Reviewed, UniProtKB/Swiss-Prot O43251 (RBM9_HUMAN)

Names and origin

Protein names

Recommended name:
    RNA-binding protein 9
Alternative name(s):
    RNA-binding motif protein 9
    Fox-1 homolog B
    Hexaribonucleotide-binding protein 2
    Repressor of tamoxifen transcriptional activity

Gene names

Name:	RBM9
Synonyms:	FOX2, HRNBP2, RTA

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	390 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	RNA-binding protein that regulates alternative splicing events by binding to 5'-UGCAUGU-3' elements. Prevents binding of U2AF2 to the 3'-splice site. Regulates alternative splicing of tissue-specific exons and of differentially spliced exons during erythropoiesis By similarity. RNA-binding protein that seems to act as a coregulatory factor of ER-alpha.
Subunit structure	Interacts with ER-alpha N-terminal activation domain.
Subcellular location	Nucleus. CytoplasmBy similarity.
Sequence similarities	Contains 1 RRM (RNA recognition motif) domain.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Alternative splicing
Ligand	RNA-binding
Technical term	3D-structure
Gene Ontology (GO)
Biological process	RNA splicing Inferred from electronic annotation. Source: UniProtKB-KW estrogen receptor signaling pathway Ref.1 Inferred from direct assay. Source: UniProtKB mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW negative regulation of transcription Ref.1 Inferred from direct assay. Source: UniProtKB regulation of cell proliferation Ref.1 Traceable author statement. Source: UniProtKB
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-KW nucleus Ref.1 Inferred from direct assay. Source: UniProtKB
Molecular function	RNA binding Ref.1 Inferred from direct assay. Source: UniProtKB nucleotide binding Inferred from electronic annotation. Source: InterPro transcription corepressor activity Ref.1 Inferred from direct assay. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ATXN1	P54253	1	EBI-746056,EBI-930964
FOX1	Q9NWB1	1	EBI-746056,EBI-945906
QKI	Q96PU8	1	EBI-746056,EBI-945792

Alternative products

This entry describes 8 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: O43251-1)

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: O43251-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-18: MQNEPLTPGYHGFPARDS → MEKKKMVT
     94-94: T → TQ

Isoform 3 (identifier: O43251-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-18: MQNEPLTPGYHGFPARDS → MEKKKMVT
     143-160: Missing.
     261-265: SLPLV → I

Notes: No experimental confirmation available.

Isoform 4 (identifier: O43251-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1-18: MQNEPLTPGYHGFPARDS → MEKKKMVT
     311-390: VYQDGFYGAD...RGGYSRFAPY → DMQPTDMHSL...TADLPPTEVT

Notes: No experimental confirmation available.

Isoform 5 (identifier: O43251-5)

The sequence of this isoform differs from the canonical sequence as follows:
     1-18: MQNEPLTPGYHGFPARDS → MEKKKMVT
     261-265: SLPLV → I

Notes: No experimental confirmation available.

Isoform 6 (identifier: O43251-6)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MAEGAQPQQPPQLGPGAAARGMKRESELELPVPGAGGDGADPGLSKRPRTEEAAADGGGGM

Isoform 7 (identifier: O43251-7)

The sequence of this isoform differs from the canonical sequence as follows:
     261-265: SLPLV → I
     323-390: GGYAAYRYAQ...RGGYSRFAPY → IESANCFRSN...TADLPPTEVT

Isoform 8 (identifier: O43251-8)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MAEGAQPQQPPQLGPGAAARGMKRESELELPVPGAGGDGADPGLSKRPRTEEAAADGGGGM
     94-94: T → TQ

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 390

390

RNA-binding protein 9

PRO_0000081766

Regions

Domain

121 – 197

77

RRM

Compositional bias

273 – 377

105

Ala-rich

Sites

Site

122

1

Interaction with RNA By similarity

Site

130

1

Interaction with RNA By similarity

Site

131

1

Interaction with RNA By similarity

Site

155

1

Interaction with RNA By similarity

Site

160

1

Interaction with RNA By similarity

Site

164

1

Interaction with RNA By similarity

Site

188

1

Interaction with RNA By similarity

Site

198

1

Interaction with RNA By similarity

Natural variations

Alternative sequence

1 – 18

18

MQNEP…PARDS → MEKKKMVT in isoform 2, isoform 3, isoform 4 and isoform 5.

VSP_007180

Alternative sequence

1

1

M → MAEGAQPQQPPQLGPGAAAR GMKRESELELPVPGAGGDGA DPGLSKRPRTEEAAADGGGG M in isoform 6 and isoform 8.

