Q6IQE0 (PU60B_DANRE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Poly(U)-binding-splicing factor PUF60-B

Gene names

Name:	puf60b
Synonyms:	puf60
ORF Names:	si:zc12p8.2, zgc:86806

Organism

Danio rerio (Zebrafish) (Brachydanio rerio)

Taxonomic identifier

7955 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Actinopterygii › Neopterygii › Teleostei › Ostariophysi › Cypriniformes › Cyprinidae › Danio

Protein attributes

Sequence length	516 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	DNA- and RNA-binding protein, involved in transcription repression and pre-mRNA splicing By similarity.
Subcellular location	Nucleus By similarity.
Domain	The third RNA recognition motif, called PUMP domain, is atypical and may rather mediate homodimerization and/or protein-protein interactions.
Sequence similarities	Belongs to the RRM half pint family. Contains 3 RRM (RNA recognition motif) domains.

Ontologies

Keywords
Biological process	Apoptosis Transcription Transcription regulation mRNA processing mRNA splicing
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Repeat
Ligand	DNA-binding RNA-binding
Molecular function	Repressor Ribonucleoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	RNA splicing Inferred from electronic annotation. Source: UniProtKB-KW apoptotic process Inferred from electronic annotation. Source: UniProtKB-KW mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell ribonucleoprotein complex Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q6IQE0-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Note: No experimental confirmation available.

Isoform 2 (identifier: Q6IQE0-2)

The sequence of this isoform differs from the canonical sequence as follows:
     57-73: Missing.

Note: No experimental confirmation available.

Isoform 3 (identifier: Q6IQE0-3)

The sequence of this isoform differs from the canonical sequence as follows:
     57-73: Missing.
     333-342: LSTTKTVFHL → VTPARPTLPVVPQ

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 516	516	Poly(U)-binding-splicing factor PUF60-B		PRO_0000299523
Regions
	Domain	86 – 164	79	RRM 1
	Domain	183 – 261	79	RRM 2
	Domain	419 – 506	88	RRM 3; atypical
	Compositional bias	278 – 288	11	Poly-Ala
Natural variations
	Alternative sequence	57 – 73	17	Missing in isoform 2 and isoform 3.		VSP_029175
	Alternative sequence	333 – 342	10	LSTTKTVFHL → VTPARPTLPVVPQ in isoform 3.		VSP_029176

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 13, 2007. Version 2. Checksum: 105C2A4CD905D976	FASTA	516	55,420
	10 20 30 40 50 60 MENGQGTGSK LGLPPLTPEQ QEALQKAKKY AMEQSIKSVL VKQTIAHQQQ QLTNLQMAAV 70 80 90 100 110 120 TMGFGDPLSS LQSVAAQRQR ALAIMCRVYV GSIYYELGED TIRQAFAPFG PIKSIDMSWD 130 140 150 160 170 180 SVTMKHKGFA FVEYEVPEAA QLALEQMNSV MLGGRNIKVG RPGSIGQAQP IIEQLAEEAR 190 200 210 220 230 240 AYNRIYVASI HPDLSDDDIK SVFEAFGKIK SCMLAREPTT GKHKGFGFIE YEKPQSSLDA 250 260 270 280 290 300 VSSMNLFDLG GQYLRVGKAV TPPMPLLTPT TPGGLPPAAA VAAAAATAKI TAQEAVAGTV 310 320 330 340 350 360 LSSLASPAHI LSQQMGLPQA VLAAQAPGII TGLSTTKTVF HLVGLVNPVL ASPPVTAPAS 370 380 390 400 410 420 MGTPTSAVQL HTEVKREEDS RRTAEDHSAP VGNGQDSELE RLSVSASAGR QAAIQSKSTV 430 440 450 460 470 480 MVLRNMVGPE DIDDDLEGEV MEECGKYGAV NRVIIYQERQ GEEDDAEIIV KIFVEFSDAG 490 500 510 EMNKAIQALN NRWFAGRKVV AELYDQDRFN SSDLTA
	Isoform 2 [UniParc]. Checksum: 45CC90ED48F8DBB8	FASTA	499	53,726
	10 20 30 40 50 60 MENGQGTGSK LGLPPLTPEQ QEALQKAKKY AMEQSIKSVL VKQTIAHQQQ QLTNLQVAAQ 70 80 90 100 110 120 RQRALAIMCR VYVGSIYYEL GEDTIRQAFA PFGPIKSIDM SWDSVTMKHK GFAFVEYEVP 130 140 150 160 170 180 EAAQLALEQM NSVMLGGRNI KVGRPGSIGQ AQPIIEQLAE EARAYNRIYV ASIHPDLSDD 190 200 210 220 230 240 DIKSVFEAFG KIKSCMLARE PTTGKHKGFG FIEYEKPQSS LDAVSSMNLF DLGGQYLRVG 250 260 270 280 290 300 KAVTPPMPLL TPTTPGGLPP AAAVAAAAAT AKITAQEAVA GTVLSSLASP AHILSQQMGL 310 320 330 340 350 360 PQAVLAAQAP GIITGLSTTK TVFHLVGLVN PVLASPPVTA PASMGTPTSA VQLHTEVKRE 370 380 390 400 410 420 EDSRRTAEDH SAPVGNGQDS ELERLSVSAS AGRQAAIQSK STVMVLRNMV GPEDIDDDLE 430 440 450 460 470 480 GEVMEECGKY GAVNRVIIYQ ERQGEEDDAE IIVKIFVEFS DAGEMNKAIQ ALNNRWFAGR 490 KVVAELYDQD RFNSSDLTA
	Isoform 3 [UniParc]. Checksum: 599BEDC067BA0642	FASTA	502	53,954
	10 20 30 40 50 60 MENGQGTGSK LGLPPLTPEQ QEALQKAKKY AMEQSIKSVL VKQTIAHQQQ QLTNLQVAAQ 70 80 90 100 110 120 RQRALAIMCR VYVGSIYYEL GEDTIRQAFA PFGPIKSIDM SWDSVTMKHK GFAFVEYEVP 130 140 150 160 170 180 EAAQLALEQM NSVMLGGRNI KVGRPGSIGQ AQPIIEQLAE EARAYNRIYV ASIHPDLSDD 190 200 210 220 230 240 DIKSVFEAFG KIKSCMLARE PTTGKHKGFG FIEYEKPQSS LDAVSSMNLF DLGGQYLRVG 250 260 270 280 290 300 KAVTPPMPLL TPTTPGGLPP AAAVAAAAAT AKITAQEAVA GTVLSSLASP AHILSQQMGL 310 320 330 340 350 360 PQAVLAAQAP GIITGVTPAR PTLPVVPQVG LVNPVLASPP VTAPASMGTP TSAVQLHTEV 370 380 390 400 410 420 KREEDSRRTA EDHSAPVGNG QDSELERLSV SASAGRQAAI QSKSTVMVLR NMVGPEDIDD 430 440 450 460 470 480 DLEGEVMEEC GKYGAVNRVI IYQERQGEED DAEIIVKIFV EFSDAGEMNK AIQALNNRWF 490 500 AGRKVVAELY DQDRFNSSDL TA

