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SERF1B small EDRK-rich factor 1B [ Homo sapiens (human) ]

Gene ID: 728492, updated on 5-Mar-2024

Summary

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Official Symbol
SERF1Bprovided by HGNC
Official Full Name
small EDRK-rich factor 1Bprovided by HGNC
Primary source
HGNC:HGNC:10756
See related
Ensembl:ENSG00000205572 AllianceGenome:HGNC:10756
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
h4F5; FAM2B; H4F5C
Summary
This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. This gene is the centromeric copy which is identical to the telomeric copy. Alternatively spliced transcripts have been documented but it is unclear whether alternative splicing occurs for both the centromeric and telomeric copies of the gene. The gene encodes a protein of unknown function which bears low-level homology with the RNA-binding domain of matrin-cyclophilin, a protein which colocalizes with small nuclear ribonucleoproteins (snRNPs) and the SMN1 gene product. [provided by RefSeq, Jul 2008]
Annotation information
Note: June 2007: The sequences of SERF1A and SERF1B are identical. The names were switched so that the location of each gene corresponds with the official nomenclature, which specifies telomeric and centromeric copies. [26 Jun 2007]
Expression
Broad expression in testis (RPKM 16.5), brain (RPKM 11.2) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See SERF1B in Genome Data Viewer
Location:
5q13.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (70025251..70043113)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (70844220..70862105, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (69321078..69338940)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900996 Neighboring gene GUSB pseudogene 13 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:69257484-69258124 Neighboring gene cadherin 12 pseudogene 2 Neighboring gene mitochondrial import receptor subunit TOM5 homolog Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:69351921-69352560 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:69352561-69353200 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:69384675-69385378 Neighboring gene survival of motor neuron 2, centromeric Neighboring gene NAIP pseudogene 2 Neighboring gene GUSB pseudogene 14

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. Increased Aggregation Tendency of Alpha-Synuclein in a Fully Disordered Protein Complex. Merle DA, et al. J Mol Biol, 2019 Jun 28. PMID 31034892
  2. Identification of MOAG-4/SERF as a regulator of age-related proteotoxicity. van Ham TJ, et al. Cell, 2010 Aug 20. PMID 20723760
  3. Identification of a candidate modifying gene for spinal muscular atrophy by comparative genomics. Scharf JM, et al. Nat Genet, 1998 Sep. PMID 9731538
  4. SERF protein is a direct modifier of amyloid fiber assembly. Falsone SF, et al. Cell Rep, 2012 Aug 30. PMID 22854022, Free PMC Article
  5. Comparative sequence analysis of the mouse and human Lgn1/SMA interval. Endrizzi M, et al. Genomics, 1999 Sep 1. PMID 10486205

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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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)

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

  • MGC125278, MGC125279, MGC125280

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in amyloid fibril formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nervous system development TAS
Traceable Author Statement
more info
 PubMed 
involved_in protein destabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of protein-containing complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
small EDRK-rich factor 1
Names
SMA modifier 1
protein 4F5
small EDRK-rich factor 1B (centromeric)

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_001178087.2 → NP_001171558.1  small EDRK-rich factor 1 isoform 1

    See identical proteins and their annotated locations for NP_001171558.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC139277
    Consensus CDS
    CCDS54866.1
    UniProtKB/Swiss-Prot
    O75920
    Related
    ENSP00000370127.5, ENST00000380751.10

  2. NM_022978.3 → NP_075267.1  small EDRK-rich factor 1 isoform 2

    See identical proteins and their annotated locations for NP_075267.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 3' exon, as compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, as compared to isoform 1.
    Source sequence(s)
    AC139277, BC103687, BC104738, BM686659, DB454907
    Consensus CDS
    CCDS43326.1
    UniProtKB/Swiss-Prot
    B7ZKM2, O75919, O75920, Q52LK5
    UniProtKB/TrEMBL
    D6RCL9
    Related
    ENSP00000370126.4, ENST00000380750.8
    Conserved Domains (1) summary
    pfam04419
    Location:1 → 37
    4F5; 4F5 protein family

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    70025251..70043113
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791777.1 Reference GRCh38.p14 PATCHES

    Range
    857090..874971 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187651.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    250583..268460
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    70844220..70862105 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75920.1 GenPept UniProtKB/Swiss-Prot:O75920

Gene LinkOut

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