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    NDE1 nudE neurodevelopment protein 1 [ Homo sapiens (human) ]

    Gene ID: 54820, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NDE1provided by HGNC
    Official Full Name
    nudE neurodevelopment protein 1provided by HGNC
    Primary source
    HGNC:HGNC:17619
    See related
    Ensembl:ENSG00000072864 MIM:609449; AllianceGenome:HGNC:17619
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NDE; LIS4; MHAC; NUDE; NUDE1; HOM-TES-87
    Summary
    This gene encodes a member of the nuclear distribution E (NudE) family of proteins. The encoded protein is localized at the centrosome and interacts with other centrosome components as part of a multiprotein complex that regulates dynein function. This protein plays an essential role in microtubule organization, mitosis and neuronal migration. Mutations in this gene cause lissencephaly 4, a disorder characterized by lissencephaly, severe brain atrophy, microcephaly, and severe cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]
    Expression
    Broad expression in esophagus (RPKM 68.2), prostate (RPKM 53.0) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NDE1 in Genome Data Viewer
    Location:
    16p13.11
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (15643382..15726353)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (15648287..15731290)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (15737239..15820210)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene meiosis regulator and mRNA stability factor 1 Neighboring gene uncharacterized LOC124903649 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15743803-15744304 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15744305-15744804 Neighboring gene Sharpr-MPRA regulatory region 7034 Neighboring gene microRNA 484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15766651-15767392 Neighboring gene Sharpr-MPRA regulatory region 12074 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15814393-15815196 Neighboring gene myosin heavy chain 11 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15830279-15831035 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15851025-15851658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15851659-15852292 Neighboring gene uncharacterized LOC124903650 Neighboring gene uncharacterized LOC124903651

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Comprehensive analysis indicated that NDE1 is a potential biomarker for pan-cancer and promotes bladder cancer progression. Wang P, et al. Cancer Med, 2024 Mar. PMID 38466053, Free PMC Article
    2. Deletion 16p13.11 uncovers NDE1 mutations on the non-deleted homolog and extends the spectrum of severe microcephaly to include fetal brain disruption. Paciorkowski AR, et al. Am J Med Genet A, 2013 Jul. PMID 23704059, Free PMC Article
    3. Novel NDE1 homozygous mutation resulting in microhydranencephaly and not microlyssencephaly. Guven A, et al. Neurogenetics, 2012 Aug. PMID 22526350
    4. An interaction between NDE1 and high birth weight increases schizophrenia susceptibility. Wegelius A, et al. Psychiatry Res, 2015 Dec 15. PMID 26350705
    5. Cloning of the promoter of NDE1, a gene implicated in psychiatric and neurodevelopmental disorders through copy number variation. Bradshaw NJ. Neuroscience, 2016 Jun 2. PMID 26975893

    See all (96) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Comprehensive analysis indicated that NDE1 is a potential biomarker for pan-cancer and promotes bladder cancer progression.
      Title: Comprehensive analysis indicated that NDE1 is a potential biomarker for pan-cancer and promotes bladder cancer progression.
    2. Novel lissencephaly-associated NDEL1 variant reveals distinct roles of NDE1 and NDEL1 in nucleokinesis and human cortical malformations.
      Title: Novel lissencephaly-associated NDEL1 variant reveals distinct roles of NDE1 and NDEL1 in nucleokinesis and human cortical malformations.
    3. 16p13.11 microduplication in 45 new patients: refined clinical significance and genotype-phenotype correlations.
      Title: 16p13.11 microduplication in 45 new patients: refined clinical significance and genotype-phenotype correlations.
    4. CENP-F stabilizes kinetochore-microtubule attachments and limits dynein stripping of corona cargoes.
      Title: CENP-F stabilizes kinetochore-microtubule attachments and limits dynein stripping of corona cargoes.
    5. [Microlissencephaly due to pathogenic variants of NDE1: from pathology to normal brain development].", trans "Variations pathogenes de NDE1 et microlissencephalie - De la pathologie au developpement cerebral normal.
      Title: [Microlissencephaly due to pathogenic variants of NDE1: from pathology to normal brain development].
    6. These studies identify the LIS1/NDE1 complex as an important FGF signaling regulator and provide insights into the bidirectional regulation of cell signaling and transport machinery for endocytosis.
      Title: The LIS1/NDE1 Complex Is Essential for FGF Signaling by Regulating FGF Receptor Intracellular Trafficking.
    7. Nde1 makes unique contributions to human neurodevelopment through its regulation of both dynein and proteasome function.
      Title: Nde1 promotes diverse dynein functions through differential interactions and exhibits an isoform-specific proteasome association.
    8. Our results show how evolutionary changes in cis as well as trans acting signals have played a fundamental role in determining NDE1 species specific splicing isoforms supporting the notion that alternative splicing plays a central role in human genome evolution, and possibly human cognitive predominance.
      Title: Human NDE1 splicing and mammalian brain development.
    9. the severity of NDE1-associated microcephaly results not from defects in mitosis, but rather the inability of neural progenitors to ever reach this stage
      Title: Severe NDE1-mediated microcephaly results from neural progenitor cell cycle arrests at multiple specific stages.
    10. Variation at the NDE1 locus may alter risk of mental illness, in part through modification of miR-484. NDE1 SNP rs2242549 associates with significant changes in gene expression of DISC1 network.
      Title: The NDE1 genomic locus can affect treatment of psychiatric illness through gene expression changes related to microRNA-484.
    Submit: New GeneRIF Correction See all GeneRIFs (37)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Lissencephaly 4
    MedGen: C3151461 OMIM: 614019 GeneReviews: Not available
    		Compare labs
    NDE1-related microhydranencephaly
    MedGen: C1857977 OMIM: 605013 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20101

