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Protein

Splicing factor U2AF 26 kDa subunit

Gene

U2af1l4

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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. Shows a preference for AGC or AGA.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):
Liver regeneration-related protein LRRG157/LRRG158
U2 auxiliary factor 26
U2 small nuclear RNA auxiliary factor 1-like protein 4
Short name:
U2AF1-like 4By similarity
Gene namesi
Name:U2af1l4
ORF Names:Cb2-806, Cb2-807
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 1

Organism-specific databases

RGDi1305600. 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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 220219Splicing factor U2AF 26 kDa subunitPRO_0000309742Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

PRIDEiQ7TP17.

PTM databases

PhosphoSiteiQ7TP17.

Expressioni

Gene expression databases

GenevisibleiQ7TP17. RN.

Interactioni

Subunit structurei

Interacts with GFI1, U2AF2 and C1QBP.By similarity

Structurei

3D structure databases

ProteinModelPortaliQ7TP17.
SMRiQ7TP17. Positions 15-185.
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

GeneTreeiENSGT00530000063193.
HOGENOMiHOG000178619.
HOVERGENiHBG054605.
InParanoidiQ7TP17.
KOiK12836.
OMAiLAKIERW.
OrthoDBiEOG70089G.
PhylomeDBiQ7TP17.
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. U2AF_small.
IPR000571. Znf_CCCH.
[Graphical view]
PANTHERiPTHR12620. PTHR12620. 1 hit.
PfamiPF00076. RRM_1. 1 hit.
PF00642. zf-CCCH. 2 hits.
[Graphical view]
PRINTSiPR01848. U2AUXFACTOR.
SMARTiSM00360. RRM. 1 hit.
SM00361. RRM_1. 1 hit.
SM00356. ZnF_C3H1. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
PS50103. ZF_C3H1. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q7TP17-1) [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 YFKIGACRHG DRCSRLHNKP TFSQTIVLLN
60 70 80 90 100
LYRNPQNTAQ TADGSHCHVS DVEVQEHYDN FFEEVFTELQ EKYGEIEEMN
110 120 130 140 150
VCDNLGDHLV GNVYVKFRRE EDAERAVAEL NNRWFNGQAV HAELSPVTDF
160 170 180 190 200
RESCCRQYEM GECTRGGFCN FMHLRPISRN LRRQLYGRGP RHRSPPRSHT
210 220
GHRPRERNRR RSPDHRHGRF
Length:220
Mass (Da):25,836
Last modified:October 1, 2003 - v1
Checksum:i90AC4B4126060169
GO
Isoform 2 (identifier: Q7TP17-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-43: MAEYLASIFG...SRLHNKPTFS → MVIQVVRTIT...SELRSLLNFV

Note: No experimental confirmation available.
Show »
Length:254
Mass (Da):29,358
Checksum:iDAE2DB104C3C66A0
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 4343MAEYL…KPTFS → MVIQVVRTITQKRKPTAERQ TSRKKNQGLTALFTLRLGPA GTGTGAPDFTTNRLSARVGY TLHAVPLSELRSLLNFV in isoform 2. 1 PublicationVSP_029266Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY325237 mRNA. Translation: AAP92638.1.
AY325238 mRNA. Translation: AAP92639.1.
RefSeqiNP_001008775.1. NM_001008775.1. [Q7TP17-1]
XP_006228838.1. XM_006228776.2. [Q7TP17-1]
UniGeneiRn.145185.

Genome annotation databases

EnsembliENSRNOT00000038154; ENSRNOP00000030286; ENSRNOG00000024497. [Q7TP17-1]
GeneIDi361542.
KEGGirno:361542.
UCSCiRGD:1305600. rat. [Q7TP17-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY325237 mRNA. Translation: AAP92638.1.
AY325238 mRNA. Translation: AAP92639.1.
RefSeqiNP_001008775.1. NM_001008775.1. [Q7TP17-1]
XP_006228838.1. XM_006228776.2. [Q7TP17-1]
UniGeneiRn.145185.

3D structure databases

ProteinModelPortaliQ7TP17.
SMRiQ7TP17. Positions 15-185.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

PhosphoSiteiQ7TP17.

Proteomic databases

PRIDEiQ7TP17.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000038154; ENSRNOP00000030286; ENSRNOG00000024497. [Q7TP17-1]
GeneIDi361542.
KEGGirno:361542.
UCSCiRGD:1305600. rat. [Q7TP17-1]

Organism-specific databases

CTDi199746.
RGDi1305600. U2af1l4.

Phylogenomic databases

GeneTreeiENSGT00530000063193.
HOGENOMiHOG000178619.
HOVERGENiHBG054605.
InParanoidiQ7TP17.
KOiK12836.
OMAiLAKIERW.
OrthoDBiEOG70089G.
PhylomeDBiQ7TP17.
TreeFamiTF300143.

Miscellaneous databases

NextBioi676661.
PROiQ7TP17.

Gene expression databases

GenevisibleiQ7TP17. RN.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
IPR009145. U2AF_small.
IPR000571. Znf_CCCH.
[Graphical view]
PANTHERiPTHR12620. PTHR12620. 1 hit.
PfamiPF00076. RRM_1. 1 hit.
PF00642. zf-CCCH. 2 hits.
[Graphical view]
PRINTSiPR01848. U2AUXFACTOR.
SMARTiSM00360. RRM. 1 hit.
SM00361. RRM_1. 1 hit.
SM00356. ZnF_C3H1. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
PS50103. ZF_C3H1. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Liver regeneration after PH."
    Xu C.S., Li W.Q., Li Y.C., Ma H., Wang L., Wang S.F., Han H.P., Wang G.P., Chai L.Q., Yuan J.Y., Yang K.J., Yan H.M., Chang C.F., Zhao L.F., Shi J.B., Rahman S., Wang Q.N., Zhang J.B.
    Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Tissue: Liver.

Entry informationi

Entry nameiU2AF4_RAT
AccessioniPrimary (citable) accession number: Q7TP17
Secondary accession number(s): Q7TP18
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: October 1, 2003
Last modified: May 11, 2016
This is version 94 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

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, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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 one 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.