Q9GZS1 (RPA49_HUMAN) Reviewed, UniProtKB/Swiss-Prot

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) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	481 AA.
Sequence status	Complete.
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. Ref.6
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 Reference proteome
Gene Ontology (GO)
Biological_process	rRNA transcription Inferred from sequence or structural similarity. Source: HGNC
Cellular_component	cell junction Inferred from direct assay. Source: HPA cytoplasm Inferred from direct assay. Source: HPA 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
Complete GO annotation...

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	97	1	Phosphoserine Ref.8
	Modified residue	225	1	Phosphoserine Ref.10
Natural variations
	Alternative sequence	1 – 87	87	MYQAS…GCTLT → MAAEVLPSARWQYCGAPDGS QRAVL in isoform 2.		VSP_013535
	Natural variant	254	1	D → H. Corresponds to variant rs7863488 [ dbSNP | Ensembl ].		VAR_022372
	Natural variant	418	1	V → M. Corresponds to variant rs7867180 [ dbSNP | Ensembl ].		VAR_022373
	Natural variant	445	1	R → K. Ref.4 Corresponds to variant rs10814571 [ dbSNP | Ensembl ].		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 [UniParc]. 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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[8]	"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-97, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[9]	"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].
[10]	"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-225, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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. NM_022490.1.
UniGene	Hs.591087. Hs.733126.
3D structure databases
ProteinModelPortal	Q9GZS1.
SMR	Q9GZS1. Positions 87-175.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-27546N.
IntAct	Q9GZS1. 4 interactions.
MINT	MINT-1137773.
STRING	9606.ENSP00000367029.
PTM databases
PhosphoSite	Q9GZS1.
Polymorphism databases
DMDM	62901107.
2D gel databases
SWISS-2DPAGE	Q9GZS1.
Proteomic databases
PaxDb	Q9GZS1.
PRIDE	Q9GZS1.
Protocols and materials databases
DNASU	64425.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000377792; ENSP00000367023; ENSG00000137054. ENST00000377798; ENSP00000367029; ENSG00000137054.
GeneID	64425.
KEGG	hsa:64425.
UCSC	uc003zzy.1. human. uc003zzz.1. human.
Organism-specific databases
CTD	64425.
GeneCards	GC09P037486.
HGNC	HGNC:17631. POLR1E.
HPA	HPA022527.
neXtProt	NX_Q9GZS1.
PharmGKB	PA142671136.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG301234.
HOGENOM	HOG000035116.
HOVERGEN	HBG053490.
InParanoid	Q9GZS1.
KO	K03005.
OMA	RRMNRVG.
PhylomeDB	Q9GZS1.
Gene expression databases
ArrayExpress	Q9GZS1.
Bgee	Q9GZS1.
CleanEx	HS_POLR1E.
Genevestigator	Q9GZS1.
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
GenomeRNAi	64425.
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:	May 1, 2013
This is version 101 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.