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    YJEFN3 YjeF N-terminal domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 374887, updated on 5-Mar-2024

    Summary

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    Official Symbol
    YJEFN3provided by HGNC
    Official Full Name
    YjeF N-terminal domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:24785
    See related
    Ensembl:ENSG00000250067 MIM:618607; AllianceGenome:HGNC:24785
    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 NADHX epimerase activity. Predicted to be involved in several processes, including hematopoietic stem cell proliferation; membrane raft distribution; and negative regulation of angiogenesis. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 3.9), brain (RPKM 3.2) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    19p13.11
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19528911..19537581)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19666386..19675069)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19639720..19648390)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14360 Neighboring gene NADH:ubiquinone oxidoreductase subunit A13 Neighboring gene testis specific serine kinase 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19635662-19636637 Neighboring gene Sharpr-MPRA regulatory region 9511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19638979-19639479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19640455-19641386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19650412-19651074 Neighboring gene Sharpr-MPRA regulatory region 4095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19656191-19656874 Neighboring gene cartilage intermediate layer protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19662820-19663379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19671101-19671600 Neighboring gene PBX homeobox 4 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:19686115-19686616 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:19686617-19687116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19690665-19691164 Neighboring gene PHF5A pseudogene 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. ApoA-I-binding protein (AI-BP) and its homologues hYjeF_N2 and hYjeF_N3 comprise the YjeF_N domain protein family in humans with a role in spermiogenesis and oogenesis. Rudolph C, et al. Horm Metab Res, 2007 May. PMID 17533573
    2. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Ripke S, et al. Nat Genet, 2013 Oct. PMID 23974872, Free PMC Article
    3. POH1 contributes to hyperactivation of TGF-β signaling and facilitates hepatocellular carcinoma metastasis through deubiquitinating TGF-β receptors and caveolin-1. Wang B, et al. EBioMedicine, 2019 Mar. PMID 30745168, Free PMC Article
    4. The DNA sequence and biology of human chromosome 19. Grimwood J, et al. Nature, 2004 Apr 1. PMID 15057824
    5. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Fei T, et al. Proc Natl Acad Sci U S A, 2017 Jun 27. PMID 28611215, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    EBI GWAS Catalog

    Description
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog

    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

    • FLJ44968, MGC138490

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables NADHX epimerase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in hematopoietic stem cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in membrane raft distribution ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of Notch signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cholesterol efflux ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in sprouting angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    yjeF N-terminal domain-containing protein 3
    Names
    apoA-I-binding protein 2
    apolipoprotein A1 binding protein
    hYjeF_N3
    hYjeF_N3-19p13.11
    yjeF_N3

    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_001190328.2 → NP_001177257.1  yjeF N-terminal domain-containing protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001177257.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate segment, in the 5' coding region, compared to variant 1. The resulting protein (isoform 2) is shorter when it is compared to isoform 1.
      Source sequence(s)
      BI520231, BX097402, DQ778079
      Consensus CDS
      CCDS54236.1
      UniProtKB/Swiss-Prot
      A6XGL0
      Related
      ENSP00000398520.2, ENST00000436027.9
      Conserved Domains (1) summary
      PLN03049
      Location:13 → 246
      PLN03049; pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional

    2. NM_198537.4 → NP_940939.2  yjeF N-terminal domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_940939.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform 1).
      Source sequence(s)
      AK126916, BC020948, BI520231
      Consensus CDS
      CCDS42530.1
      UniProtKB/Swiss-Prot
      A6XGK9, A6XGL0, Q4G1C0
      Related
      ENSP00000426964.1, ENST00000514277.6
      Conserved Domains (1) summary
      cl00318
      Location:70 → 299
      YjeF_N; YjeF-related protein N-terminus

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      19528911..19537581
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005259903.5 → XP_005259960.1  yjeF N-terminal domain-containing protein 3 isoform X1

      Conserved Domains (1) summary
      cl00318
      Location:143 → 372
      YjeF_N; YjeF-related protein N-terminus

    2. XM_011527996.3 → XP_011526298.1  yjeF N-terminal domain-containing protein 3 isoform X3

    3. XM_017026770.2 → XP_016882259.1  yjeF N-terminal domain-containing protein 3 isoform X2

    4. XM_011527997.2 → XP_011526299.1  yjeF N-terminal domain-containing protein 3 isoform X4

      See identical proteins and their annotated locations for XP_011526299.1

      Conserved Domains (1) summary
      cl00318
      Location:10 → 194
      YjeF_N; YjeF-related protein N-terminus

    5. XM_011527998.4 → XP_011526300.1  yjeF N-terminal domain-containing protein 3 isoform X4

      See identical proteins and their annotated locations for XP_011526300.1

      Conserved Domains (1) summary
      cl00318
      Location:10 → 194
      YjeF_N; YjeF-related protein N-terminus

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      19666386..19675069
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320916.1 → XP_054176891.1  yjeF N-terminal domain-containing protein 3 isoform X1

    2. XM_054320918.1 → XP_054176893.1  yjeF N-terminal domain-containing protein 3 isoform X3

    3. XM_054320917.1 → XP_054176892.1  yjeF N-terminal domain-containing protein 3 isoform X2

    4. XM_054320919.1 → XP_054176894.1  yjeF N-terminal domain-containing protein 3 isoform X4

    5. XM_054320920.1 → XP_054176895.1  yjeF N-terminal domain-containing protein 3 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6XGL0.1 GenPept UniProtKB/Swiss-Prot:A6XGL0

    Gene LinkOut

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

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