Pre-mRNA-splicing factor SYF1 - Homo sapiens (Human)

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Q9HCS7 (SYF1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 122. History...

Clusters with 100%, 90%, 50% identity |

Documents (5) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Pre-mRNA-splicing factor SYF1

Alternative name(s):
Protein HCNP
XPA-binding protein 2

Gene names

Name:	XAB2
Synonyms:	HCNP, KIAA1177, SYF1
ORF Names:	PP3898

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	855 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing. Ref.1
Subunit structure	Associates with RNA polymerase II, the TCR-specific proteins CKN1/CSA and ERCC6/CSB, and XPA. Identified in the spliceosome C complex. Ref.1 Ref.8
Subcellular location	Nucleus By similarity. Note: Detected in the splicing complex carrying pre-mRNA By similarity.
Sequence similarities	Belongs to the crooked-neck family. Contains 14 HAT repeats.
Sequence caution	The sequence AAF86951.1 differs from that shown. Reason: Frameshift at positions 314, 411, 426, 429 and 468. The sequence AAH08778.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened. The sequence BAB84861.1 differs from that shown. Reason: Alternative splicing. Incomplete sequence.

Ontologies

Keywords
Biological process	DNA damage DNA repair Transcription mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Coding sequence diversity	Polymorphism
Domain	Repeat
PTM	Acetylation Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	blastocyst development Inferred from electronic annotation. Source: Compara mRNA splicing, via spliceosome Inferred by curator Ref.8. Source: UniProtKB transcription, DNA-dependent Inferred from direct assay Ref.1. Source: UniProtKB transcription-coupled nucleotide-excision repair Inferred from direct assay Ref.1. Source: UniProtKB
Cellular_component	catalytic step 2 spliceosome Inferred from direct assay Ref.8. Source: UniProtKB nucleoplasm Traceable author statement. Source: Reactome
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
ERCC8	Q13216	3	EBI-295232,EBI-295260
POLR2A	P24928	2	EBI-295232,EBI-295301
XPA	P23025	2	EBI-295232,EBI-295222

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 855

855

Pre-mRNA-splicing factor SYF1

PRO_0000106414

Regions

Repeat

15 – 47

HAT 1

Repeat

48 – 80

HAT 2

Repeat

90 – 122

HAT 3

Repeat

124 – 158

HAT 4

Repeat

160 – 192

HAT 5

Repeat

198 – 230

HAT 6

Repeat

235 – 268

HAT 7

Repeat

270 – 305

HAT 8

Repeat

369 – 407

HAT 9

Repeat

498 – 530

HAT 10

Repeat

532 – 566

HAT 11

Repeat

571 – 605

HAT 12

Repeat

643 – 677

HAT 13

Repeat

679 – 713

HAT 14

Amino acid modifications

Modified residue

420

N6-acetyllysine Ref.10

Modified residue

851

Phosphoserine Ref.9

Natural variations

Natural variant

126

V → I. Ref.4
Corresponds to variant rs4134822 [ dbSNP | Ensembl ].

VAR_016248

Natural variant

454

R → Q. Ref.4
Corresponds to variant rs4134850 [ dbSNP | Ensembl ].

VAR_016249

Natural variant

702

A → T. Ref.4
Corresponds to variant rs4134865 [ dbSNP | Ensembl ].

VAR_016250

Experimental info

Sequence conflict

Y → T in AAF86951. Ref.2

Sequence conflict

140

L → M in BAB15807. Ref.1

Sequence conflict

447

E → K in AAH08778. Ref.5

Sequence conflict

467

A → V in AAF86951. Ref.2

Sequence conflict

680

E → K in AAF86951. Ref.2

Sequence conflict

751 – 753

SAT → IP in AAF86951. Ref.2

Sequences

Sequence

Length

Mass (Da)

Tools

Q9HCS7 [UniParc].

Last modified October 1, 2002. Version 2.
Checksum: CF766917CD65F6FD
Show »

FASTA

855

100,010

        10         20         30         40         50         60 
MVVMARLSRP ERPDLVFEEE DLPYEEEIMR NQFSVKCWLR YIEFKQGAPK PRLNQLYERA 

        70         80         90        100        110        120 
LKLLPCSYKL WYRYLKARRA QVKHRCVTDP AYEDVNNCHE RAFVFMHKMP RLWLDYCQFL 

       130        140        150        160        170        180 
MDQGRVTHTR RTFDRALRAL PITQHSRIWP LYLRFLRSHP LPETAVRGYR RFLKLSPESA 

       190        200        210        220        230        240 
EEYIEYLKSS DRLDEAAQRL ATVVNDERFV SKAGKSNYQL WHELCDLISQ NPDKVQSLNV 

       250        260        270        280        290        300 
DAIIRGGLTR FTDQLGKLWC SLADYYIRSG HFEKARDVYE EAIRTVMTVR DFTQVFDSYA 

       310        320        330        340        350        360 
QFEESMIAAK METASELGRE EEDDVDLELR LARFEQLISR RPLLLNSVLL RQNPHHVHEW 

       370        380        390        400        410        420 
HKRVALHQGR PREIINTYTE AVQTVDPFKA TGKPHTLWVA FAKFYEDNGQ LDDARVILEK 

       430        440        450        460        470        480 
ATKVNFKQVD DLASVWCQCG ELELRHENYD EALRLLRKAT ALPARRAEYF DGSEPVQNRV 

       490        500        510        520        530        540 
YKSLKVWSML ADLEESLGTF QSTKAVYDRI LDLRIATPQI VINYAMFLEE HKYFEESFKA 

