Q63625 (PHRF1_RAT) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
PHD and RING finger domain-containing protein 1

Alternative name(s):
CTD-binding SR-like protein rA9

Gene names

Name:

Phrf1

Organism

Rattus norvegicus (Rat) [Reference proteome]

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	1685 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Subunit structure	Interacts with POLR2A (via the C-terminal domain). Ref.1
Sequence similarities	Contains 1 PHD-type zinc finger. Contains 1 RING-type zinc finger.

Ontologies

Keywords
Coding sequence diversity	Alternative splicing
Domain	Coiled coil Zinc-finger
Ligand	Metal-binding Zinc
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	mRNA processing Inferred from mutant phenotype Ref.1. Source: RGD transcription from RNA polymerase II promoter Inferred from mutant phenotype Ref.1. Source: RGD
Molecular_function	protein domain specific binding Inferred from mutant phenotype Ref.1. Source: RGD zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q63625-1)

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. Gene prediction based on similarity to human ortholog.

Isoform 2 Ref.1 (identifier: Q63625-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-212: Missing.
     213-244: YHMECLDPPLQEVPVDEWFCPECAVPGVDPTH → MRRLKRKTRPFVKCVAGVIVRTGSYFVTAVML

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1685	1685	PHD and RING finger domain-containing protein 1		PRO_0000354663
Regions
	Zinc finger	109 – 150	42	RING-type; degenerate
	Zinc finger	188 – 238	51	PHD-type
	Coiled coil	1589 – 1615	27	Potential
	Compositional bias	267 – 409	143	Arg-rich
	Compositional bias	994 – 1188	195	Arg-rich
Amino acid modifications
	Modified residue	335	1	Phosphothreonine By similarity
	Modified residue	460	1	Phosphoserine By similarity
	Modified residue	867	1	Phosphoserine By similarity
	Modified residue	870	1	Phosphoserine By similarity
	Modified residue	922	1	Phosphoserine By similarity UniProtKB Q9P1Y6
	Modified residue	948	1	Phosphoserine By similarity
	Modified residue	1002	1	Phosphoserine By similarity UniProtKB Q9P1Y6
	Modified residue	1044	1	Phosphoserine By similarity
	Modified residue	1046	1	Phosphoserine By similarity
	Modified residue	1138	1	Phosphoserine By similarity
	Modified residue	1139	1	Phosphoserine By similarity
	Modified residue	1205	1	Phosphoserine By similarity UniProtKB Q9P1Y6
	Modified residue	1372	1	Phosphoserine By similarity
	Modified residue	1383	1	Phosphoserine By similarity
	Modified residue	1416	1	Phosphothreonine By similarity
Natural variations
	Alternative sequence	1 – 212	212	Missing in isoform 2. Ref.1		VSP_052981
