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    SCAPER S-phase cyclin A associated protein in the ER [ Homo sapiens (human) ]

    Gene ID: 49855, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SCAPERprovided by HGNC
    Official Full Name
    S-phase cyclin A associated protein in the ERprovided by HGNC
    Primary source
    HGNC:HGNC:13081
    See related
    Ensembl:ENSG00000140386 MIM:611611; AllianceGenome:HGNC:13081
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    IDDRP; ZNF291; Zfp291; MSTP063
    Summary
    Predicted to enable nucleic acid binding activity and zinc ion binding activity. Acts upstream of or within retina development in camera-type eye. Located in cytosol and nuclear speck. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 4.5), brain (RPKM 3.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SCAPER in Genome Data Viewer
    Location:
    15q24.3
    Exon count:
    46
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (76347904..76905340, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (74219067..74764374, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (76640245..77197681, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene electron transfer flavoprotein subunit alpha Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:76603062-76603562 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:76603563-76604063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9878 Neighboring gene CRISPRi-validated cis-regulatory element chr15.2471 Neighboring gene TYRO3P protein tyrosine kinase pseudogene Neighboring gene Sharpr-MPRA regulatory region 228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76629623-76630434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9881 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76632479-76633234 Neighboring gene uncharacterized LOC124903532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76638487-76638988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6688 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:76663676-76663893 Neighboring gene tRNA-Lys (anticodon CTT) 16-1 Neighboring gene ISL LIM homeobox 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:76726060-76727259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9883 Neighboring gene microRNA 3713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6689 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76991672-76992172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76992173-76992673 Neighboring gene RN7SK pseudogene 217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6690 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6691 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:77197527-77198027 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:77208364-77208864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:77208865-77209365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6693 Neighboring gene uncharacterized LOC105370904 Neighboring gene RNA, 7SL, cytoplasmic 278, pseudogene Neighboring gene reticulocalbin 2

    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. Delineating the expanding phenotype associated with SCAPER gene mutation. Fasham J, et al. Am J Med Genet A, 2019 Aug. PMID 31192531, Free PMC Article
    2. SCAPER-associated nonsyndromic autosomal recessive retinitis pigmentosa. Jauregui R, et al. Am J Med Genet A, 2019 Feb. PMID 30561111, Free PMC Article
    3. Homozygous variants in the gene SCAPER cause syndromic intellectual disability. Kahrizi K, et al. Am J Med Genet A, 2019 Jul. PMID 31069901
    4. SCAPER localizes to primary cilia and its mutation affects cilia length, causing Bardet-Biedl syndrome. Wormser O, et al. Eur J Hum Genet, 2019 Jun. PMID 30723319, Free PMC Article
    5. Double identity of SCAPER: a substrate and regulator of cyclin A/Cdk2. Tsang WY, et al. Cell Cycle, 2008 Mar 15. PMID 18245951

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Absence of SCAPER causes male infertility in humans and Drosophila by modulating microtubule dynamics during meiosis.
      Title: Absence of SCAPER causes male infertility in humans and Drosophila by modulating microtubule dynamics during meiosis.
    2. Male sterility and reduced female fertility in SCAPER-deficient mice.
      Title: Male sterility and reduced female fertility in SCAPER-deficient mice.
    3. Delineating the expanding phenotype associated with SCAPER gene mutation.
      Title: Delineating the expanding phenotype associated with SCAPER gene mutation.
    4. As SCAPER expression is known to peak at late G1 and S phase, overlapping the timing of ciliary resorption, our data suggest a possible role of SCAPER in ciliary dynamics and disassembly, also affecting microtubule-related mitotic progression.
      Title: SCAPER localizes to primary cilia and its mutation affects cilia length, causing Bardet-Biedl syndrome.
    5. Homozygous variants in the gene SCAPER cause syndromic intellectual disability.
      Title: Homozygous variants in the gene SCAPER cause syndromic intellectual disability.
    6. Unique to our patient's presentation is the absence of intellectual disability and attention-deficit/hyperactivity disorder, suggesting that SCAPER-associated retinitis pigmentosa can also present without systemic manifestations.
      Title: SCAPER-associated nonsyndromic autosomal recessive retinitis pigmentosa.
    7. By sequestering cyclin A/Cdk2, SCAPER is capable of directing the activity of this kinase complex away from the nucleus and regulating cyclin A/Cdk2 equilibrium in distinct subcellular compartments.
      Title: Double identity of SCAPER: a substrate and regulator of cyclin A/Cdk2.
    8. An unstable [CCTG](n) repeat in the second intron of the ZNF291 gene, on chromosome 15q21-24, was identified.
      Title: Detection of an unstable non-coding tandem repeat in the ZNF291 gene.
    9. Study describes the biochemically purification and identification of SCAPER, a novel protein that specifically interacts with cyclin A/Cdk2 in vivo.
      Title: SCAPER, a novel cyclin A-interacting protein that regulates cell cycle progression.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Intellectual developmental disorder and retinitis pigmentosa; IDDRP
    MedGen: C4748658 OMIM: 618195 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ31533, FLJ31953, FLJ46212, KIAA1454