VSP_030889

Alternative sequence

94

1

T → TQ in isoform 2 and isoform 8.

VSP_030890

Alternative sequence

143 – 160

18

Missing in isoform 3.

VSP_007181

Alternative sequence

261 – 265

5

SLPLV → I in isoform 3, isoform 5 and isoform 7.

VSP_007182

Alternative sequence

311 – 390

80

VYQDG…RFAPY → DMQPTDMHSLLLQPQPPLLQ PLQPLTVTVMAGCTQPTPTM PLPLPLAMELALWRVYTEVA TADLPPTEVT in isoform 4.

VSP_007183

Alternative sequence

323 – 390

68

GGYAA…RFAPY → IESANCFRSNRVDMQPTDMH SLLLQPQPPLLQPLQPLTVT VMAGCTQPTPTMPLPLPLAM ELALWRVYTEVATADLPPTE VT in isoform 7.

VSP_030891

Experimental info

Sequence conflict

116

1

S → G in AAX84843. Ref.6

Sequence conflict

231

1

S → F in BAB70875. Ref.4

Sequence conflict

346

1

A → V in AAH13115. Ref.8

Sequence conflict

350

1

S → G in BAB70875. Ref.4

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

390

Helix Strand Turn

Details...

Beta strand

122 – 127

6

Helix

134 – 140

7

Helix

141 – 143

3

Beta strand

147 – 153

7

Turn

156 – 159

4

Beta strand

162 – 168

7

Helix

170 – 180

11

Beta strand

191 – 194

4

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified April 11, 2003. Version 3. Checksum: 40D6C8C40764B317	FASTA	390	41,374
	10 20 30 40 50 60 MQNEPLTPGY HGFPARDSQG NQEPTTTPDA MVQPFTTIPF PPPPQNGIPT EYGVPHTQDY 70 80 90 100 110 120 AGQTGEHNLT LYGSTQAHGE QSSNSPSTQN GSLTTEGGAQ TDGQQSQTQS SENSESKSTP 130 140 150 160 170 180 KRLHVSNIPF RFRDPDLRQM FGQFGKILDV EIIFNERGSK GFGFVTFENS ADADRAREKL 190 200 210 220 230 240 HGTVVEGRKI EVNNATARVM TNKKMVTPYA NGWKLSPVVG AVYGPELYAA SSFQADVSLG 250 260 270 280 290 300 NDAAVPLSGR GGINTYIPLI SLPLVPGFPY PTAATTAAAF RGAHLRGRGR TVYGAVRAVP 310 320 330 340 350 360 PTAIPAYPGV VYQDGFYGAD LYGGYAAYRY AQPATATAAT AAAAAAAAYS DGYGRVYTAD 370 380 390 PYHALAPAAS YGVGAVASLY RGGYSRFAPY
	Isoform 2. Checksum: 553FE52BD48F7062		381	40,479
	10 20 30 40 50 60 MEKKKMVTQG NQEPTTTPDA MVQPFTTIPF PPPPQNGIPT EYGVPHTQDY AGQTGEHNLT 70 80 90 100 110 120 LYGSTQAHGE QSSNSPSTQN GSLTQTEGGA QTDGQQSQTQ SSENSESKST PKRLHVSNIP 130 140 150 160 170 180 FRFRDPDLRQ MFGQFGKILD VEIIFNERGS KGFGFVTFEN SADADRAREK LHGTVVEGRK 190 200 210 220 230 240 IEVNNATARV MTNKKMVTPY ANGWKLSPVV GAVYGPELYA ASSFQADVSL GNDAAVPLSG 250 260 270 280 290 300 RGGINTYIPL ISLPLVPGFP YPTAATTAAA FRGAHLRGRG RTVYGAVRAV PPTAIPAYPG 310 320 330 340 350 360 VVYQDGFYGA DLYGGYAAYR YAQPATATAA TAAAAAAAAY SDGYGRVYTA DPYHALAPAA 370 380 SYGVGAVASL YRGGYSRFAP Y
	Isoform 3. Checksum: BA4B3740D2DA6E7A		358	37,879
	10 20 30 40 50 60 MEKKKMVTQG NQEPTTTPDA MVQPFTTIPF PPPPQNGIPT EYGVPHTQDY AGQTGEHNLT 70 80 90 100 110 120 LYGSTQAHGE QSSNSPSTQN GSLTTEGGAQ TDGQQSQTQS SENSESKSTP KRLHVSNIPF 130 140 150 160 170 180 RFRDPDLRQM FGGFGFVTFE NSADADRARE KLHGTVVEGR KIEVNNATAR VMTNKKMVTP 190 200 210 220 230 240 YANGWKLSPV VGAVYGPELY AASSFQADVS LGNDAAVPLS GRGGINTYIP LIIPGFPYPT 250 260 270 280 290 300 AATTAAAFRG AHLRGRGRTV YGAVRAVPPT AIPAYPGVVY QDGFYGADLY GGYAAYRYAQ 310 320 330 340 350 PATATAATAA AAAAAAYSDG YGRVYTADPY HALAPAASYG VGAVASLYRG GYSRFAPY
	Isoform 4. Checksum: 725D8B1C719AEB10		370	39,783
