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Protein

Splicing factor 3B subunit 6

Gene

SF3B6

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 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.1 Publication

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-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
Short name:
SF3B14a
Spliceosome-associated protein, 14-kDa
Splicing factor 3b, subunit 6, 14kDa
Gene namesi
Name:SF3B6
Synonyms:SAP14, SF3B14, SF3B14A
ORF Names:CGI-110, HSPC175, HT006
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:30096. SF3B6.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Polymorphism and mutation databases

BioMutaiSF3B14.
DMDMi12585536.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 125125Splicing factor 3B subunit 6PRO_0000081725Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Acetylation, Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ9Y3B4.
MaxQBiQ9Y3B4.
PaxDbiQ9Y3B4.
PeptideAtlasiQ9Y3B4.
PRIDEiQ9Y3B4.
TopDownProteomicsiQ9Y3B4.

PTM databases

iPTMnetiQ9Y3B4.
PhosphoSiteiQ9Y3B4.
SwissPalmiQ9Y3B4.

Expressioni

Gene expression databases

BgeeiQ9Y3B4.
GenevisibleiQ9Y3B4. HS.

Organism-specific databases

HPAiHPA034829.
HPA034830.

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. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome.5 Publications

Protein-protein interaction databases

BioGridi119651. 66 interactions.
DIPiDIP-44132N.
IntActiQ9Y3B4. 13 interactions.
MINTiMINT-3085643.
STRINGi9606.ENSP00000233468.

Structurei

Secondary structure

1
125
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi19 – 257Combined sources
Helixi32 – 409Combined sources
Beta strandi45 – 517Combined sources
Turni54 – 585Combined sources
Beta strandi60 – 667Combined sources
Helixi67 – 7711Combined sources
Beta strandi81 – 844Combined sources
Beta strandi88 – 914Combined sources
Helixi94 – 974Combined sources
Turni98 – 1003Combined sources
Helixi103 – 11715Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2F9DX-ray2.50A/B1-125[»]
2F9JX-ray3.00A/B1-125[»]
2FHONMR-B8-93[»]
3LQVX-ray2.38A/B11-125[»]
ProteinModelPortaliQ9Y3B4.
SMRiQ9Y3B4. Positions 12-125.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y3B4.

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 siteAdd
BLAST

Sequence similaritiesi

Belongs to the SF3B6 family.Curated
Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0114. Eukaryota.
ENOG4111IHX. LUCA.
GeneTreeiENSGT00390000005908.
HOGENOMiHOG000276232.
HOVERGENiHBG039634.
InParanoidiQ9Y3B4.
KOiK12833.
OMAiVVYDDVM.
OrthoDBiEOG7JT6Z3.
PhylomeDBiQ9Y3B4.

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.

Q9Y3B4-1 [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:November 1, 1999 - v1
Checksum:iA1439DACB78A3208
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF401310 mRNA. Translation: AAK94041.1.
AF151868 mRNA. Translation: AAD34105.1.
AF161523 mRNA. Translation: AAF29138.1.
AF184213 mRNA. Translation: AAG09698.1.
AK311908 mRNA. Translation: BAG34849.1.
AC008073 Genomic DNA. Translation: AAY14664.1.
CH471053 Genomic DNA. Translation: EAX00767.1.
BC015463 mRNA. Translation: AAH15463.1.
CCDSiCCDS1707.1.
RefSeqiNP_057131.1. NM_016047.3.
UniGeneiHs.177861.

Genome annotation databases

EnsembliENST00000233468; ENSP00000233468; ENSG00000115128.
GeneIDi51639.
KEGGihsa:51639.
UCSCiuc002rev.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF401310 mRNA. Translation: AAK94041.1.
AF151868 mRNA. Translation: AAD34105.1.
AF161523 mRNA. Translation: AAF29138.1.
AF184213 mRNA. Translation: AAG09698.1.
AK311908 mRNA. Translation: BAG34849.1.
AC008073 Genomic DNA. Translation: AAY14664.1.
CH471053 Genomic DNA. Translation: EAX00767.1.
BC015463 mRNA. Translation: AAH15463.1.
CCDSiCCDS1707.1.
RefSeqiNP_057131.1. NM_016047.3.
UniGeneiHs.177861.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2F9DX-ray2.50A/B1-125[»]
2F9JX-ray3.00A/B1-125[»]
2FHONMR-B8-93[»]
3LQVX-ray2.38A/B11-125[»]
ProteinModelPortaliQ9Y3B4.
SMRiQ9Y3B4. Positions 12-125.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119651. 66 interactions.
DIPiDIP-44132N.
IntActiQ9Y3B4. 13 interactions.
MINTiMINT-3085643.
STRINGi9606.ENSP00000233468.