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables microtubule binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables microtubule binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in centrosome duplication ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in centrosome localization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cerebral cortex development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromosome segregation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in establishment of chromosome localization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in establishment of chromosome localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in establishment of mitotic spindle orientation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in establishment of mitotic spindle orientation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in microtubule nucleation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic centrosome separation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neuroblast proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron migration IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle transport along microtubule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cleavage furrow IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of kinesin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in kinetochore IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in kinetochore IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    located_in microtubule IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in spindle pole centrosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    nuclear distribution protein nudE homolog 1
    Names
    LIS1-interacting protein NUDE1, rat homolog
    epididymis secretory sperm binding protein
    nudE nuclear distribution E homolog 1
    nudE nuclear distribution gene E homolog 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_021210.1 RefSeqGene

      Range
      11979..88087
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001143979.2 → NP_001137451.1  nuclear distribution protein nudE homolog 1

      See identical proteins and their annotated locations for NP_001137451.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC026401, AF001548, AK000108, BC001421, BC033900
      Consensus CDS
      CCDS10564.1
      UniProtKB/Swiss-Prot
      Q49AQ2, Q9NXR1
      UniProtKB/TrEMBL
      A0A6Q8PGV6, X5DR54
      Related
      ENSP00000379643.1, ENST00000396355.5
      Conserved Domains (2) summary
      pfam04880
      Location:134 → 309
      NUDE_C; NUDE protein, C-terminal conserved region
      cl25732
      Location:27 → 186
      SMC_N; RecF/RecN/SMC N terminal domain

    2. NM_017668.3 → NP_060138.1  nuclear distribution protein nudE homolog 1

      See identical proteins and their annotated locations for NP_060138.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AF001548, BC001421
      Consensus CDS
      CCDS10564.1
      UniProtKB/Swiss-Prot
      Q49AQ2, Q9NXR1
      UniProtKB/TrEMBL
      A0A6Q8PGV6, X5DR54
      Related
      ENSP00000379642.1, ENST00000396354.6
      Conserved Domains (2) summary
      pfam04880
      Location:134 → 309
      NUDE_C; NUDE protein, C-terminal conserved region
      cl25732
      Location:27 → 186
      SMC_N; RecF/RecN/SMC N terminal domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      15643382..15726353
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434261.1 → XP_047290217.1  nuclear distribution protein nudE homolog 1 isoform X8

    2. XM_047434259.1 → XP_047290215.1  nuclear distribution protein nudE homolog 1 isoform X5

    3. XM_047434264.1 → XP_047290220.1  nuclear distribution protein nudE homolog 1 isoform X12

    4. XM_047434260.1 → XP_047290216.1  nuclear distribution protein nudE homolog 1 isoform X7

    5. XM_047434258.1 → XP_047290214.1  nuclear distribution protein nudE homolog 1 isoform X4

    6. XM_006720897.5 → XP_006720960.1  nuclear distribution protein nudE homolog 1 isoform X3

      See identical proteins and their annotated locations for XP_006720960.1

      Conserved Domains (3) summary
      PRK14160
      Location:33 → 220
      PRK14160; heat shock protein GrpE; Provisional
      pfam04880
      Location:166 → 344
      NUDE_C; NUDE protein, C-terminal conserved region
      cl03075
      Location:66 → 159
      GrpE; nucleotide exchange factor GrpE