	Alternative sequence	213 – 244	32	YHMEC…VDPTH → MRRLKRKTRPFVKCVAGVIV RTGSYFVTAVML in isoform 2. Ref.1		VSP_052982
Experimental info
	Sequence conflict	615	1	T → S in AAC52658. Ref.1
	Sequence conflict	793	1	Q → P in AAC52658. Ref.1
	Sequence conflict	855 – 856	2	SG → PD in AAC52658. Ref.1
	Sequence conflict	1549	1	S → G in AAC52658. Ref.1
	Sequence conflict	1592	1	K → T in AAC52658. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 25, 2008. Version 2. Checksum: 54D4ACFA2FD8BAC2	FASTA	1,685	184,214
	10 20 30 40 50 60 MDDDNLDELV AHSPGPDGPP QVGSSELASD AEESSNGHSE DSEDDTGSEQ DDDTDGEETE 70 80 90 100 110 120 GLSEEEDPED RSGSEDSEDG IEVPTAAVET QRKLEASSTP NSDDDAESCP ICLNAFRDQA 130 140 150 160 170 180 VGTPETCAHY FCLDCIIEWS RNANSCPVDR TIFKCICIRA QFNGKILKKI PVENTRACED 190 200 210 220 230 240 EEAEEEDPTF CEVCGRSDRE DRLLLCDGCD AGYHMECLDP PLQEVPVDEW FCPECAVPGV 250 260 270 280 290 300 DPTHDAAPVS DEEVSLLLAD VVPTTSRLRP RVGRTRAIAR TRQSERVRAT VNRNRISSAR 310 320 330 340 350 360 RVQHVPRYLM SSLLDETIEA VATGLSTAVY QRPLTPRVPA KRKRKAGRRK KVLGRKKTRS 370 380 390 400 410 420 RSSVKSKSGG TRAKKRQHRV RRTKGRKLKN EVTARSRIAR TLGLRRPVRG TSMPSVYKPV 430 440 450 460 470 480 DPSLGLMRAD IGAASLSLFG DPYALDPFDS NGEQSADPPS PLSAKRRVLS RSALQSHQPV 490 500 510 520 530 540 ARPVAMGLAR RQLPAVAPEP SVEEAPVPDL LGSILCGQSL LMMSSADVVI HRDGSLSAKR 550 560 570 580 590 600 AAPVSLQRNS VTQSREESRL RDNLQPGALP SESVSGGLIG DRRPNSGLSC GDRTALRCLP 610 620 630 640 650 660 AQIVQTPVRS DSSVTPRSGL SGNLSDESRP KWKHSNSPRL NGSNVRVGSA STKTMTHSNF 670 680 690 700 710 720 PSKNIAPGHP QKTDPRRPDF SKLPRIPKIR RDGSNSTQDQ APASGQTVEL PSACISRLTG 730 740 750 760 770 780 REGPGQPGRG RADSEPSSRG PQETGSHTSG SRPPAPSSHG NLAPLGPSRG KGIGSSFESF 790 800 810 820 830 840 RINIPGNTAH CSQLSSPGFC NTFRPVDSKV QRKENPSPLF SIKKPKQLKS EIYDPFDPTG 850 860 870 880 890 900 SDSSPPSSSP ESLGSGLLPS EITRTISINS PKAPAFQTVR CVTSYRVESV FGTEMDPDPQ 910 920 930 940 950 960 PPGEPVSGML ELLGKGPAEG ASDLEQEGLG EIEPTEIQGS SARAQRPSPP DPWDDEDGVS 970 980 990 1000 1010 1020 CTPFFGSEER TVTCVTVEEP SVPSPDAPQI TTHRIVEFRA SSRSRSTSSS RSRKKTKKKK 1030 1040 1050 1060 1070 1080 KVAREHQRTR SSTRSGSRDR TSRSVSPFTE EHTKRHRAKT KSRRSSSDRA SSQDRAKRRK 1090 1100 1110 1120 1130 1140 DRDREHRRGP WGHGRCWRKS RSRSGSPGSS SCERHESRRR KRRHSGSRSR GRDGSPHSSL 1150 1160 1170 1180 1190 1200 ERDRRHKHRE RSRERMDKKE SMTRSRERRR WRSRSPSVEH RTRRPHSREK HPHSPEKKGA 1210 1220 1230 1240 1250 1260 VREVSPAPAP QGEPRQDGDH STKPPVSEVS VLPEVVSVLP EVVVADLNPP EVPPVLAESV 1270 1280 1290 1300 1310 1320 SCVPEDLDYG DSVEAGHVFE DFSNEAIFIQ LDDMSSPPSP ESTDSSPERD FLPNPILPPA 1330 1340 1350 1360 1370 1380 SLPQNSTLPV TQREVLPIHS EDISKPAPQP LAPSDQCLLR QDTVETTATT LSTPGVLPMG 1390 1400 1410 1420 1430 1440 KDSPLLSGRG CEVVRPKDAV APAPLLRSRT LVKRVTWNLQ EAEASTPALD RDPRTPLQRP 1450 1460 1470 1480 1490 1500 QRPQEGDWDA EDRALIGFQQ APFSELPPPI HVLQESGLPD ADPSQPPGVP RAEGPPAVGT 1510 1520 1530 1540 1550 1560 LHSAGGILAQ VYSPNMPPPL AQPSSIPPYA LVNQPSVQLI LQGTLPLASC GAAQNLAPVP 1570 1580 1590 1600 1610 1620 TMPATASELA VPTTNNSEER TATPKTAAEK TKKEEYMKKL HMQERAVEEV KLAIKPFYQK 1630 1640 1650 1660 1670 1680 REVTKEEYKD ILRKAVQKIC HSKSGEINPV KVANLVKAYV DKYRHMRKHK KTEAGEEPPT QGAET