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in antral ovarian follicle growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within retina development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in seminiferous tubule development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in ooplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in sperm head IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    S phase cyclin A-associated protein in the endoplasmic reticulum
    Names
    zinc finger protein 291

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001145923.2 → NP_001139395.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AC016343, AC027243, AF119814, BX647285
      Consensus CDS
      CCDS53961.1
      UniProtKB/Swiss-Prot
      Q9BY12
      Related
      ENSP00000442190.2, ENST00000538941.6
      Conserved Domains (2) summary
      PTZ00121
      Location:146 → 524
      PTZ00121; MAEBL; Provisional
      smart00451
      Location:544 → 576
      ZnF_U1; U1-like zinc finger

    2. NM_001353009.2 → NP_001339938.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform c

      Status: VALIDATED

      Source sequence(s)
      AC015798, AC016343, AC027243, AC051643, AC090179, AC090751
      Conserved Domains (3) summary
      smart00451
      Location:796 → 828
      ZnF_U1; U1-like zinc finger
      pfam16501
      Location:89 → 183
      SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
      cl26511
      Location:395 → 776
      Neuromodulin_N; Gap junction protein N-terminal region

    3. NM_001353010.2 → NP_001339939.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform d

      Status: VALIDATED

      Source sequence(s)
      AC015798, AC016343, AC027243, AC051643, AC090179, AC090751
      Conserved Domains (3) summary
      smart00451
      Location:656 → 688
      ZnF_U1; U1-like zinc finger
      pfam16501
      Location:1 → 49
      SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
      cl26511
      Location:258 → 636
      Neuromodulin_N; Gap junction protein N-terminal region

    4. NM_001353011.2 → NP_001339940.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform e

      Status: VALIDATED

      Source sequence(s)
      AC015798, AC016343, AC027243, AC051643, AC090179, AC090751
      Conserved Domains (3) summary
      smart00451
      Location:662 → 694
      ZnF_U1; U1-like zinc finger
      pfam16501
      Location:1 → 49
      SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
      cl26511
      Location:261 → 642
      Neuromodulin_N; Gap junction protein N-terminal region

    5. NM_001353012.2 → NP_001339941.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform d

      Status: VALIDATED

      Source sequence(s)
      AC015798, AC016343, AC027243, AC051643, AC090179, AC090751
      Conserved Domains (3) summary
      smart00451
      Location:656 → 688
      ZnF_U1; U1-like zinc finger
      pfam16501
      Location:1 → 49
      SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
      cl26511
      Location:258 → 636
      Neuromodulin_N; Gap junction protein N-terminal region

    6. NM_020843.4 → NP_065894.2  S phase cyclin A-associated protein in the endoplasmic reticulum isoform a

      See identical proteins and their annotated locations for NP_065894.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform a.
      Source sequence(s)
      AC015798, AC016343, AC027243, AC051643, AC090179, AC090751
      Consensus CDS
      CCDS53962.1
      UniProtKB/Swiss-Prot
      F5H7X8, H3BNR7, Q3B7X7, Q96BS9, Q9BY12, Q9H3D8, Q9NT03, Q9P274
      Related
      ENSP00000454973.1, ENST00000563290.6
      Conserved Domains (5) summary
      smart00451
      Location:790 → 822
      ZnF_U1; U1-like zinc finger
      pfam00836
      Location:529 → 626
      Stathmin; Stathmin family
      pfam16501
      Location:89 → 183
      SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
      cd16269
      Location:760 → 770
      GBP_C; coiled coil [structural motif]
      cl20817
      Location:670 → 774
      GBP_C; Guanylate-binding protein, C-terminal domain