	10 20 30 40 50 60 MEKKKMVTQG NQEPTTTPDA MVQPFTTIPF PPPPQNGIPT EYGVPHTQDY AGQTGEHNLT 70 80 90 100 110 120 LYGSTQAHGE QSSNSPSTQN GSLTTEGGAQ TDGQQSQTQS SENSESKSTP KRLHVSNIPF 130 140 150 160 170 180 RFRDPDLRQM FGQFGKILDV EIIFNERGSK GFGFVTFENS ADADRAREKL HGTVVEGRKI 190 200 210 220 230 240 EVNNATARVM TNKKMVTPYA NGWKLSPVVG AVYGPELYAA SSFQADVSLG NDAAVPLSGR 250 260 270 280 290 300 GGINTYIPLI SLPLVPGFPY PTAATTAAAF RGAHLRGRGR TVYGAVRAVP PTAIPAYPGV 310 320 330 340 350 360 DMQPTDMHSL LLQPQPPLLQ PLQPLTVTVM AGCTQPTPTM PLPLPLAMEL ALWRVYTEVA 370 TADLPPTEVT
	Isoform 5. Checksum: A50D5086B4436165		376	39,954
	10 20 30 40 50 60 MEKKKMVTQG NQEPTTTPDA MVQPFTTIPF PPPPQNGIPT EYGVPHTQDY AGQTGEHNLT 70 80 90 100 110 120 LYGSTQAHGE QSSNSPSTQN GSLTTEGGAQ TDGQQSQTQS SENSESKSTP KRLHVSNIPF 130 140 150 160 170 180 RFRDPDLRQM FGQFGKILDV EIIFNERGSK GFGFVTFENS ADADRAREKL HGTVVEGRKI 190 200 210 220 230 240 EVNNATARVM TNKKMVTPYA NGWKLSPVVG AVYGPELYAA SSFQADVSLG NDAAVPLSGR 250 260 270 280 290 300 GGINTYIPLI IPGFPYPTAA TTAAAFRGAH LRGRGRTVYG AVRAVPPTAI PAYPGVVYQD 310 320 330 340 350 360 GFYGADLYGG YAAYRYAQPA TATAATAAAA AAAAYSDGYG RVYTADPYHA LAPAASYGVG 370 AVASLYRGGY SRFAPY
	Isoform 6. Checksum: C0AAA21A2D4161B0		450	47,206
	10 20 30 40 50 60 MAEGAQPQQP PQLGPGAAAR GMKRESELEL PVPGAGGDGA DPGLSKRPRT EEAAADGGGG 70 80 90 100 110 120 MQNEPLTPGY HGFPARDSQG NQEPTTTPDA MVQPFTTIPF PPPPQNGIPT EYGVPHTQDY 130 140 150 160 170 180 AGQTGEHNLT LYGSTQAHGE QSSNSPSTQN GSLTTEGGAQ TDGQQSQTQS SENSESKSTP 190 200 210 220 230 240 KRLHVSNIPF RFRDPDLRQM FGQFGKILDV EIIFNERGSK GFGFVTFENS ADADRAREKL 250 260 270 280 290 300 HGTVVEGRKI EVNNATARVM TNKKMVTPYA NGWKLSPVVG AVYGPELYAA SSFQADVSLG 310 320 330 340 350 360 NDAAVPLSGR GGINTYIPLI SLPLVPGFPY PTAATTAAAF RGAHLRGRGR TVYGAVRAVP 370 380 390 400 410 420 PTAIPAYPGV VYQDGFYGAD LYGGYAAYRY AQPATATAAT AAAAAAAAYS DGYGRVYTAD 430 440 450 PYHALAPAAS YGVGAVASLY RGGYSRFAPY
	Isoform 7. Checksum: 6A4D8B3E2FAA5726		400	43,179
	10 20 30 40 50 60 MQNEPLTPGY HGFPARDSQG NQEPTTTPDA MVQPFTTIPF PPPPQNGIPT EYGVPHTQDY 70 80 90 100 110 120 AGQTGEHNLT LYGSTQAHGE QSSNSPSTQN GSLTTEGGAQ TDGQQSQTQS SENSESKSTP 130 140 150 160 170 180 KRLHVSNIPF RFRDPDLRQM FGQFGKILDV EIIFNERGSK GFGFVTFENS ADADRAREKL 190 200 210 220 230 240 HGTVVEGRKI EVNNATARVM TNKKMVTPYA NGWKLSPVVG AVYGPELYAA SSFQADVSLG 250 260 270 280 290 300 NDAAVPLSGR GGINTYIPLI IPGFPYPTAA TTAAAFRGAH LRGRGRTVYG AVRAVPPTAI 310 320 330 340 350 360 PAYPGVVYQD GFYGADLYIE SANCFRSNRV DMQPTDMHSL LLQPQPPLLQ PLQPLTVTVM 370 380 390 400 AGCTQPTPTM PLPLPLAMEL ALWRVYTEVA TADLPPTEVT
	Isoform 8. Checksum: BCEF50C7FF45F304		451	47,334
	10 20 30 40 50 60 MAEGAQPQQP PQLGPGAAAR GMKRESELEL PVPGAGGDGA DPGLSKRPRT EEAAADGGGG 70 80 90 100 110 120 MQNEPLTPGY HGFPARDSQG NQEPTTTPDA MVQPFTTIPF PPPPQNGIPT EYGVPHTQDY 130 140 150 160 170 180 AGQTGEHNLT LYGSTQAHGE QSSNSPSTQN GSLTQTEGGA QTDGQQSQTQ SSENSESKST 190 200 210 220 230 240 PKRLHVSNIP FRFRDPDLRQ MFGQFGKILD VEIIFNERGS KGFGFVTFEN SADADRAREK 250 260 270 280 290 300 LHGTVVEGRK IEVNNATARV MTNKKMVTPY ANGWKLSPVV GAVYGPELYA ASSFQADVSL 310 320 330 340 350 360 GNDAAVPLSG RGGINTYIPL ISLPLVPGFP YPTAATTAAA FRGAHLRGRG RTVYGAVRAV 370 380 390 400 410 420 PPTAIPAYPG VVYQDGFYGA DLYGGYAAYR YAQPATATAA TAAAAAAAAY SDGYGRVYTA 430 440 450 DPYHALAPAA SYGVGAVASL YRGGYSRFAP Y

