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Protein

Splicing factor U2AF 26 kDa subunit

Gene

U2AF1L4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

RNA-binding protein that function as a pre-mRNA splicing factor. Plays a critical role in both constitutive and enhancer-dependent splicing by mediating protein-protein interactions and protein-RNA interactions required for accurate 3'-splice site selection. Acts by enhancing the binding of U2AF2 to weak pyrimidine tracts. Also participates in the regulation of alternative pre-mRNA splicing. Activates exon 5 skipping of PTPRC during T-cell activation; an event reversed by GFI1. Binds to RNA at the AG dinucleotide at the 3'-splice site (By similarity). Shows a preference for AGC or AGA (By similarity).By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri12 – 4029C3H1-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri149 – 17628C3H1-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

Metal-binding, RNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Splicing factor U2AF 26 kDa subunit
Alternative name(s):
U2 auxiliary factor 26
U2 small nuclear RNA auxiliary factor 1-like protein 4
Short name:
U2AF1-like 4By similarity
U2(RNU2) small nuclear RNA auxiliary factor 1-like protein 3
Short name:
U2 small nuclear RNA auxiliary factor 1-like protein 3
Short name:
U2AF1-like protein 3
Gene namesi
Name:U2AF1L4
Synonyms:U2AF1-RS3, U2AF1L3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:23020. U2AF1L4.

Subcellular locationi

  • Nucleus By similarity
  • Nucleus speckle By similarity
  • Cytoplasm By similarity

  • Note: Interaction with C1QBP is required for the nuclear translocation. Displays active nucleo-cytoplasmic shuttling.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA164742763.

Polymorphism and mutation databases

DMDMi160358766.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 220219Splicing factor U2AF 26 kDa subunitPRO_0000309740Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ8WU68.
PaxDbiQ8WU68.
PRIDEiQ8WU68.

PTM databases

PhosphoSiteiQ8WU68.

Expressioni

Tissue specificityi

Isoform 2 is widely expressed. Isoform 3 is highly expressed in heart, brain and lung, lower expressed in thymus and much lower expressed in peripheral blood leukocytes.1 Publication

Gene expression databases

BgeeiQ8WU68.
CleanExiHS_U2AF1L4.
ExpressionAtlasiQ8WU68. baseline.
GenevisibleiQ8WU68. HS.

Organism-specific databases

HPAiHPA052083.
HPA061644.

Interactioni

Subunit structurei

Interacts with GFI1, U2AF2 and C1QBP.By similarity

Protein-protein interaction databases

BioGridi128270. 4 interactions.
IntActiQ8WU68. 2 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ8WU68.
SMRiQ8WU68. Positions 43-146.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini65 – 14783RRMPROSITE-ProRule annotationAdd
BLAST

Domaini

The second zinc finger in necessary for interaction with GFI1 and for alternative pre-mRNA splicing events.By similarity
The region 162-220 is essential for the nuclear import of the protein in spite of the absence of a nuclear localization signal (NLS). This region is essential for the interaction with C1QBP, interaction which is required for the nuclear translocation. This region may be involved in the localization in nuclear dot-like structures and it also confers the ability of nucleo-cytoplasmic shuttling.By similarity

Sequence similaritiesi

Belongs to the splicing factor SR family.Curated
Contains 2 C3H1-type zinc fingers.PROSITE-ProRule annotation
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri12 – 4029C3H1-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri149 – 17628C3H1-type 2PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG252826.
GeneTreeiENSGT00530000063193.
HOGENOMiHOG000178619.
HOVERGENiHBG054605.
InParanoidiQ8WU68.
KOiK12836.
OMAiDEAGHYP.
PhylomeDBiQ8WU68.
TreeFamiTF300143.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
IPR009145. U2_small.
IPR000571. Znf_CCCH.
[Graphical view]
PANTHERiPTHR12620. PTHR12620. 1 hit.
PfamiPF00076. RRM_1. 1 hit.
PF00642. zf-CCCH. 2 hits.
[Graphical view]
PRINTSiPR01848. U2AUXFACTOR.
SMARTiSM00361. RRM_1. 1 hit.
SM00356. ZnF_C3H1. 2 hits.
[Graphical view]
PROSITEiPS50102. RRM. 1 hit.
PS50103. ZF_C3H1. 2 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8WU68-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAEYLASIFG TEKDKVNCSF YFKIGVCRHG DRCSRLHNKP TFSQTIVLLN
60 70 80 90 100
LYRNPQNTAQ TADGSHCHVS DVEVQEHYDS FFEEVFTELQ EKYGEIEEMN
110 120 130 140 150
VCDNLGDHLV GNVYVKFRRE EDGERAVAEL SNRWFNGQAV HGELSPVTDF
160 170 180 190 200
RESCCRQYEM GECTRGGFCN FMHLRPISQN LQRQLYGRGP RRRSPPRFHT
210 220
GHHPRERNHR CSPDHWHGRF
Note: No experimental confirmation available.
Length:220
Mass (Da):25,744
Last modified:November 13, 2007 - v2
Checksum:i64BA09EEDE3FB093
GO
Isoform 2 (identifier: Q8WU68-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     45-83: Missing.
     143-220: ELSPVTDFRE...CSPDHWHGRF → NVPEVASATS...ILPRLPGSIM

Show »
Length:202
Mass (Da):22,017
Checksum:iE7001729AA18DD96
GO
Isoform 3 (identifier: Q8WU68-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     45-83: Missing.

