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    GSG1 germ cell associated 1 [ Homo sapiens (human) ]

    Gene ID: 83445, updated on 5-Mar-2024

    Summary

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    Official Symbol
    GSG1provided by HGNC
    Official Full Name
    germ cell associated 1provided by HGNC
    Primary source
    HGNC:HGNC:19716
    See related
    Ensembl:ENSG00000111305 AllianceGenome:HGNC:19716
    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
    Summary
    Predicted to enable RNA polymerase binding activity. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Restricted expression toward testis (RPKM 69.4) See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12p13.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (13083532..13103667, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (12957742..12977872, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (13236466..13256601, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene GPRC5D and HEBP1 antisense RNA 1 Neighboring gene ribosomal protein S26 pseudogene 46 Neighboring gene family with sequence similarity 234 member B Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:13237538-13238737 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:13239727-13240549 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:13240550-13241371 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:13241372-13242194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:13242195-13243015 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:13243112-13243710 Neighboring gene uncharacterized LOC105369666 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4273 Neighboring gene Sharpr-MPRA regulatory region 6445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:13277735-13278236 Neighboring gene uncharacterized LOC124902882 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:13318180-13319379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6033 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:13336996-13337496 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:13337497-13337997 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:13351700-13352200 Neighboring gene epithelial membrane protein 1

    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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    Related articles in PubMed

    1. Mapping of six germ-cell-specific genes to mouse chromosomes. Matsui M, et al. Mamm Genome, 1997. PMID 9337410
    2. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. Oshikawa M, et al. Invest Ophthalmol Vis Sci, 2011 Aug 22. PMID 21697133
    3. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Otsuki T, et al. DNA Res, 2005. PMID 16303743
    4. The sequence of the human genome. Venter JC, et al. Science, 2001 Feb 16. PMID 11181995
    5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC3146, MGC111023

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    germ cell-specific gene 1 protein
    Names
    testicular secretory protein Li 20

    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.

    mRNA and Protein(s)

    1. NM_001080554.4 → NP_001074023.1  germ cell-specific gene 1 protein isoform 3

      See identical proteins and their annotated locations for NP_001074023.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region, and includes an alternate in-frame exon in the central coding region, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is longer than isoform 1.
      Source sequence(s)
      AC023790, AC079628
      Consensus CDS
      CCDS44836.1
      UniProtKB/TrEMBL
      G3XAB9
      Related
      ENSP00000336857.6, ENST00000351606.10
      Conserved Domains (1) summary
      pfam07803
      Location:24 → 160
      GSG-1; GSG1-like protein

    2. NM_001080555.4 → NP_001074024.1  germ cell-specific gene 1 protein isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, includes an alternate in-frame exon in the central coding region, and uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (4) has distinct N- and C-termini and is longer than isoform 1.
      Source sequence(s)
      AC023790, AC079628
      UniProtKB/TrEMBL
      A0A494C0G6
      Related
      ENSP00000498528.1, ENST00000651961.1
      Conserved Domains (1) summary
      pfam07803
      Location:24 → 160
      GSG-1; GSG1-like protein

    3. NM_001206842.3 → NP_001193771.1  germ cell-specific gene 1 protein isoform 5

      See identical proteins and their annotated locations for NP_001193771.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and 5' coding region, and uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (5) has distinct N- and C-termini and is longer than isoform 1.
      Source sequence(s)
      AC023790, AC079628
      Consensus CDS
      CCDS55808.1
      UniProtKB/Swiss-Prot
      Q2KHT4
      UniProtKB/TrEMBL
      F1T0A1
      Related
      ENSP00000405032.2, ENST00000432710.7
      Conserved Domains (1) summary
      pfam07803
      Location:24 → 137
      GSG-1; GSG1-like protein

    4. NM_001206843.3 → NP_001193772.1  germ cell-specific gene 1 protein isoform 6

      See identical proteins and their annotated locations for NP_001193772.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) includes an alternate in-frame exon in the central coding region and uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (6) has a distinct C-terminus and is longer than isoform 1.
      Source sequence(s)
      AC023790
      Consensus CDS
      CCDS55807.1
      UniProtKB/Swiss-Prot
      Q2KHT4
      UniProtKB/TrEMBL
      F1T0A1
      Related
      ENSP00000441718.1, ENST00000537302.5
      Conserved Domains (1) summary
      pfam07803
      Location:11 → 147
      GSG-1; GSG1-like protein

    5. NM_001206845.3 → NP_001193774.1  germ cell-specific gene 1 protein isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) uses an alternate splice site and lacks an alternate exon, resulting in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (7) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC023790
      Consensus CDS
      CCDS55806.1
      UniProtKB/Swiss-Prot
      Q2KHT4
      UniProtKB/TrEMBL
      F1T0A1
      Related
      ENSP00000398384.2, ENST00000457134.6
      Conserved Domains (1) summary
      pfam07803
      Location:11 → 124
      GSG-1; GSG1-like protein

    6. NM_001367358.2 → NP_001354287.1  germ cell-specific gene 1 protein isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC023790, AC079628
      Conserved Domains (1) summary
      pfam07803
      Location:24 → 160
      GSG-1; GSG1-like protein

