Reviewed, UniProtKB/Swiss-Prot Q9GZS1 (RPA49_HUMAN)

Names and origin

Protein names

Recommended name:
    DNA-directed RNA polymerase I subunit RPA49
      Short name=RNA polymerase I subunit A49
Alternative name(s):
    DNA-directed RNA polymerase I subunit E
    RNA polymerase I-associated factor 1
    RNA polymerase I-associated factor 53

Gene names

Name:	POLR1E
Synonyms:	PAF53, PRAF1

Organism

Homo sapiens (Human) [Complete 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	481 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Appears to be involved in the formation of the initiation complex at the promoter by mediating the interaction between Pol I and UBTF/UBF By similarity.
Subunit structure	Component of the RNA polymerase I (Pol I) complex consisting of at least 13 subunits By similarity. Interacts with PAF49/CD3EAP. Also binds UBTF/UBF By similarity.
Subcellular location	Nucleus › nucleolus. Ref.5
Sequence similarities	Belongs to the eukaryotic RPA49/POLR1E RNA polymerase subunit family.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	rRNA transcription Inferred from sequence or structural similarity. Source: HGNC
Cellular component	nucleolus Inferred from sequence or structural similarity. Source: HGNC
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
DDX20	Q9UHI6	1	EBI-359458,EBI-347658
DDX6	P26196	1	EBI-359458,EBI-351257
HNRNPUL1	Q9BUJ2	1	EBI-359458,EBI-1018153
MYO1C	O00159	1	EBI-359458,EBI-350423
POLR1C	O15160	1	EBI-359458,EBI-1055079
QPCTL	Q9NXS2	1	EBI-359458,EBI-1052839

Alternative products

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

Isoform 1 (identifier: Q9GZS1-1)

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.

Isoform 2 (identifier: Q9GZS1-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-87: MYQASAVSLL...LISFLGCTLT → MAAEVLPSARWQYCGAPDGSQRAVL

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 481	481	DNA-directed RNA polymerase I subunit RPA49		PRO_0000073956
Amino acid modifications
	Modified residue	225	1	Phosphoserine Ref.7
Natural variations
	Alternative sequence	1 – 87	87	MYQAS…GCTLT → MAAEVLPSARWQYCGAPDGS QRAVL in isoform 2.		VSP_013535
	Natural variant	254	1	D → H: dbSNP rs7863488.		VAR_022372
	Natural variant	418	1	V → M: dbSNP rs7867180.		VAR_022373
	Natural variant	445	1	R → K: dbSNP rs10814571. Ref.4		VAR_022374
Experimental info
	Sequence conflict	56	1	T → A in BAC03629. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified April 26, 2005. Version 2. Checksum: 8E43E238D0C669CB	FASTA	481	53,962
	10 20 30 40 50 60 MYQASAVSLL PRDIPSCHSP SPGFSHLPTS SSQLAPDLLQ FPLGQDPSFL AIPILTLPPS 70 80 90 100 110 120 DSLVPPYIVW YIVWPSALIS FLGCTLTVQF SNGKLQSPGN MRFTLYENKD STNPRKRNQR 130 140 150 160 170 180 ILAAETDRLS YVGNNFGTGA LKCNTLCRHF VGILNKTSGQ MEVYDAELFN MQPLFSDVSV 190 200 210 220 230 240 ESELALESQT KTYREKMDSC IEAFGTTKQK RALNTRRMNR VGNESLNRAV AKAAETIIDT 250 260 270 280 290 300 KGVTALVSDA IHNDLQDDSL YLPPCYDDAA KPEDVYKFED LLSPAEYEAL QSPSEAFRNV 310 320 330 340 350 360 TSEEILKMIE ENSHCTFVIE ALKSLPSDVE SRDRQARCIW FLDTLIKFRA HRVVKRKSAL 370 380 390 400 410 420 GPGVPHIINT KLLKHFTCLT YNNGRLRNLI SDSMKAKITA YVIILALHIH DFQIDLTVLQ 430 440 450 460 470 480 RDLKLSEKRM MEIAKAMRLK ISKRRVSVAA GSEEDHKLGT LSLPLPPAQT SDRLAKRRKI T
	Isoform 2. Checksum: AB9EF3B9E8230053	FASTA	419	47,260
	10 20 30 40 50 60 MAAEVLPSAR WQYCGAPDGS QRAVLVQFSN GKLQSPGNMR FTLYENKDST NPRKRNQRIL 70 80 90 100 110 120 AAETDRLSYV GNNFGTGALK CNTLCRHFVG ILNKTSGQME VYDAELFNMQ PLFSDVSVES 130 140 150 160 170 180 ELALESQTKT YREKMDSCIE AFGTTKQKRA LNTRRMNRVG NESLNRAVAK AAETIIDTKG 190 200 210 220 230 240 VTALVSDAIH NDLQDDSLYL PPCYDDAAKP EDVYKFEDLL SPAEYEALQS PSEAFRNVTS 250 260 270 280 290 300 EEILKMIEEN SHCTFVIEAL KSLPSDVESR DRQARCIWFL DTLIKFRAHR VVKRKSALGP 310 320 330 340 350 360 GVPHIINTKL LKHFTCLTYN NGRLRNLISD SMKAKITAYV IILALHIHDF QIDLTVLQRD 370 380 390 400 410 LKLSEKRMME IAKAMRLKIS KRRVSVAAGS EEDHKLGTLS LPLPPAQTSD RLAKRRKIT

