Rbfox1 Gene Detail

Summary

• Symbol
  Rbfox1
• Name
  RNA binding protein, fox-1 homolog (C. elegans) 1
• Synonyms
  A2bp, A2bp1, FOX1, HRNBP1

• Feature Type
  protein coding gene
• IDs
  MGI:1926224
  NCBI Gene: 268859
• Alliance
  gene page
• Transcription Start Sites
  72 TSS

Location &
Maps

• Sequence Map
  Chr16:5703219-7229390 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 16, 3.34 cM
• Mapping Data
  1 experiment

Strain
Comparison

• SNPs within 2kb
  20338 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1926224	protein coding gene	Chr16:5702566-7230344 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0022490	protein coding gene	Chr16:3429752-4069285 (+)
A/J	MGP_AJ_G0022452	protein coding gene	Chr16:3182139-3801677 (+)
AKR/J	MGP_AKRJ_G0022429	protein coding gene	Chr16:3413469-4039694 (+)
BALB/cJ	MGP_BALBcJ_G0022457	protein coding gene	Chr16:3333458-3945668 (+)
C3H/HeJ	MGP_C3HHeJ_G0022224	protein coding gene	Chr16:3423402-4031042 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0022906	protein coding gene	Chr16:3512693-4137041 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0020427	protein coding gene	Chr16:3068624-3671166 (+)
CAST/EiJ	MGP_CASTEiJ_G0021750	protein coding gene	Chr16:3466958-4100314 (+)
CBA/J	MGP_CBAJ_G0022193	protein coding gene	Chr16:3706259-4362225 (+)
DBA/2J	MGP_DBA2J_G0022324	protein coding gene	Chr16:3234244-3850517 (+)
FVB/NJ	MGP_FVBNJ_G0022299	protein coding gene	Chr16:3237047-3850908 (+)
LP/J	MGP_LPJ_G0022392	protein coding gene	Chr16:3393463-4040146 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0022321	protein coding gene	Chr16:3514609-4149610 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0022918	protein coding gene	Chr16:3379863-4004963 (+)
PWK/PhJ	MGP_PWKPhJ_G0021490	protein coding gene	Chr16:3390551-4005556 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0021321	protein coding gene	Chr16:3455679-4082114 (+)
WSB/EiJ	MGP_WSBEiJ_G0021799	protein coding gene	Chr16:3402139-4025924 (+)

Homology

• Human Ortholog
  RBFOX1, RNA binding fox-1 homolog 1

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  RBFOX1, RNA binding fox-1 homolog 1
  
• Synonyms
  2BP1, A2BP1, FOX1, FOX-1, HRNBP1
• Links
  HGNC:18222

  NCBI Gene ID: 54715

  neXtProt AC: NX_Q9NWB1

  UniProt: Q9NWB1

  
  
• Chr Location
  16p13.3; chr16:5239749-7713343 (+)  GRCh38.p7

---

• Alliance of Genome Resources
  Rbfox1 stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: RBFOX1
• Protein SuperFamily
  Ataxin_2_bd_A2BP
• Gene Tree
  Rbfox1
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  11 phenotypes from 2 alleles in 2 genetic backgrounds
  10 phenotypes from multigenic genotypes
  17 phenotype references
  

• All Mutations and Alleles
  6
• Endonuclease-mediated
  2
• Targeted
  4
• Incidental Mutations
  Mutagenetix , APF , CvDC
• Find Mice (IMSR)
  19 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Mice homozygous for a conditional allele activated in the brain exhibit reduced fertility, infrequent spontaneous seizures, increased susceptibility to kainic acid-induced seizures and lethality, and increased neuronal excitation.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  21
• GO References
  9

Expression

• Assay Results
  1061
• Tissues
  129
• cDNA Data
  16
• Literature Summary
  18

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase rbfox1
  ZFIN rbfox1

Interactions

• Rbfox1 interacts with 308 markers (Mir1a-1, Mir1a-2, Mir1b, ...) View All

Sequences &
Gene Models

• All Sequences
  165
• RefSeq
  106
• UniProt
  5
• CCDS
  CCDS27936.1, CCDS37245.1

• Ensembl
  ENSMUSG00000008658 (Evidence)
• NCBI Gene
  268859

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000008658	Ensembl Gene Model | MGI Sequence Detail	1526172	C57BL/6J
transcript	ENSMUST00000229741	Ensembl | MGI Sequence Detail	1407	Not Applicable
polypeptide	ENSMUSP00000155364	Ensembl | MGI Sequence Detail	417	Not Applicable

Protein
Information

• UniProt
  5 Sequences
• Protein Ontology
  PR:000007601 RNA binding protein fox-1 homolog 1
  (term hierarchy)
• InterPro Domains
  IPR025670 Fox-1 C-terminal domain
  IPR034237 FOX1, RNA recognition motif
  IPR012677 Nucleotide-binding alpha-beta plait domain superfamily
  IPR035979 RNA-binding domain superfamily
  IPR017325 RNA binding protein Fox-1
  IPR000504 RNA recognition motif domain

Molecular
Reagents

• All nucleic 18

  cDNA 16

  Primer pair 2

  
  

  Microarray probesets 3

References

• Summaries
  All 69

  Developmental Gene Expression 18

  Gene Ontology 9

  Phenotypes 17
• Earliest
  J:70808 Kiehl TR, et al., Identification and expression of a mouse ortholog of A2BP1. Mamm Genome. 2001 Aug;12(8):595-601
• Latest
  J:314130 Gu L, et al., Loss of Rbfox1 Does Not Affect Survival of Retinal Ganglion Cells Injured by Optic Nerve Crush. Front Neurosci. 2021;15:687690

