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LETMD1 LETM1 domain containing 1 [ Homo sapiens (human) ]

Gene ID: 25875, updated on 3-Nov-2024

Summary

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Official Symbol
LETMD1provided by HGNC
Official Full Name
LETM1 domain containing 1provided by HGNC
Primary source
HGNC:HGNC:24241
See related
Ensembl:ENSG00000050426 MIM:619070; AllianceGenome:HGNC:24241
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
HCCR; HCCR1; HCCR2; HCCR-1; HCCR-2; HCRR-2; SLC55A3; 1110019O13Rik
Summary
This gene encodes a mitochondrial outer membrane protein. It has a potential role in tumorigenesis, which may result from negative regulation of the p53 tumor suppressor gene. Alternatively spliced transcript variants have been noted for this gene. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in thyroid (RPKM 15.5), fat (RPKM 12.3) and 25 other tissues See more
Orthologs
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Genomic context

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See LETMD1 in Genome Data Viewer
Location:
12q13.12
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (51048220..51068958)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (51011103..51031877)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (51442003..51462741)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 11 member 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51419127-51419740 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51419741-51420352 Neighboring gene RNA, U6 small nuclear 87, pseudogene Neighboring gene RNA, U6 small nuclear 1273, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6367 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51441816-51442354 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51442355-51442893 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51463214-51463714 Neighboring gene cysteine and serine rich nuclear protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51477804-51478430 Neighboring gene transcription factor CP2 Neighboring gene ribosomal protein L35a pseudogene 29 Neighboring gene PHB1 pseudogene 19

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
  • 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LETMD1, a target of KLF4, hinders endothelial inflammation and pyroptosis: A protective mechanism in the pathogenesis of atherosclerosis.
    Title: LETMD1, a target of KLF4, hinders endothelial inflammation and pyroptosis: A protective mechanism in the pathogenesis of atherosclerosis.
  2. MiR-494 Inhibits the Proliferation, Migration and Invasion of Cervical Cancer Cells by Regulating LETMD1.
    Title: MiR-494 Inhibits the Proliferation, Migration and Invasion of Cervical Cancer Cells by Regulating LETMD1.
  3. The regulating role of miR-494 on HCCR1 in cervical cancer cells.
    Title: The regulating role of miR-494 on HCCR1 in cervical cancer cells.
  4. Knockdown of SNHG1 inhibits cervical cancer growth through sponging miR-194 to regulate HCCR.
    Title: Knockdown of SNHG1 inhibits cervical cancer growth through sponging miR-194 to regulate HCCR.
  5. LETMD1 Regulates Phagocytosis and Inflammatory Responses to Lipopolysaccharide via Reactive Oxygen Species Generation and NF-kappaB Activation in Macrophages.
    Title: LETMD1 Regulates Phagocytosis and Inflammatory Responses to Lipopolysaccharide via Reactive Oxygen Species Generation and NF-κB Activation in Macrophages.
  6. HCCR-1 siRNA transfection causes significant increase in the apoptosis and decreases in the proliferation of MCF-7 cellsThese effects are related to the upregulation of the Bax expression in the MCF-7 cells.
    Title: Interaction of HCCR-1 and Bax in breast cancer.
  7. Data show that the activation of STAT3 protein upregulated human cervical cancer oncogene (HCCR) expression in gastric cancer cells.
    Title: Targeting HCCR expression resensitizes gastric cancer cells to chemotherapy via down-regulating the activation of STAT3.
  8. Demonstrate that HBx-HCCR-E-cadherin regulation pathway might play an important role in HBV-induced hepatocarcinogenesis.
    Title: Up-regulation of human cervical cancer proto-oncogene contributes to hepatitis B virus-induced malignant transformation of hepatocyte by down-regulating E-cadherin.
  9. These findings suggest that HCCR gene is over-expressed in acute leukemia patients and may be a useful biomarker for monitoring minimal residual disease.
    Title: Quantitative detection of the human cervical cancer oncogene for monitoring the minimal residual disease in acute leukemia.
  10. HCCR2 gene plays an important role in the tumorigenesis of leukemia.
    Title: Silencing HCCR2 expression inhibits the proliferation of leukemia cells by inducing apoptosis and promoting cell cycle arrest.
Submit: New GeneRIF Correction See all GeneRIFs (25)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp586A011

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular adaptor activity IEA
Inferred from Electronic Annotation
more info
  
enables molecular adaptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ribosome binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in mitochondrion organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of cold-induced thermogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in regulation of inflammatory response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of phagocytosis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrial outer membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion HTP PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
LETM1 domain-containing protein 1
Names
cervical cancer 1 proto-oncogene protein p40
cervical cancer proto-oncogene 2 protein
epididymis secretory sperm binding protein
human cervical cancer oncogene
regulator of TP53

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_029858.3 RefSeqGene

    Range
    5109..17206
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243689.2 → NP_001230618.1  LETM1 domain-containing protein 1 isoform b