    7. XM_047434267.1 → XP_047290223.1  nuclear distribution protein nudE homolog 1 isoform X17

    8. XM_047434262.1 → XP_047290218.1  nuclear distribution protein nudE homolog 1 isoform X1

    9. XM_017023353.3 → XP_016878842.1  nuclear distribution protein nudE homolog 1 isoform X6

      UniProtKB/TrEMBL
      I3L3G9, X5DRB5
      Conserved Domains (3) summary
      PRK14160
      Location:1 → 188
      PRK14160; heat shock protein GrpE; Provisional
      pfam04880
      Location:134 → 312
      NUDE_C; NUDE protein, C-terminal conserved region
      cl03075
      Location:34 → 127
      GrpE; nucleotide exchange factor GrpE

    10. XM_017023349.3 → XP_016878838.1  nuclear distribution protein nudE homolog 1 isoform X2

      UniProtKB/Swiss-Prot
      Q9NXR1
      Conserved Domains (3) summary
      PRK14160
      Location:1 → 188
      PRK14160; heat shock protein GrpE; Provisional
      pfam04880
      Location:134 → 312
      NUDE_C; NUDE protein, C-terminal conserved region
      cl03075
      Location:34 → 127
      GrpE; nucleotide exchange factor GrpE

    11. XM_017023354.3 → XP_016878843.1  nuclear distribution protein nudE homolog 1 isoform X13

      UniProtKB/TrEMBL
      I3L3G9, X5DRB5

    12. XM_047434263.1 → XP_047290219.1  nuclear distribution protein nudE homolog 1 isoform X10

    13. XM_047434265.1 → XP_047290221.1  nuclear distribution protein nudE homolog 1 isoform X14

    14. XM_017023355.3 → XP_016878844.1  nuclear distribution protein nudE homolog 1 isoform X16

      UniProtKB/TrEMBL
      I3L3G9, X5DRB5
      Related
      ENSP00000460436.2, ENST00000572756.6

    15. XM_047434266.1 → XP_047290222.1  nuclear distribution protein nudE homolog 1 isoform X15

    16. XM_017023352.3 → XP_016878841.1  nuclear distribution protein nudE homolog 1 isoform X11

      UniProtKB/TrEMBL
      A0A6Q8PG46, X5DP35
      Conserved Domains (3) summary
      PRK14160
      Location:1 → 188
      PRK14160; heat shock protein GrpE; Provisional
      pfam04880
      Location:134 → 265
      NUDE_C; NUDE protein, C-terminal conserved region
      cl03075
      Location:34 → 127
      GrpE; nucleotide exchange factor GrpE

    17. XM_017023350.2 → XP_016878839.1  nuclear distribution protein nudE homolog 1 isoform X9

    18. XM_005255396.6 → XP_005255453.1  nuclear distribution protein nudE homolog 1 isoform X1

      See identical proteins and their annotated locations for XP_005255453.1

      Conserved Domains (3) summary
      PRK14160
      Location:1 → 188
      PRK14160; heat shock protein GrpE; Provisional
      pfam04880
      Location:134 → 312
      NUDE_C; NUDE protein, C-terminal conserved region
      cl03075
      Location:34 → 127
      GrpE; nucleotide exchange factor GrpE

    19. XM_047434268.1 → XP_047290224.1  nuclear distribution protein nudE homolog 1 isoform X18

    20. XM_006720900.5 → XP_006720963.1  nuclear distribution protein nudE homolog 1 isoform X1

      See identical proteins and their annotated locations for XP_006720963.1

      Conserved Domains (3) summary
      PRK14160
      Location:1 → 188
      PRK14160; heat shock protein GrpE; Provisional
      pfam04880
      Location:134 → 312
      NUDE_C; NUDE protein, C-terminal conserved region
      cl03075
      Location:34 → 127
      GrpE; nucleotide exchange factor GrpE

    21. XM_017023357.3 → XP_016878846.1  nuclear distribution protein nudE homolog 1 isoform X19

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187607.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      1301393..1384364
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329110.1 → XP_054185085.1  nuclear distribution protein nudE homolog 1 isoform X8

