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Q9NWB1 (RFOX1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 123. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
RNA binding protein fox-1 homolog 1
Alternative name(s):
Ataxin-2-binding protein 1
Fox-1 homolog A
Hexaribonucleotide-binding protein 1
Gene names
Name:RBFOX1
Synonyms:A2BP, A2BP1, FOX1, HRNBP1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length397 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

RNA-binding protein that regulates alternative splicing events by binding to 5'-UGCAUGU-3' elements. Regulates alternative splicing of tissue-specific exons and of differentially spliced exons during erythropoiesis. Ref.7

Subunit structure

Binds to the C-terminus of ATXN2. Ref.1

Subcellular location

Nucleus By similarity. Cytoplasm By similarity.

Tissue specificity

Predominantly expressed in muscle and brain.

Sequence similarities

Contains 1 RRM (RNA recognition motif) domain.

Sequence caution

The sequence AAF78291.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Alternative products

This entry describes 5 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9NWB1-1)

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: Q9NWB1-2)

Also known as: Gamma;

The sequence of this isoform differs from the canonical sequence as follows:
     1-9: MNCEREQLR → MLASQGVLLHPYGVPMIVPAAPYLPGLIQ
     302-310: DGFYGADIY → EPVYGNKLLQ
Isoform 3 (identifier: Q9NWB1-3)

Also known as: 1;

The sequence of this isoform differs from the canonical sequence as follows:
     226-253: GTVLLCQANQEGSSMYSAPSSLVYTSAM → V
Isoform 4 (identifier: Q9NWB1-4)

Also known as: Alpha;

The sequence of this isoform differs from the canonical sequence as follows:
     1-9: MNCEREQLR → MLASQGVLLHPYGVPMIVPAAPYLPGLIQ
     302-310: DGFYGADIY → EPVYGNKLLQ
     358-383: Missing.
Isoform 5 (identifier: Q9NWB1-5)

Also known as: Beta;

The sequence of this isoform differs from the canonical sequence as follows:
     1-9: MNCEREQLR → MLASQGVLLHPYGVPMIVPAAPYLPGLIQ
     302-310: DGFYGADIY → EPVYGNKLLQ
     332-397: SYGRVYAADP...RGGYNRFAPY → RNQFVFVAAD...LQPPPTALVP

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 397397RNA binding protein fox-1 homolog 1
PRO_0000081480

Regions

Domain117 – 19377RRM

Sites

Site1181Interaction with RNA
Site1261Interaction with RNA
Site1271Interaction with RNA
Site1511Interaction with RNA
Site1561Interaction with RNA
Site1601Interaction with RNA
Site1841Interaction with RNA
Site1941Interaction with RNA

Natural variations

Alternative sequence1 – 99MNCEREQLR → MLASQGVLLHPYGVPMIVPA APYLPGLIQ in isoform 2, isoform 4 and isoform 5.
VSP_030874
Alternative sequence226 – 25328GTVLL…YTSAM → V in isoform 3.
VSP_030875
Alternative sequence302 – 3109DGFYGADIY → EPVYGNKLLQ in isoform 2, isoform 4 and isoform 5.
VSP_030876
Alternative sequence332 – 39766SYGRV…RFAPY → RNQFVFVAADEISCNTSAVT DEFMLPTPTTTHLLQPPPTA LVP in isoform 5.
VSP_030877
Alternative sequence358 – 38326Missing in isoform 4.
VSP_030878

Experimental info

Mutagenesis1201H → A: Reduces RNA-binding affinity 160-fold. Ref.8
Mutagenesis1261F → A, I or R: Reduces RNA-binding affinity 1500-fold. Ref.8
Mutagenesis1261F → H or W: Reduces RNA-binding affinity 15-fold. Ref.8
Mutagenesis1261F → Y: No effect on RNA-binding. Ref.8
Mutagenesis1581F → A: Reduces RNA-binding affinity 700-fold. Ref.8
Mutagenesis1601F → A: Reduces RNA-binding affinity 30'000-fold. Ref.8
Sequence conflict921T → A in BAA91472. Ref.4

Secondary structure

.............. 397
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified February 5, 2008. Version 2.
Checksum: EA96AA7B6E144D80

FASTA39742,784
        10         20         30         40         50         60 
MNCEREQLRG NQEAAAAPDT MAQPYASAQF APPQNGIPAE YTAPHPHPAP EYTGQTTVPE 

        70         80         90        100        110        120 
HTLNLYPPAQ THSEQSPADT SAQTVSGTAT QTDDAAPTDG QPQTQPSENT ENKSQPKRLH 