    RNA

    1. NR_148227.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC015798, AC016343, AC027243, AC051643, AC090179, AC090751

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      76347904..76905340 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017022273.2 → XP_016877762.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X9

      Conserved Domains (3) summary
      smart00451
      Location:656 → 688
      ZnF_U1; U1-like zinc finger
      pfam16501
      Location:1 → 49
      SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
      cl26511
      Location:258 → 636
      Neuromodulin_N; Gap junction protein N-terminal region

    2. XM_011521653.4 → XP_011519955.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X8

      See identical proteins and their annotated locations for XP_011519955.1

      Conserved Domains (3) summary
      smart00451
      Location:662 → 694
      ZnF_U1; U1-like zinc finger
      pfam16501
      Location:1 → 49
      SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
      cl26511
      Location:261 → 642
      Neuromodulin_N; Gap junction protein N-terminal region

    3. XM_047432625.1 → XP_047288581.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X6

    4. XM_047432621.1 → XP_047288577.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X2

    5. XM_047432624.1 → XP_047288580.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X5

    6. XM_047432620.1 → XP_047288576.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X1

    7. XM_047432623.1 → XP_047288579.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X4

    8. XM_047432622.1 → XP_047288578.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X3

    9. XM_047432626.1 → XP_047288582.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X7

    10. XM_047432627.1 → XP_047288583.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X10

    11. XM_011521656.4 → XP_011519958.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X20

      Conserved Domains (5) summary
      smart00451
      Location:176 → 208
      ZnF_U1; U1-like zinc finger
      pfam11600
      Location:28 → 182
      CAF-1_p150; Chromatin assembly factor 1 complex p150 subunit, N-terminal
      cd16269
      Location:146 → 156
      GBP_C; coiled coil [structural motif]
      cl00220
      Location:543 → 584
      cysteine_hydrolases; Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It ...
      cl20817
      Location:56 → 160
      GBP_C; Guanylate-binding protein, C-terminal domain

    12. XM_047432633.1 → XP_047288589.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X22

    13. XM_047432629.1 → XP_047288585.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X15

    14. XM_047432628.1 → XP_047288584.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X14

    15. XM_024449942.2 → XP_024305710.2  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X13

    16. XM_024449941.2 → XP_024305709.2  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X12

    17. XM_024449940.2 → XP_024305708.2  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X11

    18. XM_047432630.1 → XP_047288586.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X16

    19. XM_047432632.1 → XP_047288588.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X21

    20. XM_047432631.1 → XP_047288587.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X18

    21. XM_024449944.2 → XP_024305712.2  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X17

    22. XM_017022283.2 → XP_016877772.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X19

      UniProtKB/TrEMBL
      H3BS25
      Related
      ENSP00000456508.1, ENST00000564590.5

    23. XM_047432634.1 → XP_047288590.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X23

    RNA

    1. XR_007064448.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      74219067..74764374 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378112.1 → XP_054234087.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X9

    2. XM_054378111.1 → XP_054234086.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X8

    3. XM_054378109.1 → XP_054234084.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X6

    4. XM_054378105.1 → XP_054234080.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X2

    5. XM_054378108.1 → XP_054234083.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X5

    6. XM_054378104.1 → XP_054234079.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X1

    7. XM_054378107.1 → XP_054234082.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X4

    8. XM_054378106.1 → XP_054234081.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X3

    9. XM_054378110.1 → XP_054234085.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X7

    10. XM_054378113.1 → XP_054234088.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X10

    11. XM_054378123.1 → XP_054234098.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X20

    12. XM_054378125.1 → XP_054234100.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X22

    13. XM_054378118.1 → XP_054234093.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X15

    14. XM_054378116.1 → XP_054234091.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X13

    15. XM_054378115.1 → XP_054234090.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X12

    16. XM_054378117.1 → XP_054234092.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X14

    17. XM_054378114.1 → XP_054234089.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X11

    18. XM_054378119.1 → XP_054234094.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X16

    19. XM_054378124.1 → XP_054234099.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X21

    20. XM_054378121.1 → XP_054234096.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X18

    21. XM_054378120.1 → XP_054234095.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X17

    22. XM_054378122.1 → XP_054234097.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X19

    23. XM_054378126.1 → XP_054234101.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X23

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BY12.2 GenPept UniProtKB/Swiss-Prot:Q9BY12

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