Show »
Length:181
Mass (Da):21,283
Checksum:iEE3B93447ABA55AF
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti109 – 1091L → V in AAH21186 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei45 – 8339Missing in isoform 2 and isoform 3. 2 PublicationsVSP_029264Add
BLAST
Alternative sequencei143 – 22078ELSPV…WHGRF → NVPEVASATSCICGPFPRTS RGSSMGGDPGAGHPRGSILA TIPERGTIGVPLITGMAASE ALAPLPFTPNRDRCSWQDLS SKPPSLSCPILPRLPGSIM in isoform 2. 1 PublicationVSP_029265Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY569437 mRNA. Translation: AAT72770.3.
AD000671 Genomic DNA. No translation available.
BC021186 mRNA. Translation: AAH21186.1.
CCDSiCCDS12473.1. [Q8WU68-2]
CCDS42551.1. [Q8WU68-3]
RefSeqiNP_001035515.1. NM_001040425.2. [Q8WU68-3]
NP_659424.2. NM_144987.3. [Q8WU68-2]
UniGeneiHs.351558.

Genome annotation databases

EnsembliENST00000292879; ENSP00000292879; ENSG00000161265. [Q8WU68-2]
ENST00000378975; ENSP00000368258; ENSG00000161265. [Q8WU68-3]
ENST00000412391; ENSP00000397645; ENSG00000161265.
GeneIDi199746.
KEGGihsa:199746.
UCSCiuc002obe.3. human. [Q8WU68-3]
uc002obf.3. human. [Q8WU68-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY569437 mRNA. Translation: AAT72770.3.
AD000671 Genomic DNA. No translation available.
BC021186 mRNA. Translation: AAH21186.1.
CCDSiCCDS12473.1. [Q8WU68-2]
CCDS42551.1. [Q8WU68-3]
RefSeqiNP_001035515.1. NM_001040425.2. [Q8WU68-3]
NP_659424.2. NM_144987.3. [Q8WU68-2]
UniGeneiHs.351558.

3D structure databases

ProteinModelPortaliQ8WU68.
SMRiQ8WU68. Positions 43-146.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi128270. 4 interactions.
IntActiQ8WU68. 2 interactions.

PTM databases

PhosphoSiteiQ8WU68.

Polymorphism and mutation databases

DMDMi160358766.

Proteomic databases

MaxQBiQ8WU68.
PaxDbiQ8WU68.
PRIDEiQ8WU68.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000292879; ENSP00000292879; ENSG00000161265. [Q8WU68-2]
ENST00000378975; ENSP00000368258; ENSG00000161265. [Q8WU68-3]
ENST00000412391; ENSP00000397645; ENSG00000161265.
GeneIDi199746.
KEGGihsa:199746.
UCSCiuc002obe.3. human. [Q8WU68-3]
uc002obf.3. human. [Q8WU68-2]

Organism-specific databases

CTDi199746.
GeneCardsiGC19M036233.
HGNCiHGNC:23020. U2AF1L4.
HPAiHPA052083.
HPA061644.
MIMi601080. gene.
neXtProtiNX_Q8WU68.
PharmGKBiPA164742763.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG252826.
GeneTreeiENSGT00530000063193.
HOGENOMiHOG000178619.
HOVERGENiHBG054605.
InParanoidiQ8WU68.
KOiK12836.
OMAiDEAGHYP.
PhylomeDBiQ8WU68.
TreeFamiTF300143.

Miscellaneous databases

GenomeRNAii199746.
NextBioi89722.
PROiQ8WU68.
SOURCEiSearch...

Gene expression databases

BgeeiQ8WU68.
CleanExiHS_U2AF1L4.
ExpressionAtlasiQ8WU68. baseline.
GenevisibleiQ8WU68. HS.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
IPR009145. U2_small.
IPR000571. Znf_CCCH.
[Graphical view]
PANTHERiPTHR12620. PTHR12620. 1 hit.
PfamiPF00076. RRM_1. 1 hit.
PF00642. zf-CCCH. 2 hits.
[Graphical view]
PRINTSiPR01848. U2AUXFACTOR.
SMARTiSM00361. RRM_1. 1 hit.
SM00356. ZnF_C3H1. 2 hits.
[Graphical view]
PROSITEiPS50102. RRM. 1 hit.
PS50103. ZF_C3H1. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and characterization of a novel splice variant of human U2AF1L3 gene."
    Chen F., Ji C., Dou T., Zheng N., Qiu R., Peng J., Fang W., Feng C., Xie Y., Mao Y.
    DNA Seq. 17:282-286(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), TISSUE SPECIFICITY.
  2. "The DNA sequence and biology of human chromosome 19."
    Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V.
    , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.
    Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
    Tissue: Brain.
  4. Bienvenut W.V., Zebisch A., Kolch W.
    Submitted (OCT-2008) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 2-13, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY.
    Tissue: Colon carcinoma.

Entry informationi

Entry nameiU2AF4_HUMAN
AccessioniPrimary (citable) accession number: Q8WU68
Secondary accession number(s): A6NKI8, Q56UU3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: November 13, 2007
Last modified: July 22, 2015
This is version 128 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Caution

Orthologs of U2AF1L4 do not appear to exist in lower eukaryotes, Drosophila, C. elegans, plants, or vertebrates such as Xenopus or zebrafish. Existence of circadian and light-inducible alternative splicing of U2AF1L4 similar to the mouse in human and rat is not yet proven.Curated

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.