       130        140        150        160        170        180 
VSNIPFRFRD PDLRQMFGQF GKILDVEIIF NERGSKGFGF VTFENSADAD RAREKLHGTV 

       190        200        210        220        230        240 
VEGRKIEVNN ATARVMTNKK TVNPYTNGWK LNPVVGAVYS PEFYAGTVLL CQANQEGSSM 

       250        260        270        280        290        300 
YSAPSSLVYT SAMPGFPYPA ATAAAAYRGA HLRGRGRTVY NTFRAAAPPP PIPAYGGVVY 

       310        320        330        340        350        360 
QDGFYGADIY GGYAAYRYAQ PTPATAAAYS DSYGRVYAAD PYHHALAPAP TYGVGAMNAF 

       370        380        390 
APLTDAKTRS HADDVGLVLS SLQASIYRGG YNRFAPY 

« Hide

Isoform 2 (Gamma) [UniParc].

Checksum: 47D6FC140F75D01A
Show »

FASTA41844,793
Isoform 3 (1) [UniParc].

Checksum: 26DBC3263B7E5EA9
Show »

FASTA37040,005
Isoform 4 (Alpha) [UniParc].

Checksum: 68F8CEFE2FC6D674
Show »

FASTA39242,084
Isoform 5 (Beta) [UniParc].

Checksum: 2299F9127AA1DE39
Show »

FASTA39542,402

References

« Hide 'large scale' references
[1]"A novel protein with RNA-binding motifs interacts with ataxin-2."
Shibata H., Huynh D.P., Pulst S.-M.
Hum. Mol. Genet. 9:1303-1313(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH ATXN2.
[2]"Molecular cloning and chromosomal localization of a human brain, heart and skeletal muscle specific RNA binding protein gene homologous to fox-1 in Caenorhabditis elegans."
Chen W., Chu Z.-L., Blough R.I., Liu L., Hoppes B., Winkelmann J.C.
Submitted (SEP-1998) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORMS 2; 4 AND 5).
[3]"An alternative splicing of a novel protein with RNA-binding motifs interacts with ataxin-2."
Yu L., Guo J., She X.
Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
[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. expand/collapse author list , 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] (ISOFORM 1).
[5]"The sequence and analysis of duplication-rich human chromosome 16."
Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J. expand/collapse author list , Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J., Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D., Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M., Rubin E.M., Pennacchio L.A.
Nature 432:988-994(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"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 5).
[7]"Fox-2 splicing factor binds to a conserved intron motif to promote inclusion of protein 4.1R alternative exon 16."
Ponthier J.L., Schluepen C., Chen W., Lersch R.A., Gee S.L., Hou V.C., Lo A.J., Short S.A., Chasis J.A., Winkelmann J.C., Conboy J.G.
J. Biol. Chem. 281:12468-12474(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"Molecular basis of RNA recognition by the human alternative splicing factor Fox-1."
Auweter S.D., Fasan R., Reymond L., Underwood J.G., Black D.L., Pitsch S., Allain F.H.-T.
EMBO J. 25:163-173(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 109-196 IN COMPLEX WITH RNA, MUTAGENESIS OF HIS-120; PHE-126; PHE-158 AND PHE-160.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF107203 mRNA. Translation: AAF78291.1. Different initiation.
AF229057 mRNA. Translation: AAL71904.1.
AF094849 mRNA. Translation: AAL83405.1.
AF109106 mRNA. Translation: AAL83406.1.
AF109120 expand/collapse EMBL AC list , AF109107, AF109108, AF109109, AF109110, AF109111, AF109112, AF109113, AF109114, AF109115, AF109116, AF109117, AF109118, AF109119 Genomic DNA. Translation: AAL83407.1.
AF109120 expand/collapse EMBL AC list , AF109107, AF109108, AF109109, AF109110, AF109111, AF109112, AF109113, AF109114, AF109115, AF109116, AF109117, AF109119 Genomic DNA. Translation: AAL83408.1.
AF109120 expand/collapse EMBL AC list , AF109107, AF109108, AF109109, AF109110, AF109111, AF109112, AF109113, AF109114, AF109115, AF109116, AF109117, AF109119 Genomic DNA. Translation: AAL83409.1.
AF448859 mRNA. Translation: AAP41925.1.
AK001027 mRNA. Translation: BAA91472.1.
AC005774 Genomic DNA. No translation available.
AC006075 Genomic DNA. No translation available.
AC006112 Genomic DNA. No translation available.
AC007012 Genomic DNA. No translation available.
AC007217 Genomic DNA. No translation available.
AC007222 Genomic DNA. No translation available.
AC007223 Genomic DNA. No translation available.
AC009135 Genomic DNA. No translation available.
AC022206 Genomic DNA. No translation available.
AC023829 Genomic DNA. No translation available.
AC027683 Genomic DNA. No translation available.
AC079410 Genomic DNA. No translation available.
AC125796 Genomic DNA. No translation available.
AC131390 Genomic DNA. No translation available.
BC113691 mRNA. Translation: AAI13692.1.
CCDSCCDS10531.1. [Q9NWB1-2]
CCDS10532.1. [Q9NWB1-5]
CCDS45405.1. [Q9NWB1-4]
CCDS55983.1. [Q9NWB1-1]
CCDS55984.1. [Q9NWB1-3]
RefSeqNP_001135805.1. NM_001142333.1. [Q9NWB1-3]
NP_001135806.1. NM_001142334.1. [Q9NWB1-1]
NP_061193.2. NM_018723.3. [Q9NWB1-1]
NP_665898.1. NM_145891.2. [Q9NWB1-2]
NP_665899.1. NM_145892.2. [Q9NWB1-4]
NP_665900.1. NM_145893.2. [Q9NWB1-5]
UniGeneHs.459842.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2ERRNMR-A109-196[»]
ProteinModelPortalQ9NWB1.
SMRQ9NWB1. Positions 75-196.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid120107. 23 interactions.
IntActQ9NWB1. 22 interactions.
MINTMINT-2854938.
STRING9606.ENSP00000309117.

