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Phf5a PHD finger protein 5A [ Mus musculus (house mouse) ]

Gene ID: 68479, updated on 12-May-2024

Summary

Official Symbol
Phf5aprovided by MGI
Official Full Name
PHD finger protein 5Aprovided by MGI
Primary source
MGI:MGI:2156864
See related
Ensembl:ENSMUSG00000061360 AllianceGenome:MGI:2156864
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
1110007B08Rik
Summary
Predicted to enable RNA binding activity and zinc ion binding activity. Acts upstream of or within stem cell differentiation. Located in nuclear matrix and nuclear speck. Is expressed in several structures, including brain ventricular layer; branchial arch; limb; maxillary process; and sensory organ. Orthologous to human PHF5A (PHD finger protein 5A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in liver E14 (RPKM 43.6), CNS E11.5 (RPKM 39.2) and 28 other tissues See more
Orthologs
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Genomic context

Location:
15 E1; 15 38.26 cM
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (81748717..81756093, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (81864516..81871892, complement)

Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E8599 Neighboring gene predicted gene 8444 Neighboring gene STARR-positive B cell enhancer ABC_E7399 Neighboring gene STARR-positive B cell enhancer ABC_E481 Neighboring gene transducer of ERBB2, 2 Neighboring gene aconitase 2, mitochondrial Neighboring gene STARR-seq mESC enhancer starr_39272 Neighboring gene polymerase (RNA) III (DNA directed) polypeptide H Neighboring gene STARR-positive B cell enhancer ABC_E2447 Neighboring gene cold shock domain containing C2, RNA binding

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Targeted (1)  1 citation
  • Transgenic (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA binding ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
contributes_to protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables zinc ion binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in mRNA splicing, via spliceosome ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in stem cell differentiation IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
part_of U12-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of U12-type spliceosomal complex ISO
Inferred from Sequence Orthology
more info
 
part_of U2 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of U2 snRNP ISO
Inferred from Sequence Orthology
more info
 
part_of U2-type precatalytic spliceosome ISO
Inferred from Sequence Orthology
more info
 
part_of U2-type spliceosomal complex ISO
Inferred from Sequence Orthology
more info
 
located_in nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
PubMed 
NOT located_in nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of precatalytic spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of spliceosomal complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
PHD finger-like domain-containing protein 5A
Names
PHD finger-like domain protein 5A
SF3b14b
splicing factor 3B-associated 14 kDa 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.

mRNA and Protein(s)

  1. NM_026737.3NP_081013.1  PHD finger-like domain-containing protein 5A

    See identical proteins and their annotated locations for NP_081013.1

    Status: PROVISIONAL

    Source sequence(s)
    AK143590
    Consensus CDS
    CCDS27674.1
    UniProtKB/Swiss-Prot
    P83870, Q3TQX7
    Related
    ENSMUSP00000023117.9, ENSMUST00000023117.10
    Conserved Domains (1) summary
    pfam03660
    Location:1104
    PHF5; PHF5-like protein

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000081.7 Reference GRCm39 C57BL/6J

    Range
    81748717..81756093 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)