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Protein

Splicing factor 3B subunit 6

Gene

Sf3b6

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Necessary for the splicing of pre-mRNA. Directly contacts the pre-mRNA branch site adenosine for the first catalytic step of splicing. Enters the spliceosome and associates with the pre-mRNA branch site as part of the 17S U2 or, in the case of the minor spliceosome, as part of the 18S U11/U12 snRNP complex, and thus may facilitate the interaction of these snRNP with the branch sites of U2 and U12 respectively (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

  • blastocyst formation Source: MGI
  • mRNA splicing, via spliceosome Source: MGI
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-72163. mRNA Splicing - Major Pathway.
R-MMU-72165. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Splicing factor 3B subunit 6
Alternative name(s):
Pre-mRNA branch site protein p14
SF3b 14 kDa subunit
Gene namesi
Name:Sf3b6
Synonyms:Sf3b14
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 12

Organism-specific databases

MGIiMGI:1913305. Sf3b6.

Subcellular locationi

GO - Cellular componenti

  • nucleoplasm Source: MGI
  • nucleus Source: MGI
  • U12-type spliceosomal complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 125125Splicing factor 3B subunit 6PRO_0000081726Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei29 – 291N6-acetyllysine; alternateBy similarity
Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei41 – 411N6-acetyllysineBy similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiP59708.
MaxQBiP59708.
PaxDbiP59708.
PRIDEiP59708.

PTM databases

iPTMnetiP59708.
PhosphoSiteiP59708.

Expressioni

Gene expression databases

BgeeiP59708.
CleanExiMM_0610009D07RIK.
GenevisibleiP59708. MM.

Interactioni

Subunit structurei

Component of splicing factor SF3B complex which is composed of at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6, PHF5A/SF3B14B, and DDX42/SF3B125. Interacts with SF3B1. Interacts to a lesser extent with SF3B3. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome.

Protein-protein interaction databases

BioGridi211182. 1 interaction.
IntActiP59708. 2 interactions.
MINTiMINT-1868268.
STRINGi10090.ENSMUSP00000043662.

Structurei

3D structure databases

ProteinModelPortaliP59708.
SMRiP59708. Positions 12-125.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini19 – 9476RRMPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni16 – 2914Interaction with pre-mRNA branch siteBy similarityAdd
BLAST

Sequence similaritiesi

Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0114. Eukaryota.
ENOG4111IHX. LUCA.
GeneTreeiENSGT00390000005908.
HOGENOMiHOG000276232.
HOVERGENiHBG039634.
InParanoidiP59708.
KOiK12833.
OMAiVVYDDVM.
OrthoDBiEOG7JT6Z3.
PhylomeDBiP59708.
TreeFamiTF314161.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P59708-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAMQAAKRAN IRLPPEVNRI LYIRNLPYKI TAEEMYDIFG KYGPIRQIRV
60 70 80 90 100
GNTPETRGTA YVVYEDIFDA KNACDHLSGF NVCNRYLVVL YYNANRAFQK
110 120
MDTKKKEEQL KLLKEKYGIN TDPPK
Length:125
Mass (Da):14,585
Last modified:June 6, 2003 - v1
Checksum:iA1439DACB78A3208
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK002375 mRNA. Translation: BAB22052.1.
AK003683 mRNA. Translation: BAB22936.1.
AK151648 mRNA. Translation: BAE30577.1.
BC019535 mRNA. Translation: AAH19535.1.
CCDSiCCDS25791.1.
RefSeqiNP_079599.1. NM_025323.2.
UniGeneiMm.102627.

Genome annotation databases

EnsembliENSMUST00000046207; ENSMUSP00000043662; ENSMUSG00000037361.
GeneIDi66055.
KEGGimmu:66055.
UCSCiuc007myi.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK002375 mRNA. Translation: BAB22052.1.
AK003683 mRNA. Translation: BAB22936.1.
AK151648 mRNA. Translation: BAE30577.1.
BC019535 mRNA. Translation: AAH19535.1.
CCDSiCCDS25791.1.
RefSeqiNP_079599.1. NM_025323.2.
UniGeneiMm.102627.

3D structure databases

ProteinModelPortaliP59708.
SMRiP59708. Positions 12-125.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi211182. 1 interaction.
IntActiP59708. 2 interactions.
MINTiMINT-1868268.
STRINGi10090.ENSMUSP00000043662.

PTM databases

iPTMnetiP59708.
PhosphoSiteiP59708.

Proteomic databases

EPDiP59708.
MaxQBiP59708.
PaxDbiP59708.
PRIDEiP59708.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000046207; ENSMUSP00000043662; ENSMUSG00000037361.
GeneIDi66055.
KEGGimmu:66055.
UCSCiuc007myi.1. mouse.

Organism-specific databases

CTDi51639.
MGIiMGI:1913305. Sf3b6.

Phylogenomic databases

eggNOGiKOG0114. Eukaryota.
ENOG4111IHX. LUCA.
GeneTreeiENSGT00390000005908.
HOGENOMiHOG000276232.
HOVERGENiHBG039634.
InParanoidiP59708.
KOiK12833.
OMAiVVYDDVM.
OrthoDBiEOG7JT6Z3.
PhylomeDBiP59708.
TreeFamiTF314161.

Enzyme and pathway databases

ReactomeiR-MMU-72163. mRNA Splicing - Major Pathway.
R-MMU-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

NextBioi320494.
PROiP59708.
SOURCEiSearch...

Gene expression databases

BgeeiP59708.
CleanExiMM_0610009D07RIK.
GenevisibleiP59708. MM.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 1 hit.
[Graphical view]
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Bone marrow.
  2. "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].
    Strain: FVB/N.
    Tissue: Mammary tumor.
  3. "Comprehensive identification of phosphorylation sites in postsynaptic density preparations."
    Trinidad J.C., Specht C.G., Thalhammer A., Schoepfer R., Burlingame A.L.
    Mol. Cell. Proteomics 5:914-922(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain.
  4. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Pancreas, Spleen and Testis.

Entry informationi

Entry nameiSF3B6_MOUSE
AccessioniPrimary (citable) accession number: P59708
Secondary accession number(s): Q3U9T9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 6, 2003
Last sequence update: June 6, 2003
Last modified: May 11, 2016
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  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.