	Isoform 2 [UniParc]. Checksum: 0BB2E97F2BFA0F58	FASTA	1,473	161,239
	10 20 30 40 50 60 MRRLKRKTRP FVKCVAGVIV RTGSYFVTAV MLDAAPVSDE EVSLLLADVV PTTSRLRPRV 70 80 90 100 110 120 GRTRAIARTR QSERVRATVN RNRISSARRV QHVPRYLMSS LLDETIEAVA TGLSTAVYQR 130 140 150 160 170 180 PLTPRVPAKR KRKAGRRKKV LGRKKTRSRS SVKSKSGGTR AKKRQHRVRR TKGRKLKNEV 190 200 210 220 230 240 TARSRIARTL GLRRPVRGTS MPSVYKPVDP SLGLMRADIG AASLSLFGDP YALDPFDSNG 250 260 270 280 290 300 EQSADPPSPL SAKRRVLSRS ALQSHQPVAR PVAMGLARRQ LPAVAPEPSV EEAPVPDLLG 310 320 330 340 350 360 SILCGQSLLM MSSADVVIHR DGSLSAKRAA PVSLQRNSVT QSREESRLRD NLQPGALPSE 370 380 390 400 410 420 SVSGGLIGDR RPNSGLSCGD RTALRCLPAQ IVQTPVRSDS SVTPRSGLSG NLSDESRPKW 430 440 450 460 470 480 KHSNSPRLNG SNVRVGSAST KTMTHSNFPS KNIAPGHPQK TDPRRPDFSK LPRIPKIRRD 490 500 510 520 530 540 GSNSTQDQAP ASGQTVELPS ACISRLTGRE GPGQPGRGRA DSEPSSRGPQ ETGSHTSGSR 550 560 570 580 590 600 PPAPSSHGNL APLGPSRGKG IGSSFESFRI NIPGNTAHCS QLSSPGFCNT FRPVDSKVQR 610 620 630 640 650 660 KENPSPLFSI KKPKQLKSEI YDPFDPTGSD SSPPSSSPES LGSGLLPSEI TRTISINSPK 670 680 690 700 710 720 APAFQTVRCV TSYRVESVFG TEMDPDPQPP GEPVSGMLEL LGKGPAEGAS DLEQEGLGEI 730 740 750 760 770 780 EPTEIQGSSA RAQRPSPPDP WDDEDGVSCT PFFGSEERTV TCVTVEEPSV PSPDAPQITT 790 800 810 820 830 840 HRIVEFRASS RSRSTSSSRS RKKTKKKKKV AREHQRTRSS TRSGSRDRTS RSVSPFTEEH 850 860 870 880 890 900 TKRHRAKTKS RRSSSDRASS QDRAKRRKDR DREHRRGPWG HGRCWRKSRS RSGSPGSSSC 910 920 930 940 950 960 ERHESRRRKR RHSGSRSRGR DGSPHSSLER DRRHKHRERS RERMDKKESM TRSRERRRWR 970 980 990 1000 1010 1020 SRSPSVEHRT RRPHSREKHP HSPEKKGAVR EVSPAPAPQG EPRQDGDHST KPPVSEVSVL 1030 1040 1050 1060 1070 1080 PEVVSVLPEV VVADLNPPEV PPVLAESVSC VPEDLDYGDS VEAGHVFEDF SNEAIFIQLD 1090 1100 1110 1120 1130 1140 DMSSPPSPES TDSSPERDFL PNPILPPASL PQNSTLPVTQ REVLPIHSED ISKPAPQPLA 1150 1160 1170 1180 1190 1200 PSDQCLLRQD TVETTATTLS TPGVLPMGKD SPLLSGRGCE VVRPKDAVAP APLLRSRTLV 1210 1220 1230 1240 1250 1260 KRVTWNLQEA EASTPALDRD PRTPLQRPQR PQEGDWDAED RALIGFQQAP FSELPPPIHV 1270 1280 1290 1300 1310 1320 LQESGLPDAD PSQPPGVPRA EGPPAVGTLH SAGGILAQVY SPNMPPPLAQ PSSIPPYALV 1330 1340 1350 1360 1370 1380 NQPSVQLILQ GTLPLASCGA AQNLAPVPTM PATASELAVP TTNNSEERTA TPKTAAEKTK 1390 1400 1410 1420 1430 1440 KEEYMKKLHM QERAVEEVKL AIKPFYQKRE VTKEEYKDIL RKAVQKICHS KSGEINPVKV 1450 1460 1470 ANLVKAYVDK YRHMRKHKKT EAGEEPPTQG AET