       550        560        570        580        590        600 
YERGISLFKW PNVSDIWSTY LTKFIARYGG RKLERARDLF EQALDGCPPK YAKTLYLLYA 

       610        620        630        640        650        660 
QLEEEWGLAR HAMAVYERAT RAVEPAQQYD MFNIYIKRAA EIYGVTHTRG IYQKAIEVLS 

       670        680        690        700        710        720 
DEHAREMCLR FADMECKLGE IDRARAIYSF CSQICDPRTT GAFWQTWKDF EVRHGNEDTI 

       730        740        750        760        770        780 
KEMLRIRRSV QATYNTQVNF MASQMLKVSG SATGTVSDLA PGQSGMDDMK LLEQRAEQLA 

       790        800        810        820        830        840 
AEAERDQPLR AQSKILFVRS DASREELAEL AQQVNPEEIQ LGEDEDEDEM DLEPNEVRLE 

       850 
QQSVPAAVFG SLKED

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"XAB2, a novel tetratricopeptide repeat protein, involved in transcription-coupled DNA repair and transcription." Nakatsu Y., Asahina H., Citterio E., Rademakers S., Vermeulen W., Kamiuchi S., Yeo J.-P., Khaw M.-C., Saijo M., Kodo N., Matsuda T., Hoeijmakers J.H.J., Tanaka K. J. Biol. Chem. 275:34931-34937(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBUNIT.
[2]	"A novel gene expressed in human adrenal gland." Li Y., Wu T., Xu S., Ren S., Chen Z., Han Z. Submitted (JAN-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Adrenal gland.
[3]	"Large-scale cDNA transfection screening for genes related to cancer development and progression." Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X. Gu J. Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]	NIEHS SNPs program Submitted (SEP-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS ILE-126; GLN-454 AND THR-702.
[5]	"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: Lung.
[6]	"The nucleotide sequence of a long cDNA clone isolated from human spleen." Ohara O., Nagase T., Kikuno R., Okumura K. Submitted (JAN-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 28-855. Tissue: Spleen.
[7]	"Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain." Hirosawa M., Nagase T., Ishikawa K., Kikuno R., Nomura N., Ohara O. DNA Res. 6:329-336(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 101-855. Tissue: Brain.
[8]	"Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis." Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J. RNA 8:426-439(2002) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOMAL C COMPLEX.
[9]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-851, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[10]	"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-420, MASS SPECTROMETRY.
[11]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Web resources

NIEHS-SNPs

Cross-references

Sequence databases
EMBL GenBank DDBJ	AB026111 mRNA. Translation: BAB15807.1. AF226051 mRNA. Translation: AAF86951.1. Frameshift. AF258567 mRNA. Translation: AAG23770.1. AF547265 Genomic DNA. Translation: AAN17847.1. BC007208 mRNA. Translation: AAH07208.1. BC008778 mRNA. Translation: AAH08778.1. Different initiation. AK074035 mRNA. Translation: BAB84861.1. Sequence problems. AB033003 mRNA. Translation: BAA86491.1.
IPI	IPI00163084.
RefSeq	NP_064581.2. NM_020196.2.
UniGene	Hs.9822.
3D structure databases
ProteinModelPortal	Q9HCS7.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9HCS7. 9 interactions.
MINT	MINT-1475513.
STRING	9606.ENSP00000351137.
PTM databases
PhosphoSite	Q9HCS7.
Polymorphism databases
DMDM	25091548.
Proteomic databases
PaxDb	Q9HCS7.
PeptideAtlas	Q9HCS7.
PRIDE	Q9HCS7.
Protocols and materials databases
DNASU	56949.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000358368; ENSP00000351137; ENSG00000076924.
GeneID	56949.
KEGG	hsa:56949.
UCSC	uc002mgx.3. human.
Organism-specific databases
CTD	56949.
GeneCards	GC19M007684.
HGNC	HGNC:14089. XAB2.
MIM	610850. gene.
neXtProt	NX_Q9HCS7.
PharmGKB	PA134905925.
HUGE	Search...
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG289100.
HOGENOM	HOG000176133.
HOVERGEN	HBG024066.
InParanoid	Q9HCS7.
KO	K12867.
OMA	PRSYKLW.
OrthoDB	EOG4G4GPQ.
Enzyme and pathway databases
Reactome	REACT_216. DNA Repair.
Gene expression databases
ArrayExpress	Q9HCS7.
Bgee	Q9HCS7.
CleanEx	HS_XAB2.
Genevestigator	Q9HCS7.
GermOnline	ENSG00000076924. Homo sapiens.
Family and domain databases
Gene3D	1.25.40.10. 4 hits.
InterPro	IPR003107. HAT. IPR013026. TPR-contain_dom. IPR011990. TPR-like_helical. IPR013105. TPR_2. IPR019734. TPR_repeat. [Graphical view]
Pfam	PF07719. TPR_2. 2 hits. [Graphical view]
SMART	SM00386. HAT. 11 hits. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	XAB2. human.
GenomeRNAi	56949.
NextBio	62545.
SOURCE	Search...

Entry information

Entry name

SYF1_HUMAN

Accession

Primary (citable) accession number: Q9HCS7
Secondary accession number(s): Q8TET6

Q9ULP3

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 15, 2002
Last sequence update:	October 1, 2002
Last modified:	May 1, 2013
This is version 122 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.

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Human chromosome 19: entries, gene names and cross-references to MIM

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List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Natural variations

Experimental info

Sequences

References

Web resources

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Polymorphism databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents