Q9NV88 (INT9_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Integrator complex subunit 9
Short name=Int9

Alternative name(s):
Protein related to CPSF subunits of 74 kDa
Short name=RC-74

Gene names

Name:	INTS9
Synonyms:	RC74

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	658 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the Integrator complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes.
Subunit structure	Belongs to the multiprotein complex Integrator, at least composed of INTS1, INTS2, INTS3, INTS4, INTS5, INTS6, INTS7, INTS8, INTS9/RC74, INTS10, CPSF3L/INTS11 and INTS12. Ref.5
Subcellular location	Nucleus Ref.6.
Miscellaneous	Although strongly related to RNA-specific endonuclease proteins, it lacks the HXHXDH motif that binds zinc and participates in the catalytic center. Its function as endonuclease is therefore unsure.
Sequence similarities	Belongs to the metallo-beta-lactamase superfamily. RNA-metabolizing metallo-beta-lactamase-like family. INTS9 subfamily.
Sequence caution	The sequence AAB67601.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	snRNA processing Inferred from direct assay Ref.5. Source: HGNC
Cellular_component	integrator complex Inferred from direct assay Ref.5. Source: HGNC
Complete GO annotation...

Alternative products

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

Isoform 1 (identifier: Q9NV88-1)

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: Q9NV88-2)

The sequence of this isoform differs from the canonical sequence as follows:
     67-87: Missing.

Note: No experimental confirmation available.

Isoform 3 (identifier: Q9NV88-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-24: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 658	658	Integrator complex subunit 9		PRO_0000259557
Natural variations
	Alternative sequence	1 – 24	24	Missing in isoform 3.		VSP_044306
	Alternative sequence	67 – 87	21	Missing in isoform 2.		VSP_043011
Experimental info
	Sequence conflict	324	1	V → A in BAA91867. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified October 31, 2006. Version 2. Checksum: 81F1A24B99704684	FASTA	658	73,814
	10 20 30 40 50 60 MKLYCLSGHP TLPCNVLKFK STTIMLDCGL DMTSTLNFLP LPLVQSPRLS NLPGWSLKDG 70 80 90 100 110 120 NAFLDKELKE CSGHVFVDSV PEFCLPETEL IDLSTVDVIL ISNYHCMMAL PYITEHTGFT 130 140 150 160 170 180 GTVYATEPTV QIGRLLMEEL VNFIERVPKA QSASLWKNKD IQRLLPSPLK DAVEVSTWRR 190 200 210 220 230 240 CYTMQEVNSA LSKIQLVGYS QKIELFGAVQ VTPLSSGYAL GSSNWIIQSH YEKVSYVSGS 250 260 270 280 290 300 SLLTTHPQPM DQASLKNSDV LVLTGLTQIP TANPDGMVGE FCSNLALTVR NGGNVLVPCY 310 320 330 340 350 360 PSGVIYDLLE CLYQYIDSAG LSSVPLYFIS PVANSSLEFS QIFAEWLCHN KQSKVYLPEP 370 380 390 400 410 420 PFPHAELIQT NKLKHYPSIH GDFSNDFRQP CVVFTGHPSL RFGDVVHFME LWGKSSLNTV 430 440 450 460 470 480 IFTEPDFSYL EALAPYQPLA MKCIYCPIDT RLNFIQVSKL LKEVQPLHVV CPEQYTQPPP 490 500 510 520 530 540 AQSHRMDLMI DCQPPAMSYR RAEVLALPFK RRYEKIEIMP ELADSLVPME IKPGISLATV 550 560 570 580 590 600 SAVLHTKDNK HLLQPPPRPA QPTSGKKRKR VSDDVPDCKV LKPLLSGSIP VEQFVQTLEK 610 620 630 640 650 HGFSDIKVED TAKGHIVLLQ EAETLIQIEE DSTHIICDND EMLRVRLRDL VLKFLQKF
	Isoform 2 [UniParc]. Checksum: DF93CBBDE1A6061E	FASTA	637	71,468
	10 20 30 40 50 60 MKLYCLSGHP TLPCNVLKFK STTIMLDCGL DMTSTLNFLP LPLVQSPRLS NLPGWSLKDG 70 80 90 100 110 120 NAFLDKTELI DLSTVDVILI SNYHCMMALP YITEHTGFTG TVYATEPTVQ IGRLLMEELV 130 140 150 160 170 180 NFIERVPKAQ SASLWKNKDI QRLLPSPLKD AVEVSTWRRC YTMQEVNSAL SKIQLVGYSQ 190 200 210 220 230 240 KIELFGAVQV TPLSSGYALG SSNWIIQSHY EKVSYVSGSS LLTTHPQPMD QASLKNSDVL 250 260 270 280 290 300 VLTGLTQIPT ANPDGMVGEF CSNLALTVRN GGNVLVPCYP SGVIYDLLEC LYQYIDSAGL 310 320 330 340 350 360 SSVPLYFISP VANSSLEFSQ IFAEWLCHNK QSKVYLPEPP FPHAELIQTN KLKHYPSIHG 370 380 390 400 410 420 DFSNDFRQPC VVFTGHPSLR FGDVVHFMEL WGKSSLNTVI FTEPDFSYLE ALAPYQPLAM 430 440 450 460 470 480 KCIYCPIDTR LNFIQVSKLL KEVQPLHVVC PEQYTQPPPA QSHRMDLMID CQPPAMSYRR 490 500 510 520 530 540 AEVLALPFKR RYEKIEIMPE LADSLVPMEI KPGISLATVS AVLHTKDNKH LLQPPPRPAQ 550 560 570 580 590 600 PTSGKKRKRV SDDVPDCKVL KPLLSGSIPV EQFVQTLEKH GFSDIKVEDT AKGHIVLLQE 610 620 630 AETLIQIEED STHIICDNDE MLRVRLRDLV LKFLQKF
	Isoform 3 [UniParc]. Checksum: 327CFB70D6AB0649	FASTA	634	71,137
	10 20 30 40 50 60 MLDCGLDMTS TLNFLPLPLV QSPRLSNLPG WSLKDGNAFL DKELKECSGH VFVDSVPEFC 70 80 90 100 110 120 LPETELIDLS TVDVILISNY HCMMALPYIT EHTGFTGTVY ATEPTVQIGR LLMEELVNFI 130 140 150 160 170 180 ERVPKAQSAS LWKNKDIQRL LPSPLKDAVE VSTWRRCYTM QEVNSALSKI QLVGYSQKIE 190 200 210 220 230 240 LFGAVQVTPL SSGYALGSSN WIIQSHYEKV SYVSGSSLLT THPQPMDQAS LKNSDVLVLT 250 260 270 280 290 300 GLTQIPTANP DGMVGEFCSN LALTVRNGGN VLVPCYPSGV IYDLLECLYQ YIDSAGLSSV 310 320 330 340 350 360 PLYFISPVAN SSLEFSQIFA EWLCHNKQSK VYLPEPPFPH AELIQTNKLK HYPSIHGDFS 370 380 390 400 410 420 NDFRQPCVVF TGHPSLRFGD VVHFMELWGK SSLNTVIFTE PDFSYLEALA PYQPLAMKCI 430 440 450 460 470 480 YCPIDTRLNF IQVSKLLKEV QPLHVVCPEQ YTQPPPAQSH RMDLMIDCQP PAMSYRRAEV 490 500 510 520 530 540 LALPFKRRYE KIEIMPELAD SLVPMEIKPG ISLATVSAVL HTKDNKHLLQ PPPRPAQPTS 550 560 570 580 590 600 GKKRKRVSDD VPDCKVLKPL LSGSIPVEQF VQTLEKHGFS DIKVEDTAKG HIVLLQEAET 610 620 630 LIQIEEDSTH IICDNDEMLR VRLRDLVLKF LQKF