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Tissue: Placenta.
[2]	"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)." Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B. Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
[3]	"DNA sequence and analysis of human chromosome 9." Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I. Nature 429:369-374(2004) [PubMed: 15164053] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT LYS-445. Tissue: Cervix and Lung.
[5]	"Functional proteomic analysis of human nucleolus." Scherl A., Coute Y., Deon C., Calle A., Kindbeiter K., Sanchez J.-C., Greco A., Hochstrasser D.F., Diaz J.-J. Mol. Biol. Cell 13:4100-4109(2002) [PubMed: 12429849] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[6]	"RNA polymerase I-specific subunit CAST/hPAF49 has a role in the activation of transcription by upstream binding factor." Panov K.I., Panova T.B., Gadal O., Nishiyama K., Saito T., Russell J., Zomerdijk J.C.B.M. Mol. Cell. Biol. 26:5436-5448(2006) [PubMed: 16809778] [Abstract] Cited for: IDENTIFICATION IN THE RNA POL I COMPLEX.
[7]	"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: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-225, MASS SPECTROMETRY.
[8]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AK023452 mRNA. Translation: BAB14579.1. AK024032 mRNA. Translation: BAB14791.1. AK091294 mRNA. Translation: BAC03629.1. CR457313 mRNA. Translation: CAG33594.1. AL158156 Genomic DNA. Translation: CAH73518.1. AL158156 Genomic DNA. Translation: CAH73519.1. BC001337 mRNA. Translation: AAH01337.1. BC014331 mRNA. Translation: AAH14331.1.
IPI	IPI00251989. IPI00550638.
RefSeq	NP_071935.1.
UniGene	Hs.591087
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9GZS1. 22 interactions.
PTM databases
PhosphoSite	Q9GZS1.
2-D gel databases
SWISS-2DPAGE	Q9GZS1.
Proteomic databases
PRIDE	Q9GZS1.
Genome annotation databases
Ensembl	ENSG00000137054. Homo sapiens. [Contig view]
GeneID	64425.
KEGG	hsa:64425.
NMPDR	fig|9606.3.peg.31289.
UCSC	uc003zzy.1. human. uc003zzz.1. human.
Organism-specific databases
GeneCards	GC09P037477.
H-InvDB	HIX0008038.
HGNC	HGNC:17631. POLR1E.
GenAtlas	Search...
Phylogenomic databases
HOGENOM	Q9GZS1.
HOVERGEN	Q9GZS1.
OMA	Q9GZS1. NKTSGQM.
Gene expression databases
ArrayExpress	Q9GZS1.
Bgee	Q9GZS1.
CleanEx	HS_POLR1E.
GermOnline	ENSG00000137054. Homo sapiens.
Family and domain databases
InterPro	IPR009668. RNA_pol-assoc_fac_A49-like. [Graphical view]
Pfam	PF06870. RNA_pol_I_A49. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	66425.

Entry information

Entry name

RPA49_HUMAN

Accession

Primary (citable) accession number: Q9GZS1
Secondary accession number(s): Q5VZT3, Q8NBA9, Q96L20

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 26, 2005
Last sequence update:	April 26, 2005
Last modified:	July 7, 2009
This is version 65 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)