    See identical proteins and their annotated locations for NP_001230618.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame donor splice site at an internal exon in the 5' coding region compared to variant 1. This results in a longer isoform (b, also known as 3) containing a 13 aa protein segment not found in isoform 1.
    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS58231.1
    UniProtKB/TrEMBL
    B2RCH7
    Related
    ENSP00000389903.2, ENST00000418425.6
    Conserved Domains (1) summary
    pfam07766
    Location:80 → 351
    LETM1; LETM1-like protein

  2. NM_001300765.2 → NP_001287694.1  LETM1 domain-containing protein 1 isoform c

    See identical proteins and their annotated locations for NP_001287694.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks three alternate in-frame exons in the central coding region, compared to variant 1. The encoded isoform (c, also known as 7) is shorter than isoform 1.
    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS73469.1
    UniProtKB/TrEMBL
    F8W1Z2
    Related
    ENSP00000447419.1, ENST00000547008.5
    Conserved Domains (1) summary
    pfam07766
    Location:79 → 221
    LETM1; LETM1-like protein

  3. NM_001351312.2 → NP_001338241.1  LETM1 domain-containing protein 1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), as well as variant 12, encodes isoform d.
    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS44883.1
    UniProtKB/TrEMBL
    B7Z7F8
    Related
    ENSP00000450163.1, ENST00000550929.5
    Conserved Domains (1) summary
    pfam07766
    Location:23 → 289
    LETM1; LETM1-like protein

  4. NM_001351313.2 → NP_001338242.1  LETM1 domain-containing protein 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variants 25-27, encodes isoform e.
    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1 → 188
    LETM1; LETM1-like protein

  5. NM_001351315.2 → NP_001338244.1  LETM1 domain-containing protein 1 isoform f

    Status: REVIEWED

    Source sequence(s)
    AC087884
    UniProtKB/TrEMBL
    B2RCH7
    Conserved Domains (1) summary
    pfam07766
    Location:86 → 352
    LETM1; LETM1-like protein

  6. NM_001351316.2 → NP_001338245.1  LETM1 domain-containing protein 1 isoform g

    Status: REVIEWED

    Source sequence(s)
    AC087884
    UniProtKB/TrEMBL
    B2RCH7
    Conserved Domains (1) summary
    pfam07766
    Location:86 → 312
    LETM1; LETM1-like protein

  7. NM_001351317.2 → NP_001338246.1  LETM1 domain-containing protein 1 isoform h

    Status: REVIEWED

    Source sequence(s)
    AC087884
    UniProtKB/TrEMBL
    B2RCH7
    Conserved Domains (1) summary
    pfam07766
    Location:79 → 305
    LETM1; LETM1-like protein

  8. NM_001351319.2 → NP_001338248.1  LETM1 domain-containing protein 1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12), as well as variant 2, encodes isoform d.
    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS44883.1
    UniProtKB/TrEMBL
    B7Z7F8
    Conserved Domains (1) summary
    pfam07766
    Location:23 → 289
    LETM1; LETM1-like protein

  9. NM_001351320.2 → NP_001338249.1  LETM1 domain-containing protein 1 isoform k

    Status: REVIEWED

    Source sequence(s)
    AC087884
    UniProtKB/TrEMBL
    F8VZA2
    Conserved Domains (1) summary
    pfam07766
    Location:23 → 249
    LETM1; LETM1-like protein

  10. NM_001351321.2 → NP_001338250.1  LETM1 domain-containing protein 1 isoform l

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:79 → 255
    LETM1; LETM1-like protein

  11. NM_001351322.2 → NP_001338251.1  LETM1 domain-containing protein 1 isoform m

    Status: REVIEWED

    Source sequence(s)
    AC087884
    UniProtKB/TrEMBL
    B7Z7F8
    Conserved Domains (1) summary
    pfam07766
    Location:1 → 251
    LETM1; LETM1-like protein

  12. NM_001351323.2 → NP_001338252.1  LETM1 domain-containing protein 1 isoform m

    Status: REVIEWED

    Source sequence(s)
    AC087884
    UniProtKB/TrEMBL
    B7Z7F8
    Conserved Domains (1) summary
    pfam07766
    Location:1 → 251
    LETM1; LETM1-like protein

  13. NM_001351324.2 → NP_001338253.1  LETM1 domain-containing protein 1 isoform m

    Status: REVIEWED

    Source sequence(s)
    AC087884
    UniProtKB/TrEMBL
    B7Z7F8
    Conserved Domains (1) summary
    pfam07766
    Location:1 → 251
    LETM1; LETM1-like protein

  14. NM_001351325.2 → NP_001338254.1  LETM1 domain-containing protein 1 isoform n

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:116 → 244
    LETM1; LETM1-like protein

  15. NM_001351326.2 → NP_001338255.1  LETM1 domain-containing protein 1 isoform o

    Status: REVIEWED

    Source sequence(s)
    AC087884
    UniProtKB/TrEMBL
    B7Z7F8
    Conserved Domains (1) summary
    pfam07766
    Location:37 → 239
    LETM1; LETM1-like protein