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; 2 AND 3).
[2]	"DNA sequence and analysis of human chromosome 8." Nusbaum C., Mikkelsen T.S., Zody M.C., Asakawa S., Taudien S., Garber M., Kodira C.D., Schueler M.G., Shimizu A., Whittaker C.A., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Yang X., Allen N.R., Anderson S., Asakawa T. , Blechschmidt K., Bloom T., Borowsky M.L., Butler J., Cook A., Corum B., DeArellano K., DeCaprio D., Dooley K.T., Dorris L. III, Engels R., Gloeckner G., Hafez N., Hagopian D.S., Hall J.L., Ishikawa S.K., Jaffe D.B., Kamat A., Kudoh J., Lehmann R., Lokitsang T., Macdonald P., Major J.E., Matthews C.D., Mauceli E., Menzel U., Mihalev A.H., Minoshima S., Murayama Y., Naylor J.W., Nicol R., Nguyen C., O'Leary S.B., O'Neill K., Parker S.C.J., Polley A., Raymond C.K., Reichwald K., Rodriguez J., Sasaki T., Schilhabel M., Siddiqui R., Smith C.L., Sneddon T.P., Talamas J.A., Tenzin P., Topham K., Venkataraman V., Wen G., Yamazaki S., Young S.K., Zeng Q., Zimmer A.R., Rosenthal A., Birren B.W., Platzer M., Shimizu N., Lander E.S. Nature 439:331-335(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"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 1). Tissue: Brain.
[4]	"Human chromosome 8 BAC clone CIT987SK-2A8 complete sequence." Adams M.D. Submitted (APR-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 163-658.
[5]	"Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II." Baillat D., Hakimi M.-A., Naeaer A.M., Shilatifard A., Cooch N., Shiekhattar R. Cell 123:265-276(2005) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE INTEGRATOR COMPLEX.
[6]	"A CPSF-73 homologue is required for cell cycle progression but not cell growth and interacts with a protein having features of CPSF-100." Dominski Z., Yang X.-C., Purdy M., Wagner E.J., Marzluff W.F. Mol. Cell. Biol. 25:1489-1500(2005) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION, SUBCELLULAR LOCATION, INTERACTION WITH CPSF3L.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AK001733 mRNA. Translation: BAA91867.1. AK298468 mRNA. Translation: BAH12796.1. AK300593 mRNA. Translation: BAH13311.1. AC040975 Genomic DNA. No translation available. AC131969 Genomic DNA. No translation available. BC025267 mRNA. Translation: AAH25267.1. U96629 Genomic DNA. Translation: AAB67601.1. Sequence problems. BK005726 mRNA. Translation: DAA05726.1. BK005674 mRNA. Translation: DAA05670.1.
IPI	IPI00290514. IPI00871167.
RefSeq	NP_001138631.1. NM_001145159.2. NP_001166033.1. NM_001172562.1. NP_060720.2. NM_018250.3.
UniGene	Hs.162397.
3D structure databases
ProteinModelPortal	Q9NV88.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9NV88. 1 interaction.
STRING	9606.ENSP00000398208.
PTM databases
PhosphoSite	Q9NV88.
Polymorphism databases
DMDM	119371246.
Proteomic databases
PaxDb	Q9NV88.
PRIDE	Q9NV88.
Protocols and materials databases
DNASU	55756.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000416984; ENSP00000398208; ENSG00000104299. ENST00000521022; ENSP00000429065; ENSG00000104299. ENST00000521777; ENSP00000430943; ENSG00000104299.
GeneID	55756.
KEGG	hsa:55756.
UCSC	uc003xha.3. human.
Organism-specific databases
CTD	55756.
GeneCards	GC08M028625.
HGNC	HGNC:25592. INTS9.
MIM	611352. gene.
neXtProt	NX_Q9NV88.
PharmGKB	PA162392192.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG1236.
HOGENOM	HOG000045359.
HOVERGEN	HBG081802.
InParanoid	Q9NV88.
KO	K13146.
OMA	PLAMKCV.
OrthoDB	EOG415GCW.
PhylomeDB	Q9NV88.
Gene expression databases
ArrayExpress	Q9NV88.
Bgee	Q9NV88.
CleanEx	HS_INTS9.
Genevestigator	Q9NV88.
GermOnline	ENSG00000104299. Homo sapiens.
Family and domain databases
InterPro	IPR022712. Beta_Casp. IPR027074. Integrator_9su. [Graphical view]
PANTHER	PTHR11203:SF2. PTHR11203:SF2. 1 hit.
Pfam	PF10996. Beta-Casp. 1 hit. [Graphical view]
SMART	SM01027. Beta-Casp. 1 hit. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	INTS9. human.
GenomeRNAi	55756.
NextBio	60763.
SOURCE	Search...

Entry information

Entry name

INT9_HUMAN

Accession

Primary (citable) accession number: Q9NV88
Secondary accession number(s): B7Z560 , B7Z6M5, O00224, Q8TB16

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 31, 2006
Last sequence update:	October 31, 2006
Last modified:	May 1, 2013
This is version 79 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.