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Protein

Splicing factor U2af small subunit B

Gene

U2AF35B

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Necessary for the splicing of pre-mRNA (By similarity). Probably active at the 3' splice sites.By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri12 – 4029C3H1-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri148 – 17528C3H1-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • mRNA splicing, via spliceosome Source: InterPro
  • photoperiodism, flowering Source: TAIR
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

DNA-binding, Metal-binding, RNA-binding, Zinc

Enzyme and pathway databases

ReactomeiR-ATH-72163. mRNA Splicing - Major Pathway.
R-ATH-72187. mRNA 3'-end processing.

Names & Taxonomyi

Protein namesi
Recommended name:
Splicing factor U2af small subunit B
Alternative name(s):
U2 auxiliary factor 35 kDa subunit B
U2 small nuclear ribonucleoprotein auxiliary factor small subunit B
Short name:
U2 snRNP auxiliary factor small subunit B
Zinc finger CCCH domain-containing protein 60
Short name:
AtC3H60
Gene namesi
Name:U2AF35B
Synonyms:AUSB
Ordered Locus Names:At5g42820
ORF Names:MJB21.20
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G42820.

Subcellular locationi

GO - Cellular componenti

  • nuclear speck Source: UniProtKB-SubCell
  • nucleus Source: TAIR
  • spliceosomal complex Source: UniProtKB-KW
  • U2AF Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 283283Splicing factor U2af small subunit BPRO_0000371962Add
BLAST

Proteomic databases

PaxDbiQ9FMY5.
PRIDEiQ9FMY5.

Expressioni

Gene expression databases

GenevisibleiQ9FMY5. AT.

Interactioni

Subunit structurei

Component of the spliceosome. Homo- and heterodimer. Interacts with RNU1, U2AF35A and SR45.1 Publication

Protein-protein interaction databases

BioGridi19543. 8 interactions.
IntActiQ9FMY5. 3 interactions.
STRINGi3702.AT5G42820.1.

Structurei

3D structure databases

ProteinModelPortaliQ9FMY5.
SMRiQ9FMY5. Positions 15-190.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini44 – 146103RRMPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi178 – 279102Arg/Ser-rich (RS domain)Add
BLAST

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 fingeri148 – 17528C3H1-type 2PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG2202. Eukaryota.
ENOG410Z5PX. LUCA.
HOGENOMiHOG000178619.
InParanoidiQ9FMY5.
KOiK12836.
OMAiDDYHHRD.
PhylomeDBiQ9FMY5.

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.
SMARTiSM00361. 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]

Sequencei

Sequence statusi: Complete.

Q9FMY5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHNRP TISPTLLLSN
60 70 80 90 100
MYQRPDMITP GVDPQGQPLD PSKIQDHFED FYEDIFEELN KFGEVESLNV
110 120 130 140 150
CDNLADHMIG NVYVLFKEED HAAAALQALQ GRFYSGRPII ADFSPVTDFR
160 170 180 190 200
EATCRQYEEN SCNRGGYCNF MHVKQISREL RRKLFGRYRR SYRRGSRSRS
210 220 230 240 250
RSISPRRKRE HSRERERGDV RDRDRHGNGK RSSDRSERHD RDGGGRRRHG
260 270 280
SPKRSRSPRN VREGSEERRA RIEQWNRERD EGV
Length:283
Mass (Da):33,232
Last modified:March 1, 2001 - v1
Checksum:i45407ABBFC1624A5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti102 – 1021D → V in AAL06332 (PubMed:16407443).Curated
Sequence conflicti167 – 1671Y → C in AAL06332 (PubMed:16407443).Curated
Sequence conflicti239 – 2391H → Y in AAL06332 (PubMed:16407443).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF409140 mRNA. Translation: AAL06332.1.
AB007647, AB008264 Genomic DNA. Translation: BAB10638.1.
CP002688 Genomic DNA. Translation: AED94868.1.
CP002688 Genomic DNA. Translation: AED94869.1.
AY136436 mRNA. Translation: AAM97101.1.
BT000219 mRNA. Translation: AAN15538.1.
RefSeqiNP_199096.1. NM_123647.2.
NP_974870.1. NM_203141.2.
UniGeneiAt.25814.
At.8456.

Genome annotation databases

EnsemblPlantsiAT5G42820.1; AT5G42820.1; AT5G42820.
AT5G42820.2; AT5G42820.2; AT5G42820.
GeneIDi834293.
GrameneiAT5G42820.1; AT5G42820.1; AT5G42820.
AT5G42820.2; AT5G42820.2; AT5G42820.
KEGGiath:AT5G42820.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF409140 mRNA. Translation: AAL06332.1.
AB007647, AB008264 Genomic DNA. Translation: BAB10638.1.
CP002688 Genomic DNA. Translation: AED94868.1.
CP002688 Genomic DNA. Translation: AED94869.1.
AY136436 mRNA. Translation: AAM97101.1.
BT000219 mRNA. Translation: AAN15538.1.
RefSeqiNP_199096.1. NM_123647.2.
NP_974870.1. NM_203141.2.
UniGeneiAt.25814.
At.8456.

3D structure databases

ProteinModelPortaliQ9FMY5.
SMRiQ9FMY5. Positions 15-190.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi19543. 8 interactions.
IntActiQ9FMY5. 3 interactions.
STRINGi3702.AT5G42820.1.

Proteomic databases

PaxDbiQ9FMY5.
PRIDEiQ9FMY5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G42820.1; AT5G42820.1; AT5G42820.
AT5G42820.2; AT5G42820.2; AT5G42820.
GeneIDi834293.
GrameneiAT5G42820.1; AT5G42820.1; AT5G42820.
AT5G42820.2; AT5G42820.2; AT5G42820.
KEGGiath:AT5G42820.

Organism-specific databases

TAIRiAT5G42820.

Phylogenomic databases

eggNOGiKOG2202. Eukaryota.
ENOG410Z5PX. LUCA.
HOGENOMiHOG000178619.
InParanoidiQ9FMY5.
KOiK12836.
OMAiDDYHHRD.
PhylomeDBiQ9FMY5.

Enzyme and pathway databases

ReactomeiR-ATH-72163. mRNA Splicing - Major Pathway.
R-ATH-72187. mRNA 3'-end processing.

Miscellaneous databases

PROiQ9FMY5.

Gene expression databases

GenevisibleiQ9FMY5. AT.

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.
SMARTiSM00361. 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

« Hide 'large scale' publications
  1. "Molecular characterization and phylogeny of U2AF35 homologs in plants."
    Wang B.-B., Brendel V.
    Plant Physiol. 140:624-636(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION.
    Strain: cv. Columbia.
    Tissue: Leaf.
  2. "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones."
    Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N., Tabata S.
    DNA Res. 4:401-414(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice."
    Wang D., Guo Y., Wu C., Yang G., Li Y., Zheng C.
    BMC Genomics 9:44-44(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE.
  6. "Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence: insights into regulated splicing."
    Day I.S., Golovkin M., Palusa S.G., Link A., Ali G.S., Thomas J., Richardson D.N., Reddy A.S.
    Plant J. 71:936-947(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RNU1; SR45 AND U2AF35A, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiU2AFB_ARATH
AccessioniPrimary (citable) accession number: Q9FMY5
Secondary accession number(s): Q945S0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 5, 2009
Last sequence update: March 1, 2001
Last modified: May 11, 2016
This is version 116 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. 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.