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins." Yuryev A., Patturajan M., Litingtung Y., Joshi R.V., Gentile C., Gebara M., Corden J.L. Proc. Natl. Acad. Sci. U.S.A. 93:6975-6980(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), INTERACTION WITH POLR2A. Tissue: Hippocampus.
[2]	"Genome sequence of the Brown Norway rat yields insights into mammalian evolution." Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M. , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S. Nature 428:493-521(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Brown Norway.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U49057 mRNA. Translation: AAC52658.1. AC118351 Genomic DNA. No translation available.
IPI	IPI00211009. IPI00915115.
PIR	T31422.
RefSeq	NP_620793.1. NM_139093.1.
UniGene	Rn.10530.
3D structure databases
ProteinModelPortal	Q63625.
ModBase	Search...
Proteomic databases
PaxDb	Q63625.
PRIDE	Q63625.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSRNOT00000023376; ENSRNOP00000023376; ENSRNOG00000017299. ENSRNOT00000051755; ENSRNOP00000046880; ENSRNOG00000017299.
GeneID	245925.
KEGG	rno:245925.
UCSC	RGD:708360. rat.
Organism-specific databases
CTD	57661.
RGD	708360. Phrf1.
Phylogenomic databases
eggNOG	NOG300312.
GeneTree	ENSGT00530000063661.
HOGENOM	HOG000082501.
HOVERGEN	HBG108250.
InParanoid	Q63625.
OMA	YMKKLHM.
OrthoDB	EOG4MSD0F.
Gene expression databases
ArrayExpress	Q63625.
Genevestigator	Q63625.
Family and domain databases
Gene3D	3.30.40.10. 2 hits.
InterPro	IPR019786. Zinc_finger_PHD-type_CS. IPR011011. Znf_FYVE_PHD. IPR001965. Znf_PHD. IPR019787. Znf_PHD-finger. IPR001841. Znf_RING. IPR013083. Znf_RING/FYVE/PHD. IPR017907. Znf_RING_CS. [Graphical view]
Pfam	PF00628. PHD. 1 hit. PF13639. zf-RING_2. 1 hit. [Graphical view]
SMART	SM00249. PHD. 1 hit. SM00184. RING. 2 hits. [Graphical view]
SUPFAM	SSF57903. FYVE_PHD_ZnF. 1 hit.
PROSITE	PS01359. ZF_PHD_1. 1 hit. PS50016. ZF_PHD_2. 1 hit. PS00518. ZF_RING_1. 1 hit. PS50089. ZF_RING_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	623186.

Entry information

Entry name

PHRF1_RAT

Accession

Primary (citable) accession number: Q63625

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 25, 2008
Last sequence update:	November 25, 2008
Last modified:	April 3, 2013
This is version 67 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program