TSS for Rbfox1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr136920	Chr16:5702785-5702826 (+)	-413 bp
Tssr136921	Chr16:5702833-5702912 (+)	-346 bp
Tssr136922	Chr16:5703134-5703175 (+)	-64 bp
Tssr136923	Chr16:5703317-5703373 (+)	126 bp
Tssr136924	Chr16:5703443-5703456 (+)	231 bp
Tssr136925	Chr16:5720021-5720065 (+)	16,824 bp
Tssr136926	Chr16:5720457-5720459 (+)	17,239 bp
Tssr136927	Chr16:5860226-5860235 (+)	157,012 bp
Tssr136928	Chr16:5886357-5886373 (+)	183,146 bp
Tssr136929	Chr16:6116754-6116786 (+)	413,551 bp
Tssr136930	Chr16:6166369-6166385 (+)	463,158 bp
Tssr136931	Chr16:6166388-6166413 (+)	463,182 bp
Tssr136932	Chr16:6166520-6166544 (+)	463,313 bp
Tssr136933	Chr16:6166565-6166586 (+)	463,357 bp
Tssr136934	Chr16:6166596-6166634 (+)	463,396 bp
Tssr136935	Chr16:6166885-6166959 (+)	463,703 bp
Tssr4784	Chr16:6166973-6166980 (+)	463,758 bp
Tssr136936	Chr16:6166983-6167009 (+)	463,777 bp
Tssr136937	Chr16:6167025-6167036 (+)	463,812 bp
Tssr136938	Chr16:6278286-6278310 (+)	575,079 bp
Tssr136939	Chr16:6321041-6321047 (+)	617,825 bp
Tssr136940	Chr16:6335830-6335841 (+)	632,617 bp
Tssr136941	Chr16:6341441-6341451 (+)	638,227 bp
Tssr136942	Chr16:6380977-6380991 (+)	677,765 bp
Tssr136943	Chr16:6498583-6498624 (+)	795,385 bp
Tssr136944	Chr16:6516083-6516088 (+)	812,867 bp
Tssr136945	Chr16:6633980-6633996 (+)	930,769 bp
Tssr136946	Chr16:6642632-6642636 (+)	939,415 bp
Tssr136947	Chr16:6658284-6658304 (+)	955,075 bp
Tssr136948	Chr16:6660249-6660251 (+)	957,031 bp
Tssr136949	Chr16:6680864-6680866 (+)	977,646 bp
Tssr136950	Chr16:6707437-6707443 (+)	1,004,221 bp
Tssr136951	Chr16:6732124-6732133 (+)	1,028,910 bp
Tssr136952	Chr16:6732266-6732277 (+)	1,029,053 bp
Tssr136953	Chr16:6753462-6753470 (+)	1,050,247 bp
Tssr136954	Chr16:6766570-6766588 (+)	1,063,360 bp
Tssr136955	Chr16:6804563-6804572 (+)	1,101,349 bp
Tssr136956	Chr16:6814481-6814493 (+)	1,111,268 bp
Tssr136957	Chr16:6814506-6814519 (+)	1,111,294 bp
Tssr136958	Chr16:6814557-6814586 (+)	1,111,353 bp
Tssr136959	Chr16:6826889-6826898 (+)	1,123,675 bp
Tssr4785	Chr16:6857257-6857285 (+)	1,154,052 bp
Tssr136960	Chr16:6857433-6857446 (+)	1,154,221 bp
Tssr136961	Chr16:6857463-6857480 (+)	1,154,253 bp
Tssr136962	Chr16:6857566-6857598 (+)	1,154,363 bp
Tssr136963	Chr16:6857757-6857788 (+)	1,154,554 bp
Tssr136964	Chr16:6887592-6887601 (+)	1,184,378 bp
Tssr136965	Chr16:6887602-6887613 (+)	1,184,389 bp
Tssr136966	Chr16:6887652-6887657 (+)	1,184,436 bp
Tssr136967	Chr16:6887661-6887676 (+)	1,184,450 bp
Tssr136968	Chr16:6887689-6887710 (+)	1,184,481 bp
Tssr136969	Chr16:6887713-6887734 (+)	1,184,505 bp
Tssr136970	Chr16:6887735-6887754 (+)	1,184,526 bp
Tssr136971	Chr16:6887813-6887822 (+)	1,184,599 bp
Tssr4786	Chr16:6887880-6887887 (+)	1,184,665 bp
Tssr136972	Chr16:6898602-6898606 (+)	1,195,385 bp
Tssr136973	Chr16:6962559-6962572 (+)	1,259,347 bp
Tssr136974	Chr16:6967631-6967659 (+)	1,264,426 bp
Tssr136975	Chr16:6967775-6967780 (+)	1,264,559 bp
Tssr136976	Chr16:7007332-7007335 (+)	1,304,115 bp
Tssr136977	Chr16:7011581-7011611 (+)	1,308,377 bp
Tssr136978	Chr16:7035525-7035535 (+)	1,332,311 bp
Tssr136979	Chr16:7035548-7035576 (+)	1,332,343 bp
Tssr136980	Chr16:7035579-7035588 (+)	1,332,365 bp
Tssr136981	Chr16:7035592-7035597 (+)	1,332,376 bp
Tssr136982	Chr16:7035616-7035624 (+)	1,332,401 bp
Tssr136983	Chr16:7042169-7042181 (+)	1,338,956 bp
Tssr136984	Chr16:7042188-7042199 (+)	1,338,975 bp
Tssr136985	Chr16:7042272-7042281 (+)	1,339,058 bp
Tssr136986	Chr16:7096053-7096089 (+)	1,392,852 bp
Tssr136987	Chr16:7159383-7159388 (+)	1,456,167 bp
Tssr136988	Chr16:7227645-7227658 (+)	1,524,433 bp