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

Gene ID: 26240, updated on 5-Mar-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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Location:
6p25.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (3831894..3851317)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (3701518..3720954)
105.20220307 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
  • 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. 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
  2. Novel retrotransposed imprinted locus identified at human 6p25. Zhang A, et al. Nucleic Acids Res, 2011 Jul. PMID 21421564, Free PMC Article
  3. Expression of imprinted genes in placenta is associated with infant neurobehavioral development. Green BB, et al. Epigenetics, 2015. PMID 26198301, Free PMC Article
  4. 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
  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 (26) 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_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
    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

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