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    FAM50B family with sequence similarity 50 member B [ Homo sapiens (human) ]

    Gene ID: 26240, updated on 2-Nov-2024

    Summary

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    Official Symbol
    FAM50Bprovided by HGNC
    Official Full Name
    family with sequence similarity 50 member Bprovided by HGNC
    Primary source
    HGNC:HGNC:18789
    See related
    Ensembl:ENSG00000145945 MIM:614686; AllianceGenome:HGNC:18789
    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
    X5L; D6S2654E
    Summary
    This gene contains an intronless ORF that arose from ancestral retroposition. The encoded protein is related to a plant protein that plays a role in the circadian clock. This gene is adjacent to a differentially methylated region (DMR) and is imprinted and paternally expressed in many tissues. [provided by RefSeq, Nov 2015]
    Expression
    Ubiquitous expression in kidney (RPKM 6.3), testis (RPKM 5.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FAM50B in Genome Data Viewer
    Location:
    6p25.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (3831894..3851317)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (3701518..3720954)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (3849607..3851551)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3724209-3724747 Neighboring gene Sharpr-MPRA regulatory region 15708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3737712-3738338 Neighboring gene PX domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16857 Neighboring gene NANOG hESC enhancer GRCh37_chr6:3756018-3756884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:3757047-3758012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:3761087-3761600 Neighboring gene Sharpr-MPRA regulatory region 8997 Neighboring gene uncharacterized LOC124901244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3810000-3810500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3810501-3811001 Neighboring gene uncharacterized LOC107986557 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23893 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:3894715-3895268 Neighboring gene uncharacterized LOC107986558 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:3899874-3901073 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3903895-3904396 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:3911966-3912163 Neighboring gene ribosomal protein S25 pseudogene 7

    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. Novel retrotransposed imprinted locus identified at human 6p25. Zhang A, et al. Nucleic Acids Res, 2011 Jul. PMID 21421564, Free PMC Article
    2. Deep bisulfite sequencing of aberrantly methylated loci in a patient with multiple methylation defects. Beygo J, et al. PLoS One, 2013. PMID 24130816, Free PMC Article
    3. Array-based DNA methylation analysis in individuals with developmental delay/intellectual disability and normal molecular karyotype. Kolarova J, et al. Eur J Med Genet, 2015 Aug. PMID 26003415
    4. Expression of imprinted genes in placenta is associated with infant neurobehavioral development. Green BB, et al. Epigenetics, 2015. PMID 26198301, Free PMC Article
    5. Human and mouse XAP-5 and XAP-5-like (X5L) genes: identification of an ancient functional retroposon differentially expressed in testis. Sedlacek Z, et al. Genomics, 1999 Oct 15. PMID 10534398

    See all (28) 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 study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in intercellular bridge IDA
    Inferred from Direct Assay
    more info
    		  
    located_in midbody IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein FAM50B
    Names
    XAP5 like
    XAP5-like protein

    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_045226.1 RefSeqGene

      Range
      5008..6952
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1062

    mRNA and Protein(s)

    1. NM_012135.3 → NP_036267.1  protein FAM50B

      See identical proteins and their annotated locations for NP_036267.1

      Status: REVIEWED

      Source sequence(s)
      BC001261, BI488606, DB566944
      Consensus CDS
      CCDS4487.1
      UniProtKB/Swiss-Prot
      Q5T2L6, Q9Y247
      Related
      ENSP00000496837.1, ENST00000648326.1
      Conserved Domains (1) summary
      pfam04921
      Location:141 → 324
      XAP5; XAP5, circadian clock regulator

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      3831894..3851317
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017010729.2 → XP_016866218.1  protein FAM50B isoform X1

      UniProtKB/Swiss-Prot
      Q5T2L6, Q9Y247
      Conserved Domains (1) summary
      pfam04921
      Location:141 → 324
      XAP5; XAP5, circadian clock regulator

    RNA

    1. XR_001743335.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      3701518..3720954
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355142.1 → XP_054211117.1  protein FAM50B isoform X1

      UniProtKB/Swiss-Prot
      Q5T2L6, Q9Y247

    RNA

    1. XR_007076453.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y247.1 GenPept UniProtKB/Swiss-Prot:Q9Y247

    Gene LinkOut

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

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