Q9NWB1 (RFOX1_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
December 14, 2011.
Version 102.
History...
Names·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended 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 |
| ||||
| 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 | 397 AA. |
| Sequence status | Complete. |
| 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. 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 | |
| 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. |
Ontologies
| Keywords | |
|---|---|
| Biological process | mRNA processing mRNA splicing |
| Cellular component | Cytoplasm Nucleus |
| Coding sequence diversity | Alternative splicing |
| Ligand | RNA-binding |
| Technical term | 3D-structure Complete proteome Reference proteome |
| Gene Ontology (GO) | |
| Biological process | RNA splicing Inferred from electronic annotation. Source: UniProtKB-KW RNA transportNon-traceable author statement Ref.1. Source: UniProtKB mRNA processingInferred from electronic annotation. Source: UniProtKB-KW |
| Cellular component | nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell trans-Golgi networkInferred from direct assay Ref.1. Source: UniProtKB |
| Molecular function | RNA binding Non-traceable author statement Ref.1. Source: UniProtKB nucleotide bindingInferred from electronic annotation. Source: InterPro protein C-terminus bindingInferred from physical interaction Ref.1. Source: UniProtKB |
| Complete GO annotation... | |
Binary interactions
With | Entry | #Exp. | IntAct | Notes |
|---|---|---|---|---|
| ATN1 | P54259 | 2 | EBI-945906,EBI-945980 | |
| ATXN1 | P54253 | 2 | EBI-945906,EBI-930964 | |
| NUMBL | Q9Y6R0 | 2 | EBI-945906,EBI-945925 | |
| PLEKHA5 | Q9HAU0 | 2 | EBI-945906,EBI-945934 | |
| PSMF1 | Q92530 | 2 | EBI-945906,EBI-945916 | |
| QKI | Q96PU8 | 2 | EBI-945906,EBI-945792 | |
| RBFOX2 | O43251 | 2 | EBI-945906,EBI-746056 |
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 key | Position(s) | Length | Description | Graphical view | Feature identifier | |||||||||||||||||
Molecule processing | ||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 397 | 397 | RNA binding protein fox-1 homolog 1 | PRO_0000081480 | ||||||||||||||||||
Regions | ||||||||||||||||||||||
| Domain | 117 – 193 | 77 | RRM | |||||||||||||||||||
Sites | ||||||||||||||||||||||
| Site | 118 | 1 | Interaction with RNA | |||||||||||||||||||
| Site | 126 | 1 | Interaction with RNA | |||||||||||||||||||
| Site | 127 | 1 | Interaction with RNA | |||||||||||||||||||
| Site | 151 | 1 | Interaction with RNA | |||||||||||||||||||
| Site | 156 | 1 | Interaction with RNA | |||||||||||||||||||
| Site | 160 | 1 | Interaction with RNA | |||||||||||||||||||
| Site | 184 | 1 | Interaction with RNA | |||||||||||||||||||
| Site | 194 | 1 | Interaction with RNA | |||||||||||||||||||
Natural variations | ||||||||||||||||||||||
| Alternative sequence | 1 – 9 | 9 | MNCEREQLR → MLASQGVLLHPYGVPMIVPA APYLPGLIQ in isoform 2, isoform 4 and isoform 5. | VSP_030874 | ||||||||||||||||||
| Alternative sequence | 226 – 253 | 28 | GTVLL…YTSAM → V in isoform 3. | VSP_030875 | ||||||||||||||||||
| Alternative sequence | 302 – 310 | 9 | DGFYGADIY → EPVYGNKLLQ in isoform 2, isoform 4 and isoform 5. | VSP_030876 | ||||||||||||||||||
| Alternative sequence | 332 – 397 | 66 | SYGRV…RFAPY → RNQFVFVAADEISCNTSAVT DEFMLPTPTTTHLLQPPPTA LVP in isoform 5. | VSP_030877 | ||||||||||||||||||
| Alternative sequence | 358 – 383 | 26 | Missing in isoform 4. | VSP_030878 | ||||||||||||||||||
Experimental info | ||||||||||||||||||||||
| Mutagenesis | 120 | 1 | H → A: Reduces RNA-binding affinity 160-fold. Ref.8 | |||||||||||||||||||
| Mutagenesis | 126 | 1 | F → A, I or R: Reduces RNA-binding affinity 1500-fold. Ref.8 | |||||||||||||||||||
| Mutagenesis | 126 | 1 | F → H or W: Reduces RNA-binding affinity 15-fold. Ref.8 | |||||||||||||||||||
| Mutagenesis | 126 | 1 | F → Y: No effect on RNA-binding. Ref.8 | |||||||||||||||||||
| Mutagenesis | 158 | 1 | F → A: Reduces RNA-binding affinity 700-fold. Ref.8 | |||||||||||||||||||
| Mutagenesis | 160 | 1 | F → A: Reduces RNA-binding affinity 30'000-fold. Ref.8 | |||||||||||||||||||
| Sequence conflict | 92 | 1 | T → A in BAA91472. Ref.4 | |||||||||||||||||||
Secondary structure | ||||||||||||||||||||||