PTM databases

iPTMnetiQ9Y3B4.
PhosphoSiteiQ9Y3B4.
SwissPalmiQ9Y3B4.

Polymorphism and mutation databases

BioMutaiSF3B14.
DMDMi12585536.

Proteomic databases

EPDiQ9Y3B4.
MaxQBiQ9Y3B4.
PaxDbiQ9Y3B4.
PeptideAtlasiQ9Y3B4.
PRIDEiQ9Y3B4.
TopDownProteomicsiQ9Y3B4.

Protocols and materials databases

DNASUi51639.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000233468; ENSP00000233468; ENSG00000115128.
GeneIDi51639.
KEGGihsa:51639.
UCSCiuc002rev.4. human.

Organism-specific databases

CTDi51639.
GeneCardsiSF3B6.
HGNCiHGNC:30096. SF3B6.
HPAiHPA034829.
HPA034830.
MIMi607835. gene.
neXtProtiNX_Q9Y3B4.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0114. Eukaryota.
ENOG4111IHX. LUCA.
GeneTreeiENSGT00390000005908.
HOGENOMiHOG000276232.
HOVERGENiHBG039634.
InParanoidiQ9Y3B4.
KOiK12833.
OMAiVVYDDVM.
OrthoDBiEOG7JT6Z3.
PhylomeDBiQ9Y3B4.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiQ9Y3B4.
GeneWikiiSF3B14.
GenomeRNAii51639.
PROiQ9Y3B4.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y3B4.
GenevisibleiQ9Y3B4. HS.

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

« Hide 'large scale' publications
  1. "A novel U2 and U11/U12 snRNP protein that associates with the pre-mRNA branch site."
    Will C.L., Schneider C., MacMillan A.M., Katopodis N.F., Neubauer G., Wilm M., Luehrmann R., Query C.C.
    EMBO J. 20:4536-4546(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 29-39 AND 41-58.
  2. "Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics."
    Lai C.-H., Chou C.-Y., Ch'ang L.-Y., Liu C.-S., Lin W.-C.
    Genome Res. 10:703-713(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  3. "Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells."
    Zhang Q.-H., Ye M., Wu X.-Y., Ren S.-X., Zhao M., Zhao C.-J., Fu G., Shen Y., Fan H.-Y., Lu G., Zhong M., Xu X.-R., Han Z.-G., Zhang J.-W., Tao J., Huang Q.-H., Zhou J., Hu G.-X.
    , Gu J., Chen S.-J., Chen Z.
    Genome Res. 10:1546-1560(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Umbilical cord blood.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Hypothalamus.
  5. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  6. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Tissue: Testis.
  7. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  8. "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].
    Tissue: Uterus.
  9. "Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein."
    Will C.L., Urlaub H., Achsel T., Gentzel M., Wilm M., Luehrmann R.
    EMBO J. 21:4978-4988(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SF3B COMPLEX, SUBCELLULAR LOCATION.
  10. "Molecular architecture of the multiprotein splicing factor SF3b."
    Golas M.M., Sander B., Will C.L., Luhrmann R., Stark H.
    Science 300:980-984(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SF3B COMPLEX, ELECTRON MICROSCOPY OF THE SF3B COMPLEX.
  11. "The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome."
    Will C.L., Schneider C., Hossbach M., Urlaub H., Rauhut R., Elbashir S., Tuschl T., Luehrmann R.
    RNA 10:929-941(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, IDENTIFICATION BY MASS SPECTROMETRY.
  12. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
    Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
    Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-29 AND LYS-41, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "System-wide analysis of SUMOylation dynamics in response to replication stress reveals novel small ubiquitin-like modified target proteins and acceptor lysines relevant for genome stability."
    Xiao Z., Chang J.G., Hendriks I.A., Sigurdsson J.O., Olsen J.V., Vertegaal A.C.
    Mol. Cell. Proteomics 14:1419-1434(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-29, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  15. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH SF3B1, SUBUNIT, RNA-BINDING, FUNCTION, REGION.
  17. "NMR solution structure of the human spliceosomal protein complex p14-SF3B155."
    RIKEN structural genomics initiative (RSGI)
    Submitted (JAN-2007) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 8-93.
  18. "Structural model of the p14/SF3b155 - branch duplex complex."
    Schellenberg M.J., Dul E.L., MacMillan A.M.
    RNA 17:155-165(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.38 ANGSTROMS) OF 11-125 IN COMPLEX WITH SF3B1, SUBUNIT.

Entry informationi

Entry nameiSF3B6_HUMAN
AccessioniPrimary (citable) accession number: Q9Y3B4
Secondary accession number(s): Q53TM1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 24, 2001
Last sequence update: November 1, 1999
Last modified: June 8, 2016
This is version 152 of the entry and version 1 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.