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Q8WU68

- U2AF4_HUMAN

UniProt

Q8WU68 - U2AF4_HUMAN

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Protein

Splicing factor U2AF 26 kDa subunit

Gene

U2AF1L4

Organism
Homo sapiens (Human)
Status
Reviewed - 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

  1. metal ion binding Source: UniProtKB-KW
  2. nucleotide binding Source: InterPro
  3. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. mRNA processing Source: UniProtKB-KW
  2. RNA splicing Source: UniProtKB-KW
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: 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

  1. spliceosomal complex Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA164742763.

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.
GenevestigatoriQ8WU68.

Organism-specific databases

HPAiHPA046378.

Interactioni

Subunit structurei

Interacts with GFI1, U2AF2 and C1QBP.By similarity

Protein-protein interaction databases

BioGridi128270. 6 interactions.
IntActiQ8WU68. 2 interactions.
STRINGi9606.ENSP00000292879.

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.
OMAiRPVHCEL.
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. Align

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. [Q8WU68-1]
GeneIDi199746.
KEGGihsa:199746.
UCSCiuc002obe.3. human. [Q8WU68-3]
uc002obf.3. human. [Q8WU68-2]

Polymorphism databases

DMDMi160358766.

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 .
CCDSi CCDS12473.1. [Q8WU68-2 ]
CCDS42551.1. [Q8WU68-3 ]
RefSeqi NP_001035515.1. NM_001040425.2. [Q8WU68-3 ]
NP_659424.2. NM_144987.3. [Q8WU68-2 ]
UniGenei Hs.351558.

3D structure databases

ProteinModelPortali Q8WU68.
SMRi Q8WU68. Positions 43-146.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 128270. 6 interactions.
IntActi Q8WU68. 2 interactions.
STRINGi 9606.ENSP00000292879.

PTM databases

PhosphoSitei Q8WU68.

Polymorphism databases

DMDMi 160358766.

Proteomic databases

MaxQBi Q8WU68.
PaxDbi Q8WU68.
PRIDEi Q8WU68.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000292879 ; ENSP00000292879 ; ENSG00000161265 . [Q8WU68-2 ]
ENST00000378975 ; ENSP00000368258 ; ENSG00000161265 . [Q8WU68-3 ]
ENST00000412391 ; ENSP00000397645 ; ENSG00000161265 . [Q8WU68-1 ]
GeneIDi 199746.
KEGGi hsa:199746.
UCSCi uc002obe.3. human. [Q8WU68-3 ]
uc002obf.3. human. [Q8WU68-2 ]

Organism-specific databases

CTDi 199746.
GeneCardsi GC19M036233.
HGNCi HGNC:23020. U2AF1L4.
HPAi HPA046378.
MIMi 601080. gene.
neXtProti NX_Q8WU68.
PharmGKBi PA164742763.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG252826.
GeneTreei ENSGT00530000063193.
HOGENOMi HOG000178619.
HOVERGENi HBG054605.
InParanoidi Q8WU68.
OMAi RPVHCEL.
PhylomeDBi Q8WU68.
TreeFami TF300143.

Miscellaneous databases

GenomeRNAii 199746.
NextBioi 89722.
PROi Q8WU68.
SOURCEi Search...

Gene expression databases

Bgeei Q8WU68.
CleanExi HS_U2AF1L4.
ExpressionAtlasi Q8WU68. baseline.
Genevestigatori Q8WU68.

Family and domain databases

Gene3Di 3.30.70.330. 1 hit.
InterProi IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
IPR009145. U2_small.
IPR000571. Znf_CCCH.
[Graphical view ]
PANTHERi PTHR12620. PTHR12620. 1 hit.
Pfami PF00076. RRM_1. 1 hit.
PF00642. zf-CCCH. 2 hits.
[Graphical view ]
PRINTSi PR01848. U2AUXFACTOR.
SMARTi SM00361. RRM_1. 1 hit.
SM00356. ZnF_C3H1. 2 hits.
[Graphical view ]
PROSITEi PS50102. RRM. 1 hit.
PS50103. ZF_C3H1. 2 hits.
[Graphical view ]
ProtoNeti Search...

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: October 29, 2014
This is version 120 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

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