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Protein

Pre-mRNA-splicing factor SYF1

Gene

Xab2

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

Functioni

Involved in pre-mRNA splicing as component of the spliceosome. Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing.By similarity

GO - Biological processi

Keywordsi

Biological processDNA 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
R-MMU-72163 mRNA Splicing - Major Pathway

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 8

Organism-specific databases

MGIiMGI:1914689 Xab2

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Disruption phenotypei

Complete embryonic lethality before 13.5 dpc. Already at 3.5 dpc, the number of homozygous mutant embryos is lower than expected.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001064151 – 855Pre-mRNA-splicing factor SYF1Add BLAST855

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei420N6-acetyllysineBy similarity1
Modified residuei851PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9DCD2
MaxQBiQ9DCD2
PaxDbiQ9DCD2
PRIDEiQ9DCD2

PTM databases

iPTMnetiQ9DCD2
PhosphoSitePlusiQ9DCD2

Expressioni

Gene expression databases

BgeeiENSMUSG00000019470 Expressed in 296 organ(s), highest expression level in submandibular gland
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. Identified in a pentameric intron-binding (IB) complex composed of AQR, XAB2, ISY1, ZNF830 and PPIE that is incorporated into the spliceosome as a preassembled complex. The IB complex does not contain PRPF19.By similarity

Protein-protein interaction databases

BioGridi212186, 3 interactors
IntActiQ9DCD2, 1 interactor
MINTiQ9DCD2
STRINGi10090.ENSMUSP00000019614

Structurei

3D structure databases

ProteinModelPortaliQ9DCD2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati15 – 47HAT 1CuratedAdd BLAST33
Repeati48 – 80HAT 2CuratedAdd BLAST33
Repeati90 – 122HAT 3CuratedAdd BLAST33
Repeati124 – 158HAT 4CuratedAdd BLAST35
Repeati160 – 192HAT 5CuratedAdd BLAST33
Repeati198 – 230HAT 6Add BLAST33
Repeati235 – 268HAT 7Add BLAST34
Repeati270 – 305HAT 8Add BLAST36
Repeati369 – 407HAT 9Add BLAST39
Repeati498 – 530HAT 10Add BLAST33
Repeati532 – 566HAT 11Add BLAST35
Repeati571 – 605HAT 12Add BLAST35
Repeati643 – 677HAT 13Add BLAST35
Repeati679 – 713HAT 14Add BLAST35

Sequence similaritiesi

Belongs to the crooked-neck family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG2047 Eukaryota
ENOG410XPD9 LUCA
GeneTreeiENSGT00550000075140
HOGENOMiHOG000176133
HOVERGENiHBG024066
InParanoidiQ9DCD2
KOiK12867
OMAiNPYSVKC
OrthoDBiEOG091G01UP
PhylomeDBiQ9DCD2
TreeFamiTF300866

Family and domain databases

Gene3Di1.25.40.10, 3 hits
InterProiView protein in InterPro
IPR003107 HAT
IPR013026 TPR-contain_dom
IPR011990 TPR-like_helical_dom_sf
IPR019734 TPR_repeat
PfamiView protein in Pfam
PF13181 TPR_8, 2 hits
SMARTiView protein in SMART
SM00386 HAT, 10 hits
SM00028 TPR, 3 hits
SUPFAMiSSF48452 SSF48452, 4 hits

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F6TM12F6TM12_MOUSE
Pre-mRNA-splicing factor SYF1
Xab2
285Annotation score:
E0CYF8E0CYF8_MOUSE
Pre-mRNA-splicing factor SYF1
Xab2 mCG_13002
90Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti684A → T in AAH21341 (PubMed:15489334).Curated1
Sequence conflicti842Q → L in BAB25790 (PubMed:16141072).Curated1

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

Similar proteinsi

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
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi212186, 3 interactors
IntActiQ9DCD2, 1 interactor
MINTiQ9DCD2
STRINGi10090.ENSMUSP00000019614

PTM databases

iPTMnetiQ9DCD2
PhosphoSitePlusiQ9DCD2

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
OMAiNPYSVKC
OrthoDBiEOG091G01UP
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
R-MMU-72163 mRNA Splicing - Major Pathway

Miscellaneous databases

PROiPR:Q9DCD2
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000019470 Expressed in 296 organ(s), highest expression level in submandibular gland
CleanExiMM_XAB2
ExpressionAtlasiQ9DCD2 baseline and differential
GenevisibleiQ9DCD2 MM

Family and domain databases

Gene3Di1.25.40.10, 3 hits
InterProiView protein in InterPro
IPR003107 HAT
IPR013026 TPR-contain_dom
IPR011990 TPR-like_helical_dom_sf
IPR019734 TPR_repeat
PfamiView protein in Pfam
PF13181 TPR_8, 2 hits
SMARTiView protein in SMART
SM00386 HAT, 10 hits
SM00028 TPR, 3 hits
SUPFAMiSSF48452 SSF48452, 4 hits
ProtoNetiSearch...

Entry informationi

Entry nameiSYF1_MOUSE
AccessioniPrimary (citable) accession number: Q9DCD2
Secondary accession number(s): Q8VDT5, Q9CVD8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 15, 2002
Last sequence update: June 1, 2001
Last modified: November 7, 2018
This is version 146 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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Main funding by: National Institutes of Health

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