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Protein

Pre-mRNA-splicing factor SYF1

Gene

Xab2

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing.By similarity

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair, mRNA processing, mRNA splicing, Transcription

Enzyme and pathway databases

ReactomeiR-MMU-6781823. Formation of TC-NER Pre-Incision Complex.
R-MMU-6782135. Dual incision in TC-NER.
R-MMU-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-splicing factor SYF1
Alternative name(s):
XPA-binding protein 2
Gene namesi
Name:Xab2
Synonyms:Syf1
OrganismiMus musculus (Mouse)Imported
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 8

Organism-specific databases

MGIiMGI:1914689. Xab2.

Subcellular locationi

  • Nucleus By similarity

  • Note: Detected in the splicing complex carrying pre-mRNA.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 855855Pre-mRNA-splicing factor SYF1PRO_0000106415Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei420 – 4201N6-acetyllysineBy similarity
Modified residuei851 – 8511PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9DCD2.
MaxQBiQ9DCD2.
PaxDbiQ9DCD2.
PRIDEiQ9DCD2.

PTM databases

iPTMnetiQ9DCD2.
PhosphoSiteiQ9DCD2.

Expressioni

Gene expression databases

BgeeiQ9DCD2.
CleanExiMM_XAB2.
ExpressionAtlasiQ9DCD2. baseline and differential.
GenevisibleiQ9DCD2. MM.

Interactioni

Subunit structurei

Associates with RNA polymerase II, the TCR-specific proteins CKN1/CSA and ERCC6/CSB, and XPA. Identified in the spliceosome C complex. Component of the XAB2 complex, a multimeric protein complex composed of XAB2, PRPF19, AQR, ZNF830, ISY1, and PPIE.By similarity

Protein-protein interaction databases

BioGridi212186. 3 interactions.
IntActiQ9DCD2. 1 interaction.
MINTiMINT-4140395.
STRINGi10090.ENSMUSP00000019614.

Structurei

3D structure databases

ProteinModelPortaliQ9DCD2.
SMRiQ9DCD2. Positions 154-187, 241-287, 487-546.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati15 – 4733HAT 1CuratedAdd
BLAST
Repeati48 – 8033HAT 2CuratedAdd
BLAST
Repeati90 – 12233HAT 3CuratedAdd
BLAST
Repeati124 – 15835HAT 4CuratedAdd
BLAST
Repeati160 – 19233HAT 5CuratedAdd
BLAST
Repeati198 – 23033HAT 6Add
BLAST
Repeati235 – 26834HAT 7Add
BLAST
Repeati270 – 30536HAT 8Add
BLAST
Repeati369 – 40739HAT 9Add
BLAST
Repeati498 – 53033HAT 10Add
BLAST
Repeati532 – 56635HAT 11Add
BLAST
Repeati571 – 60535HAT 12Add
BLAST
Repeati643 – 67735HAT 13Add
BLAST
Repeati679 – 71335HAT 14Add
BLAST

Sequence similaritiesi

Belongs to the crooked-neck family.Curated
Contains 14 HAT repeats.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG2047. Eukaryota.
ENOG410XPD9. LUCA.
GeneTreeiENSGT00550000075140.
HOGENOMiHOG000176133.
HOVERGENiHBG024066.
InParanoidiQ9DCD2.
KOiK12867.
OMAiGAQENEQ.
OrthoDBiEOG7RV9FD.
PhylomeDBiQ9DCD2.
TreeFamiTF300866.

Family and domain databases

Gene3Di1.25.40.10. 5 hits.
InterProiIPR003107. HAT.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR019734. TPR_repeat.
[Graphical view]
PfamiPF13181. TPR_8. 2 hits.
[Graphical view]
SMARTiSM00386. HAT. 10 hits.
SM00028. TPR. 3 hits.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 4 hits.

Sequencei

Sequence statusi: Complete.