    2. XM_054329107.1 → XP_054185082.1  nuclear distribution protein nudE homolog 1 isoform X5

    3. XM_054329116.1 → XP_054185091.1  nuclear distribution protein nudE homolog 1 isoform X12

    4. XM_054329109.1 → XP_054185084.1  nuclear distribution protein nudE homolog 1 isoform X7

    5. XM_054329106.1 → XP_054185081.1  nuclear distribution protein nudE homolog 1 isoform X4

    6. XM_054329105.1 → XP_054185080.1  nuclear distribution protein nudE homolog 1 isoform X3

    7. XM_054329120.1 → XP_054185095.1  nuclear distribution protein nudE homolog 1 isoform X17

    8. XM_054329112.1 → XP_054185087.1  nuclear distribution protein nudE homolog 1 isoform X1

    9. XM_054329108.1 → XP_054185083.1  nuclear distribution protein nudE homolog 1 isoform X6

    10. XM_054329104.1 → XP_054185079.1  nuclear distribution protein nudE homolog 1 isoform X2

    11. XM_054329117.1 → XP_054185092.1  nuclear distribution protein nudE homolog 1 isoform X13

    12. XM_054329118.1 → XP_054185093.1  nuclear distribution protein nudE homolog 1 isoform X15

    13. XM_054329114.1 → XP_054185089.1  nuclear distribution protein nudE homolog 1 isoform X10

    14. XM_054329119.1 → XP_054185094.1  nuclear distribution protein nudE homolog 1 isoform X14

    15. XM_054329115.1 → XP_054185090.1  nuclear distribution protein nudE homolog 1 isoform X11

      UniProtKB/TrEMBL
      X5DP35

    16. XM_054329113.1 → XP_054185088.1  nuclear distribution protein nudE homolog 1 isoform X9

    17. XM_054329103.1 → XP_054185078.1  nuclear distribution protein nudE homolog 1 isoform X1

    18. XM_054329121.1 → XP_054185096.1  nuclear distribution protein nudE homolog 1 isoform X18

    19. XM_054329111.1 → XP_054185086.1  nuclear distribution protein nudE homolog 1 isoform X1

    20. XM_054329122.1 → XP_054185097.1  nuclear distribution protein nudE homolog 1 isoform X19

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      15648287..15731290
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054380543.1 → XP_054236518.1  nuclear distribution protein nudE homolog 1 isoform X8

    2. XM_054380540.1 → XP_054236515.1  nuclear distribution protein nudE homolog 1 isoform X5

    3. XM_054380549.1 → XP_054236524.1  nuclear distribution protein nudE homolog 1 isoform X12

    4. XM_054380542.1 → XP_054236517.1  nuclear distribution protein nudE homolog 1 isoform X7

    5. XM_054380539.1 → XP_054236514.1  nuclear distribution protein nudE homolog 1 isoform X4

    6. XM_054380538.1 → XP_054236513.1  nuclear distribution protein nudE homolog 1 isoform X3

    7. XM_054380545.1 → XP_054236520.1  nuclear distribution protein nudE homolog 1 isoform X1

    8. XM_054380541.1 → XP_054236516.1  nuclear distribution protein nudE homolog 1 isoform X6

    9. XM_054380537.1 → XP_054236512.1  nuclear distribution protein nudE homolog 1 isoform X2

    10. XM_054380550.1 → XP_054236525.1  nuclear distribution protein nudE homolog 1 isoform X13

    11. XM_054380551.1 → XP_054236526.1  nuclear distribution protein nudE homolog 1 isoform X15

    12. XM_054380547.1 → XP_054236522.1  nuclear distribution protein nudE homolog 1 isoform X10

    13. XM_054380552.1 → XP_054236527.1  nuclear distribution protein nudE homolog 1 isoform X14

    14. XM_054380553.1 → XP_054236528.1  nuclear distribution protein nudE homolog 1 isoform X16

    15. XM_054380548.1 → XP_054236523.1  nuclear distribution protein nudE homolog 1 isoform X11

      UniProtKB/TrEMBL
      X5DP35

    16. XM_054380546.1 → XP_054236521.1  nuclear distribution protein nudE homolog 1 isoform X9

    17. XM_054380536.1 → XP_054236511.1  nuclear distribution protein nudE homolog 1 isoform X1

    18. XM_054380544.1 → XP_054236519.1  nuclear distribution protein nudE homolog 1 isoform X1

    19. XM_054380554.1 → XP_054236529.1  nuclear distribution protein nudE homolog 1 isoform X19

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NXR1.3 GenPept UniProtKB/Swiss-Prot:Q9NXR1

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