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A negative coregulator for the human ER." Norris J.D., Fan D., Sherk A., McDonnell D.P. Mol. Endocrinol. 16:459-468(2002) [PubMed: 11875103] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY.
[2]	"Reevaluating human gene annotation: a second-generation analysis of chromosome 22." Collins J.E., Goward M.E., Cole C.G., Smink L.J., Huckle E.J., Knowles S., Bye J.M., Beare D.M., Dunham I. Genome Res. 13:27-36(2003) [PubMed: 12529303] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4). Tissue: Placenta.
[3]	Chen W., Winkelmann J.C. Submitted (JAN-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
[4]	"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 2 AND 6). Tissue: Brain.
[5]	"A genome annotation-driven approach to cloning the human ORFeome." Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I. Genome Biol. 5:RESEARCH84.1-RESEARCH84.11(2004) [PubMed: 15461802] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 5).
[6]	"A novel isoform of RNA binding motif protein 9." Yang G., Huang S.C., Benz E.J. Jr. Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 4).
[7]	Zhou G., Nong W., Li H., Ke R., Shen C., Liang M., Tang Z., Huang B., Lin L., Yang S. Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 8).
[8]	"The DNA sequence of human chromosome 22." Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J., Ainscough R., Almeida J.P., Babbage A.K., Bagguley C., Bailey J., Barlow K.F., Bates K.N., Beasley O.P., Bird C.P., Blakey S.E., Bridgeman A.M. , Buck D., Burgess J., Burrill W.D., Burton J., Carder C., Carter N.P., Chen Y., Clark G., Clegg S.M., Cobley V.E., Cole C.G., Collier R.E., Connor R., Conroy D., Corby N.R., Coville G.J., Cox A.V., Davis J., Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M., Ellington A.G., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A., Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C., Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E., Jones M.C., Kershaw J., Kimberley A.M., King A., Laird G.K., Langford C.F., Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M., Matthews L.H., Mccann O.T.,