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U2AF1L4 U2 small nuclear RNA auxiliary factor 1 like 4 [ Homo sapiens (human) ]

Gene ID: 199746, updated on 27-Nov-2024

Summary

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Official Symbol
U2AF1L4provided by HGNC
Official Full Name
U2 small nuclear RNA auxiliary factor 1 like 4provided by HGNC
Primary source
HGNC:HGNC:23020
See related
Ensembl:ENSG00000161265 MIM:601080; AllianceGenome:HGNC:23020
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
Also known as
U2af26; U2AF1L3; U2AF1RS3; U2AF1-RS3; U2AF1L3V1
Summary
Predicted to enable pre-mRNA 3'-splice site binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be part of U2AF complex and spliceosomal complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in spleen (RPKM 9.3), thyroid (RPKM 9.1) and 25 other tissues See more
Orthologs
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Genomic context

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See U2AF1L4 in Genome Data Viewer
Location:
19q13.12
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (35742464..35745418, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38287776..38290728, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36233365..36236319, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger and BTB domain containing 32 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14494 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10532 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:36207458-36208017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10535 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:36209137-36209694 Neighboring gene lysine methyltransferase 2B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36230671-36231301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14497 Neighboring gene IGF like family receptor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36234871-36235031 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36238731-36239245 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36239246-36239760 Neighboring gene presenilin enhancer, gamma-secretase subunit Neighboring gene lin-37 DREAM MuvB core complex component

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. Functional dissection of an enhancer-like element located within the second intron of the human U2AF1L4 gene. Didych DA, et al. Biochemistry (Mosc), 2011 Aug. PMID 22022969
  2. Absence of imprinting in U2AFBPL, a human homologue of the imprinted mouse gene U2afbp-rs. Pearsall RS, et al. Biochem Biophys Res Commun, 1996 May 6. PMID 8630064
  3. Cloning and characterization of a novel splice variant of human Rab18 gene (RAB18). Dou T, et al. DNA Seq, 2005 Jun. PMID 16147880
  4. The zinc finger domains in U2AF26 and U2AF35 have diverse functionalities including a role in controlling translation. Herdt O, et al. RNA Biol, 2020 Jun. PMID 32116123, Free PMC Article
  5. Human PSENEN and U2AF1L4 genes are concertedly regulated by a genuine bidirectional promoter. Didych DA, et al. Gene, 2013 Feb 15. PMID 23246698

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The zinc finger domains in U2AF26 and U2AF35 have diverse functionalities including a role in controlling translation.
    Title: The zinc finger domains in U2AF26 and U2AF35 have diverse functionalities including a role in controlling translation.
  2. U2AF1L4 gene expression is regulated by cytokines in activated T cells.
    Title: [Cytokine-mediated regulation of expression of Gfi1 and U2afll4 genes activated by T-cells with different differentiation status in vitro].
  3. a 269 bp region located between the PSENEN and U2AF1L4 human genes is a genuine bidirectional promoter regulating a concerted divergent transcription of these genes.
    Title: Human PSENEN and U2AF1L4 genes are concertedly regulated by a genuine bidirectional promoter.
  4. One of the conservative regions is responsible for the enhancer activity and is able to interact with proteins of HeLa cell nuclear extract.
    Title: Functional dissection of an enhancer-like element located within the second intron of the human U2AF1L4 gene.
  5. Differential isoform expression and interaction with the P32 regulatory protein controls the subcellular localization of the splicing factor U2AF26
    Title: Differential isoform expression and interaction with the P32 regulatory protein controls the subcellular localization of the splicing factor U2AF26.
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

  • FLJ18593, FLJ35525, MGC33901

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables pre-mRNA 3'-splice site binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of U2AF complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
splicing factor U2AF 26 kDa subunit
Names
U2 auxiliary factor 26
U2 small nuclear RNA auxiliary factor 1-like 3
U2 small nuclear RNA auxiliary factor 1-like protein 3
U2 small nuclear RNA auxiliary factor 1-like protein 4
U2(RNU2) small nuclear RNA auxiliary factor 1-like 3
U2(RNU2) small nuclear RNA auxiliary factor 1-like protein 3
U2AF1-like 4
U2AF1-like protein 3

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_001040425.3 → NP_001035515.1  splicing factor U2AF 26 kDa subunit isoform 1

    See identical proteins and their annotated locations for NP_001035515.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) has an alternate splice site in the coding region, which results in reading frameshift, compared to variant 2. The resulting isoform (1) is shorter and has a distinct C-terminus, compared to isoform 2.
    Source sequence(s)
    AI767079, AY569437, DC415103
    Consensus CDS
    CCDS42551.1
    UniProtKB/Swiss-Prot
    A6NKI8, Q56UU3, Q8WU68
    Related
    ENSP00000368258.2, ENST00000378975.8
    Conserved Domains (2) summary
    pfam00642
    Location:110 → 136
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:41 → 107
    RRM_SF; RNA recognition motif (RRM) superfamily

  2. NM_001369824.2 → NP_001356753.1  splicing factor U2AF 26 kDa subunit isoform 3

    Status: VALIDATED

    Source sequence(s)
    AD000671
    Conserved Domains (2) summary
    pfam00642
    Location:13 → 39
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:41 → 102
    RRM_SF; RNA recognition motif (RRM) superfamily

  3. NM_144987.4 → NP_659424.2  splicing factor U2AF 26 kDa subunit isoform 2

    See identical proteins and their annotated locations for NP_659424.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) encodes the longer isoform (2).
    Source sequence(s)
    AI767079, AY569437, BC010865, BC021186, DC415103
    Consensus CDS
    CCDS12473.1
    UniProtKB/Swiss-Prot
    Q8WU68
    Related
    ENSP00000292879.4, ENST00000292879.9
    Conserved Domains (2) summary
    pfam00642
    Location:13 → 39
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    cl17169
    Location:41 → 102
    RRM_SF; RNA recognition motif (RRM) superfamily

RNA

  1. NR_110173.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) has an additional exon, compared to variant 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI767079, BC010865, BM696851

  2. NR_163169.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AD000671
    Related
    ENST00000592913.5

  3. NR_163170.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AD000671
    Related
    ENST00000587987.5

  4. NR_163171.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AD000671

  5. NR_163172.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AD000671

  6. NR_163173.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AD000671

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    35742464..35745418 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    38287776..38290728 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_110171.1: Suppressed sequence

    Description
    NR_110171.1: This RefSeq was removed because currently there is insufficient support for the transcript.

  2. NR_110172.1: Suppressed sequence

    Description
    NR_110172.1: This RefSeq was removed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WU68.2 GenPept UniProtKB/Swiss-Prot:Q8WU68

Gene LinkOut

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