Q9DCD2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVVMARVPRS ERPDLVFEEE DLPYEEEIMR NQFSVKCWLR YIEFKQGAPK
60 70 80 90 100
PRLNQLYERA LKLLPCSYKL WYRYLKARRA QVKHRCVTDP AYEDVNNCHE
110 120 130 140 150
RAFVFMHKMP RLWLDYCQFL MDQGRVTHTR RTFDRALRAL PITQHSRIWP
160 170 180 190 200
LYLRFLRSHP LPETAVRGYR RFLKLSPESA EEYIEYLKSS DRLDEAAQRL
210 220 230 240 250
ATVVNDERFV SKAGKSNYQL WHELCDLISQ NPDKVQSLNV DAIIRGGLTR
260 270 280 290 300
FTDQLGKLWC SLADYYIRSG HFEKARDVYE EAIRTVMTVR DFTQVFDSYA
310 320 330 340 350
QFEESMIAAK METASELGRE EEDDVDLELR LARFEQLISR RPLLLNSVLL
360 370 380 390 400
RQNPHHVHEW HKRVALHQGR PREIINTYTE AVQTVDPFKA TGKPHTLWVA
410 420 430 440 450
FAKFYEDNGQ LDDARVILEK ATKVNFKQVD DLASVWCQCG ELELRHENYD
460 470 480 490 500
EALKLLRKAT ALPARRAEYF DGSEPVQNRV YKSLKVWSML ADLEESLGTF
510 520 530 540 550
QSTKAVYDRI LDLRIATPQI VINYAMFLEE HKYFEESFKA YERGISLFKW
560 570 580 590 600
PNVSDIWSTY LTKFISRYGG RKLERARDLF EQALDGCPPK YAKTLYLLYA
610 620 630 640 650
QLEEEWGLAR HAMAVYDRAT RAVEPAQQYD MFNIYIKRAA EIYGVTHTRG
660 670 680 690 700
IYQKAIEVLS DEHAREMCLR FADMECKLGE IDRARAIYSF CSQICDPRTT
710 720 730 740 750
GAFWQTWKDF EVRHGNEDTI REMLRIRRSV QATYNTQVNF MASQMLKVSG
760 770 780 790 800
SATGTVSDLA PGQSGMDDMK LLEQRAEQLA AEAERDQPPR AQSKIFFVRS
810 820 830 840 850
DASREELAEL AQQANPEEIQ LGEDEDEDEM DLEPNEVRLE QQSVPAAVFG

SLKED
Length:855
Mass (Da):99,988
Last modified:June 1, 2001 - v1
Checksum:i6A5DA6A74E7FCB1D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti684 – 6841A → T in AAH21341 (PubMed:15489334).Curated
Sequence conflicti842 – 8421Q → L in BAB25790 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK002890 mRNA. Translation: BAB22435.1.
AK008628 mRNA. Translation: BAB25790.1.
BC021341 mRNA. Translation: AAH21341.1.
CCDSiCCDS22065.1.
RefSeqiNP_080432.1. NM_026156.2.
UniGeneiMm.23739.

Genome annotation databases

EnsembliENSMUST00000019614; ENSMUSP00000019614; ENSMUSG00000019470.
GeneIDi67439.
KEGGimmu:67439.
UCSCiuc009kry.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK002890 mRNA. Translation: BAB22435.1.
AK008628 mRNA. Translation: BAB25790.1.
BC021341 mRNA. Translation: AAH21341.1.
CCDSiCCDS22065.1.
RefSeqiNP_080432.1. NM_026156.2.
UniGeneiMm.23739.

3D structure databases

ProteinModelPortaliQ9DCD2.
SMRiQ9DCD2. Positions 154-187, 241-287, 487-546.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi212186. 3 interactions.
IntActiQ9DCD2. 1 interaction.
MINTiMINT-4140395.
STRINGi10090.ENSMUSP00000019614.

PTM databases

iPTMnetiQ9DCD2.
PhosphoSiteiQ9DCD2.

Proteomic databases

EPDiQ9DCD2.
MaxQBiQ9DCD2.
PaxDbiQ9DCD2.
PRIDEiQ9DCD2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000019614; ENSMUSP00000019614; ENSMUSG00000019470.
GeneIDi67439.
KEGGimmu:67439.
UCSCiuc009kry.1. mouse.

Organism-specific databases

CTDi56949.
MGIiMGI:1914689. Xab2.

Phylogenomic databases

eggNOGiKOG2047. Eukaryota.
ENOG410XPD9. LUCA.
GeneTreeiENSGT00550000075140.
HOGENOMiHOG000176133.
HOVERGENiHBG024066.
InParanoidiQ9DCD2.
KOiK12867.
OMAiGAQENEQ.
OrthoDBiEOG7RV9FD.
PhylomeDBiQ9DCD2.
TreeFamiTF300866.

Enzyme and pathway databases

ReactomeiR-MMU-6781823. Formation of TC-NER Pre-Incision Complex.
R-MMU-6782135. Dual incision in TC-NER.
R-MMU-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.

Miscellaneous databases

NextBioi324566.
PROiQ9DCD2.
SOURCEiSearch...

Gene expression databases

BgeeiQ9DCD2.
CleanExiMM_XAB2.
ExpressionAtlasiQ9DCD2. baseline and differential.
GenevisibleiQ9DCD2. MM.

Family and domain databases

Gene3Di1.25.40.10. 5 hits.
InterProiIPR003107. HAT.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR019734. TPR_repeat.
[Graphical view]
PfamiPF13181. TPR_8. 2 hits.
[Graphical view]
SMARTiSM00386. HAT. 10 hits.
SM00028. TPR. 3 hits.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 4 hits.
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: Kidney and Stomach.
  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].
  3. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Spleen.

Entry informationi

Entry nameiSYF1_MOUSE
AccessioniPrimary (citable) accession number: Q9DCD2
Secondary accession number(s): Q8VDT5, Q9CVD8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 15, 2002
Last sequence update: June 1, 2001
Last modified: May 11, 2016
This is version 128 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.