Helix Strand Turn | ||||||||||||||||||||||
| Beta strand | 118 – 123 | 6 | ||||||||||||||||||||
| Helix | 130 – 136 | 7 | ||||||||||||||||||||
| Helix | 137 – 139 | 3 | ||||||||||||||||||||
| Beta strand | 146 – 148 | 3 | ||||||||||||||||||||
| Beta strand | 158 – 162 | 5 | ||||||||||||||||||||
| Helix | 167 – 176 | 10 | ||||||||||||||||||||
| Beta strand | 187 – 190 | 4 | ||||||||||||||||||||
Sequences
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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: 10814712] [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. Sugano S.Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [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. Pennacchio L.A.Nature 432:988-994(2004) [PubMed: 15616553] [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: 15489334] [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: 16537540] [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: 16362037] [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 AF109119 Genomic DNA. Translation: AAL83407.1.AF109120 AF109119 Genomic DNA. Translation: AAL83408.1.AF109120 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. | ||||||||||||
| IPI | IPI00152050. IPI00170678. IPI00170712. IPI01021020. IPI01022902. | ||||||||||||
| RefSeq | NP_001135805.1. NM_001142333.1. NP_001135806.1. NM_001142334.1. NP_061193.2. NM_018723.3. NP_665898.1. NM_145891.2. NP_665899.1. NM_145892.2. NP_665900.1. NM_145893.2. | ||||||||||||
| UniGene | Hs.459842. | ||||||||||||
3D structure databases | |||||||||||||
| PDBe RCSB PDB PDBj |
| ||||||||||||
| ProteinModelPortal | Q9NWB1. | ||||||||||||
| SMR | Q9NWB1. Positions 109-196. | ||||||||||||
| ModBase | Search... | ||||||||||||
Protein-protein interaction databases | |||||||||||||
| IntAct | Q9NWB1. 22 interactions. | ||||||||||||
| MINT | MINT-2854938. | ||||||||||||
| STRING | Q9NWB1. | ||||||||||||
Polymorphism databases | |||||||||||||
| DMDM | 166897979. | ||||||||||||
Proteomic databases | |||||||||||||
| PRIDE | Q9NWB1. | ||||||||||||
Protocols and materials databases | |||||||||||||
| StructuralBiologyKnowledgebase | Search... | ||||||||||||
Genome annotation databases | |||||||||||||
| Ensembl | ENST00000340209; ENSP00000344196; ENSG00000078328. | ||||||||||||
| GeneID | 54715. | ||||||||||||
| KEGG | hsa:54715. | ||||||||||||
| UCSC | uc002cys.1. human. uc002cyt.1. human. uc002cyw.1. human. uc002cyx.1. human. uc002cyy.1. human. | ||||||||||||
Organism-specific databases | |||||||||||||
| CTD | 54715. | ||||||||||||
| GeneCards | GC16P006033. | ||||||||||||
| H-InvDB | HIX0018900. | ||||||||||||
| HGNC | HGNC:18222. RBFOX1. | ||||||||||||
| HPA | HPA040809. | ||||||||||||
| MIM | 605104. gene. | ||||||||||||
| neXtProt | NX_Q9NWB1. | ||||||||||||
| GenAtlas | Search... | ||||||||||||
Phylogenomic databases | |||||||||||||
| GeneTree | ENSGT00390000013767. | ||||||||||||
| HOVERGEN | HBG000044. | ||||||||||||
| OMA | YPPAQSH. | ||||||||||||
Gene expression databases | |||||||||||||
| ArrayExpress | Q9NWB1. | ||||||||||||
| Bgee | Q9NWB1. | ||||||||||||
| Genevestigator | Q9NWB1. | ||||||||||||
| GermOnline | ENSG00000078328. Homo sapiens. | ||||||||||||
Family and domain databases | |||||||||||||
| InterPro | IPR012677. Nucleotide-bd_a/b_plait. IPR017325. RNA-bd_9/Ataxin-2-bd. IPR000504. RRM_dom. [Graphical view] | ||||||||||||
| Gene3D | G3DSA:3.30.70.330. a_b_plait_nuc_bd. 1 hit. | ||||||||||||
| KO | K14946. | ||||||||||||
| Pfam | PF00076. RRM_1. 1 hit. [Graphical view] | ||||||||||||
| PIRSF | PIRSF037932. Ataxin_2_bd_A2BP. 1 hit. | ||||||||||||
| SMART | SM00360. RRM. 1 hit. [Graphical view] | ||||||||||||
| PROSITE | PS50102. RRM. 1 hit. [Graphical view] | ||||||||||||
| ProtoNet | Search... | ||||||||||||
Other | |||||||||||||
| NextBio | 57277. | ||||||||||||
| SOURCE | Search... | ||||||||||||
Entry information
| Entry name | RFOX1_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q9NWB1 Secondary accession number(s): Q7Z7I7 Q9NS20 | ||||||||
| Entry history |
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| 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. | ||||||||
Relevant documents
| Human chromosome 16 Human chromosome 16: entries, gene names and cross-references to MIM |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with