  16. NM_001351327.2 → NP_001338256.1  LETM1 domain-containing protein 1 isoform o

    Status: REVIEWED

    Source sequence(s)
    AC087884
    UniProtKB/TrEMBL
    B7Z7F8
    Conserved Domains (1) summary
    pfam07766
    Location:37 → 239
    LETM1; LETM1-like protein

  17. NM_001351328.2 → NP_001338257.1  LETM1 domain-containing protein 1 isoform p

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:86 → 228
    LETM1; LETM1-like protein

  18. NM_001351330.2 → NP_001338259.1  LETM1 domain-containing protein 1 isoform t

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS86301.1
    UniProtKB/TrEMBL
    F8VP71
    Related
    ENSP00000450333.1, ENST00000552739.5
    Conserved Domains (1) summary
    pfam07766
    Location:42 → 228
    LETM1; LETM1-like protein

  19. NM_001351332.2 → NP_001338261.1  LETM1 domain-containing protein 1 isoform u

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:93 → 228
    LETM1; LETM1-like protein

  20. NM_001351333.2 → NP_001338262.1  LETM1 domain-containing protein 1 isoform q

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:79 → 181
    LETM1; LETM1-like protein

  21. NM_001351334.2 → NP_001338263.1  LETM1 domain-containing protein 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (25), as well as variants 4, 26, and 27, encodes isoform e (also called isoform r).
    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1 → 188
    LETM1; LETM1-like protein

  22. NM_001351335.2 → NP_001338264.1  LETM1 domain-containing protein 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (26), as well as variants 4, 25, and 27, encodes isoform e (also called isoform r).
    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1 → 188
    LETM1; LETM1-like protein

  23. NM_001351336.2 → NP_001338265.1  LETM1 domain-containing protein 1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (27), as well as variants 4, 25, and 26, encodes isoform e (also called isoform r).
    Source sequence(s)
    AC087884
    Conserved Domains (1) summary
    pfam07766
    Location:1 → 188
    LETM1; LETM1-like protein

  24. NM_001351337.2 → NP_001338266.1  LETM1 domain-containing protein 1 isoform s

    Status: REVIEWED

    Source sequence(s)
    AC087884, KF455649
    Conserved Domains (1) summary
    pfam07766
    Location:79 → 181
    LETM1; LETM1-like protein

  25. NM_015416.5 → NP_056231.3  LETM1 domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_056231.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant protein-coding transcript, and encodes isoform a (also known as HCCR-1 or 1).
    Source sequence(s)
    AC087884
    Consensus CDS
    CCDS8806.1
    UniProtKB/Swiss-Prot
    A6NER7, B3KXK7, Q6P1Q0, Q6X2E4, Q6X2E5, Q7L2G9, Q7L690, Q8WXW6, Q96PK7, Q9BY59, Q9Y3X3
    UniProtKB/TrEMBL
    A0A384P5D7, B2RCH7
    Related
    ENSP00000262055.4, ENST00000262055.9
    Conserved Domains (1) summary
    pfam07766
    Location:79 → 345
    LETM1; LETM1-like protein

RNA

  1. NR_045019.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two consecutive exons compared to variant 1. It is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with the translation of the longest ORF; translation of the upstream ORF renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC087884
    Related
    ENST00000547318.5

  2. NR_045020.3 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884, KF455649

  3. NR_147098.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884, BU688852

  4. NR_147099.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  5. NR_147100.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  6. NR_147101.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  7. NR_147102.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  8. NR_147103.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  9. NR_147104.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  10. NR_147105.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  11. NR_147106.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  12. NR_147107.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  13. NR_147108.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  14. NR_147109.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  15. NR_147110.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  16. NR_147111.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  17. NR_147112.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Related
    ENST00000550100.5

  18. NR_147113.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Related
    ENST00000547555.5

  19. NR_147114.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  20. NR_147115.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884
    Related
    ENST00000380135.7

  21. NR_147116.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  22. NR_147117.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  23. NR_147118.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  24. NR_147119.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

  25. NR_147120.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087884

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    51048220..51068958
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428688.1 → XP_047284644.1  LETM1 domain-containing protein 1 isoform X2

  2. XM_047428687.1 → XP_047284643.1  LETM1 domain-containing protein 1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    51011103..51031877
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371706.1 → XP_054227681.1  LETM1 domain-containing protein 1 isoform X2

  2. XM_054371705.1 → XP_054227680.1  LETM1 domain-containing protein 1 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001024668.1: Suppressed sequence

    Description
    NM_001024668.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  2. NM_001024669.1: Suppressed sequence

    Description
    NM_001024669.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  3. NM_001024670.1: Suppressed sequence

    Description
    NM_001024670.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  4. NM_001024671.1: Suppressed sequence

    Description
    NM_001024671.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P1Q0.1 GenPept UniProtKB/Swiss-Prot:Q6P1Q0

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