References

[1]	The Danio rerio sequencing project at the Sanger Institute Submitted (DEC-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Tuebingen.
[2]	NIH - Zebrafish Gene Collection (ZGC) project Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3). Tissue: Embryo.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AL772146 Genomic DNA. Translation: CAD61098.1. AL772146 Genomic DNA. Translation: CAD61099.1. BC071467 mRNA. Translation: AAH71467.1.
IPI	IPI00495062. IPI00512039. IPI00866101.
RefSeq	NP_001002121.1. NM_001002121.1.
UniGene	Dr.90714.
3D structure databases
HSSP	HSSP built from PDB template 1O0P based on UniProtKB P26368.
ProteinModelPortal	Q6IQE0.
SMR	Q6IQE0. Positions 75-267, 405-516.
ModBase	Search...
Protein-protein interaction databases
STRING	Q6IQE0.
Proteomic databases
PRIDE	Q6IQE0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSDART00000038487; ENSDARP00000034301; ENSDARG00000001241. ENSDART00000052274; ENSDARP00000052273; ENSDARG00000001241. ENSDART00000143285; ENSDARP00000123644; ENSDARG00000001241.
GeneID	415211.
KEGG	dre:415211.
Organism-specific databases
CTD	415211.
ZFIN	ZDB-GENE-040625-116. puf60b.
Phylogenomic databases
eggNOG	fiNOG05571.
GeneTree	ENSGT00590000082817.
HOGENOM	HBG445933.
HOVERGEN	HBG055622.
OMA	CMLAREP.
OrthoDB	EOG4SQWWP.
PhylomeDB	Q6IQE0.
Gene expression databases
ArrayExpress	Q6IQE0.
Bgee	Q6IQE0.
Family and domain databases
InterPro	IPR012677. Nucleotide-bd_a/b_plait. IPR006532. PolyU-bd. IPR000504. RRM_dom. [Graphical view]
Gene3D	G3DSA:3.30.70.330. a_b_plait_nuc_bd. 3 hits.
Pfam	PF00076. RRM_1. 2 hits. [Graphical view]
SMART	SM00360. RRM. 3 hits. [Graphical view]
TIGRFAMs	TIGR01645. Half-pint. 1 hit.
PROSITE	PS50102. RRM. 3 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PU60B_DANRE

Accession

Primary (citable) accession number: Q6IQE0
Secondary accession number(s): Q7ZZ33, Q7ZZ34

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 11, 2007
Last sequence update:	November 13, 2007
Last modified:	October 19, 2011
This is version 66 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program