    7. NM_001367359.2 → NP_001354288.1  germ cell-specific gene 1 protein isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC023790, AC079628
      Conserved Domains (1) summary
      pfam07803
      Location:24 → 184
      GSG-1; GSG1-like protein

    8. NM_001367360.2 → NP_001354289.1  germ cell-specific gene 1 protein isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC023790, AC079628
      Conserved Domains (1) summary
      pfam07803
      Location:24 → 160
      GSG-1; GSG1-like protein

    9. NM_001367361.2 → NP_001354290.1  germ cell-specific gene 1 protein isoform 11

      Status: VALIDATED

      Source sequence(s)
      AC023790, AC079628
      Conserved Domains (1) summary
      pfam07803
      Location:24 → 184
      GSG-1; GSG1-like protein

    10. NM_001367362.2 → NP_001354291.1  germ cell-specific gene 1 protein isoform 12

      Status: VALIDATED

      Source sequence(s)
      AC023790, AC079628
      Conserved Domains (1) summary
      pfam07803
      Location:24 → 160
      GSG-1; GSG1-like protein

    11. NM_001367363.2 → NP_001354292.1  germ cell-specific gene 1 protein isoform 13

      Status: VALIDATED

      Source sequence(s)
      AC023790, AC079628
      Conserved Domains (1) summary
      pfam07803
      Location:24 → 160
      GSG-1; GSG1-like protein

    12. NM_001367364.2 → NP_001354293.1  germ cell-specific gene 1 protein isoform 14

      Status: VALIDATED

      Source sequence(s)
      AC023790, AC079628
      Consensus CDS
      CCDS91657.1
      UniProtKB/TrEMBL
      F5H0V9
      Related
      ENSP00000445884.2, ENST00000545401.6
      Conserved Domains (1) summary
      pfam07803
      Location:24 → 137
      GSG-1; GSG1-like protein

    13. NM_001367366.1 → NP_001354295.1  germ cell-specific gene 1 protein isoform 15

      Status: VALIDATED

      Source sequence(s)
      AA776786, AC079628

    14. NM_001368007.2 → NP_001354936.1  germ cell-specific gene 1 protein isoform 16

      Status: VALIDATED

      Source sequence(s)
      AC023790
      UniProtKB/Swiss-Prot
      Q2KHT4, Q8N4M3, Q8NBR4, Q8NBS0, Q8NBT1, Q96LP9, Q96SI6, Q9BUY4

    15. NM_031289.5 → NP_112579.2  germ cell-specific gene 1 protein isoform 1

      See identical proteins and their annotated locations for NP_112579.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AC023790
      Consensus CDS
      CCDS8659.2
      UniProtKB/TrEMBL
      F1T0A0
      Related
      ENSP00000379596.3, ENST00000396302.7
      Conserved Domains (1) summary
      pfam07803
      Location:11 → 124
      GSG-1; GSG1-like protein

    16. NM_153823.5 → NP_722545.2  germ cell-specific gene 1 protein isoform 2

      See identical proteins and their annotated locations for NP_722545.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is longer than isoform 1.
      Source sequence(s)
      AC023790
      Consensus CDS
      CCDS44835.1
      UniProtKB/TrEMBL
      F1T0A1
      Related
      ENSP00000336816.6, ENST00000337630.10
      Conserved Domains (1) summary
      pfam07803
      Location:11 → 124
      GSG-1; GSG1-like protein

    RNA

    1. NR_159953.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC079628

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      13083532..13103667 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520861.3 → XP_011519163.1  germ cell-specific gene 1 protein isoform X3

      Conserved Domains (1) summary
      pfam07803
      Location:24 → 137
      GSG-1; GSG1-like protein

    2. XM_011520863.3 → XP_011519165.1  germ cell-specific gene 1 protein isoform X5

      Conserved Domains (1) summary
      pfam07803
      Location:24 → 137
      GSG-1; GSG1-like protein

    3. XM_011520862.2 → XP_011519164.1  germ cell-specific gene 1 protein isoform X4

      Conserved Domains (1) summary
      pfam07803
      Location:24 → 160
      GSG-1; GSG1-like protein

    4. XM_011520858.2 → XP_011519160.1  germ cell-specific gene 1 protein isoform X1

      Conserved Domains (1) summary
      pfam07803
      Location:24 → 184
      GSG-1; GSG1-like protein

    5. XM_011520860.2 → XP_011519162.1  germ cell-specific gene 1 protein isoform X2

      Conserved Domains (1) summary
      pfam07803
      Location:24 → 184
      GSG-1; GSG1-like protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      12957742..12977872 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373370.1 → XP_054229345.1  germ cell-specific gene 1 protein isoform X3

    2. XM_054373372.1 → XP_054229347.1  germ cell-specific gene 1 protein isoform X5

    3. XM_054373371.1 → XP_054229346.1  germ cell-specific gene 1 protein isoform X4

    4. XM_054373368.1 → XP_054229343.1  germ cell-specific gene 1 protein isoform X1

    5. XM_054373369.1 → XP_054229344.1  germ cell-specific gene 1 protein isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2KHT4.2 GenPept UniProtKB/Swiss-Prot:Q2KHT4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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