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    FAM78B family with sequence similarity 78 member B [ Homo sapiens (human) ]

    Gene ID: 149297, updated on 10-Dec-2024

    Summary

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    Official Symbol
    FAM78Bprovided by HGNC
    Official Full Name
    family with sequence similarity 78 member Bprovided by HGNC
    Primary source
    HGNC:HGNC:13495
    See related
    Ensembl:ENSG00000188859 AllianceGenome:HGNC:13495
    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
    Expression
    Broad expression in brain (RPKM 1.6), testis (RPKM 1.0) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FAM78B in Genome Data Viewer
    Location:
    1q24.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (166055918..166167001, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (165402009..165513030, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (166025155..166136238, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:166009027-166010226 Neighboring gene RPS3A pseudogene 10 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:166033205-166033704 Neighboring gene RNA, 5S ribosomal pseudogene 64 Neighboring gene MPRA-validated peak439 silencer Neighboring gene FAM78B antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_946 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:166097641-166098142 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_966 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_978 Neighboring gene uncharacterized LOC112268276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:166135105-166136007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2025 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1510 Neighboring gene microRNA 921 Neighboring gene EWS RNA binding protein 1 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr1:166276066-166276742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:166312727-166313227 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:166322051-166322217 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:166352300-166353120 Neighboring gene long intergenic non-protein coding RNA 1675 Neighboring gene flavin containing dimethylaniline monoxygenase 7, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Pre-B-cell leukemia homeobox 1 (PBX1) shows functional and possible genetic association with bone mineral density variation. Cheung CL, et al. Hum Mol Genet, 2009 Feb 15. PMID 19064610
    2. Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study. Ehret GB, et al. Eur J Hum Genet, 2009 Dec. PMID 19536175, Free PMC Article
    3. 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
    4. The DNA sequence and biological annotation of human chromosome 1. Gregory SG, et al. Nature, 2006 May 18. PMID 16710414
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC131653

    General protein information

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    Preferred Names
    protein FAM78B

    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_001017961.5 → NP_001017961.1  protein FAM78B isoform 1

      See identical proteins and their annotated locations for NP_001017961.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AB593134, AK299946, AL596087, AL626787, BM663586
      Consensus CDS
      CCDS30931.1
      UniProtKB/Swiss-Prot
      B7Z693, Q5VT40
      UniProtKB/TrEMBL
      H7C075
      Related
      ENSP00000346404.3, ENST00000354422.4

    2. NM_001320302.2 → NP_001307231.1  protein FAM78B isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 3' terminal exon, resulting in novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AB593134, AL596087, AL626787, H15427
      UniProtKB/TrEMBL
      F1T0K0

    RNA

    1. NR_135199.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains a different 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB593134, AK299946, AL596087, AL626787, BX387125, H15427

    2. NR_163271.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL596087, AL626787

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      166055918..166167001 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      165402009..165513030 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VT40.1 GenPept UniProtKB/Swiss-Prot:Q5VT40

    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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