PTM databases

PhosphoSiteQ9NWB1.

Polymorphism databases

DMDM166897979.

Proteomic databases

PaxDbQ9NWB1.
PRIDEQ9NWB1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000311745; ENSP00000309117; ENSG00000078328. [Q9NWB1-2]
ENST00000355637; ENSP00000347855; ENSG00000078328. [Q9NWB1-5]
ENST00000436368; ENSP00000402745; ENSG00000078328. [Q9NWB1-4]
ENST00000547338; ENSP00000447717; ENSG00000078328. [Q9NWB1-1]
ENST00000550418; ENSP00000450031; ENSG00000078328. [Q9NWB1-1]
ENST00000553186; ENSP00000447753; ENSG00000078328. [Q9NWB1-3]
GeneID54715.
KEGGhsa:54715.
UCSCuc002cys.2. human. [Q9NWB1-1]
uc002cyt.2. human. [Q9NWB1-3]
uc002cyw.2. human. [Q9NWB1-5]
uc002cyx.2. human. [Q9NWB1-4]
uc002cyy.2. human. [Q9NWB1-2]

Organism-specific databases

CTD54715.
GeneCardsGC16P006033.
HGNCHGNC:18222. RBFOX1.
HPAHPA040809.
MIM605104. gene.
neXtProtNX_Q9NWB1.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG258617.
HOVERGENHBG000044.
KOK14946.
OMALVYTSTM.
PhylomeDBQ9NWB1.
TreeFamTF315942.

Gene expression databases

ArrayExpressQ9NWB1.
BgeeQ9NWB1.
GenevestigatorQ9NWB1.

Family and domain databases

Gene3D3.30.70.330. 1 hit.
InterProIPR025670. Fox-1_C_dom.
IPR012677. Nucleotide-bd_a/b_plait.
IPR017325. RNA-bd_Fox-1.
IPR000504. RRM_dom.
[Graphical view]
PfamPF12414. Fox-1_C. 1 hit.
PF00076. RRM_1. 1 hit.
[Graphical view]
PIRSFPIRSF037932. Ataxin_2_bd_A2BP. 1 hit.
SMARTSM00360. RRM. 1 hit.
[Graphical view]
PROSITEPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSRBFOX1. human.
EvolutionaryTraceQ9NWB1.
GeneWikiRBFOX1.
GenomeRNAi54715.
NextBio57277.
PROQ9NWB1.
SOURCESearch...

Entry information

Entry nameRFOX1_HUMAN
AccessionPrimary (citable) accession number: Q9NWB1
Secondary accession number(s): Q7Z7I7 expand/collapse secondary AC list , Q8TAE3, Q8TAF2, Q8WYB2, Q9NS20
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: February 5, 2008
Last modified: July 9, 2014
This is version 123 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 16

Human chromosome 16: entries, gene names and cross-references to MIM