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

    Gene ID: 199746, updated on 2-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
    mouse all
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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 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)

    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

    • 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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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