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GGNBP1 gametogenetin binding protein 1 (pseudogene) [ Homo sapiens (human) ]

Gene ID: 449520, updated on 10-Oct-2023

Summary

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Official Symbol
GGNBP1provided by HGNC
Official Full Name
gametogenetin binding protein 1 (pseudogene)provided by HGNC
Primary source
HGNC:HGNC:19427
See related
Ensembl:ENSG00000204188 MIM:609495; AllianceGenome:HGNC:19427
Gene type
pseudo
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This gene is the ortholog of the mouse gametogenetin-binding protein 1 gene. In human, the open reading frame is disrupted by a nonsense mutation after 8-aa; consequently, this gene is currently considered to be a unitary pseudogene in human even though it is functional in other mammals. [provided by RefSeq, Aug 2009]
Expression
Biased expression in testis (RPKM 1.5), lymph node (RPKM 0.2) and 2 other tissues See more
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Genomic context

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See GGNBP1 in Genome Data Viewer
Location:
6p21.31
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33583699..33589026)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33404889..33410216)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33551476..33556803)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91452 Neighboring gene RNA, 7SL, cytoplasmic 26, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33546627-33547272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33552868-33553862 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:33557672-33558871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33559025-33559664 Neighboring gene BCL2 antagonist/killer 1 Neighboring gene long intergenic non-protein coding RNA 336 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33560945-33561584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33566996-33567496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33567497-33567997 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33571503-33572004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33572005-33572504 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:33574668-33575174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33575775-33576317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33577246-33577832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33577833-33578418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17048 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33589316-33589501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33590023-33590572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33590573-33591121 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17051 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33597027-33597903 Neighboring gene uncharacterized LOC124901305 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33602349-33602895 Neighboring gene inositol 1,4,5-trisphosphate receptor type 3 Neighboring gene ITPR3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33618418-33618918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33618919-33619419 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33624122-33624658 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33625731-33626265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33626906-33627416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33636045-33636676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33636677-33637307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33641013-33641534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33658493-33659470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33659471-33660446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33660447-33661424 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:33662237-33663436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33665333-33666308 Neighboring gene microRNA 3934 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 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
  • 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. Identification and characterization of a novel testicular germ cell-specific gene Ggnbp1. Zhou Y, et al. Mol Reprod Dev, 2005 Mar. PMID 15625700
  2. Germ-cell specific protein gametogenetin protein 2 (GGN2), expression in the testis, and association with intracellular membrane. Zhao Q, et al. Mol Reprod Dev, 2005 Sep. PMID 15892049
  3. Yeast two-hybrid screens imply that GGNBP1, GGNBP2 and OAZ3 are potential interaction partners of testicular germ cell-specific protein GGN1. Zhang J, et al. FEBS Lett, 2005 Jan 17. PMID 15642376
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. Bailey SD, et al. Diabetes Care, 2010 Oct. PMID 20628086, Free PMC Article
  5. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Talmud PJ, et al. Am J Hum Genet, 2009 Nov. PMID 19913121, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  3. A testicular germ cell-specific protein interacting with GGN1. The protein seems to associate with the membrane system in the germ cell.
    Title: Identification and characterization of a novel testicular germ cell-specific gene Ggnbp1.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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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

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

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.

RNA

  1. NR_028361.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AY383627, Z93017
    Related
    ENST00000374458.5

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    33583699..33589026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    33404889..33410216
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001005478.1: Suppressed sequence

    Description
    NM_001005478.1: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5YKI7.1 GenPept UniProtKB/Swiss-Prot:Q5YKI7

Gene LinkOut

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

Chemical Information
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