XLOC_002493 (rfx3)


Basic Information

Item Value
gene id XLOC_002493
gene name rfx3
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007121.7
NCBI id CM002894.2
chromosome length 45420867
location 600164 ~ 641609 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00004660
TTTTTCCGCAGCGTCAAGTTGGTGTACGCGGCGAGCTTTATAGCAACCGTTGCCCTGAGCTGCAGCGCCATAGTCACCGTAGTCCTGGCGACTGTAACCCaccaacaataacaacaacaacctcCTCCTGTCCGCTCCATCCTTACCACCACCTTCCGACCATCCTCATCCTCATCCTCACACCGATCCAGGCGCCATGCAGACCCCAGAGGCAGGCGCTGACTCCACCGTGTCCACCGTGCCCCTCCAGACCAGCGTGCCTGTGCAGCCTGCGGTcagtggccagcaggtggcgtctCAGGTGCCCGTCCAGCAGCAGGCGCAGACTGTTCAACAGGTCCAGCATGTGTATCAAGCACAGGTTCAGTATGTGCAGGAGGAAAACAACAGCGTTTACACCAACGGAACCATACGGGCGTACTCGTACTCGGAGCCACAGCTCTACAACCAGAACAGCAGCGGGAACTACTTCGACACGCAGGGCGGCGGAGGCAGCGCGGCACAGGTCAGCACCGTAGTGTCCACTCACAGCATGGCCAACAACGGCAACGGCACCGGCGCTCTGGCTATGGGGCTCACCGGAGGCCAGATCATCAGCAGCTCAGGAGCTTATCTGATTGGAGGAAACTCCATGGATGGCTCCGCCCCTCACGGCGCCGCACAGACCACCAGAGCCTCCCCTGCTACGATTGAAATGGCGATTGAGACGCTCCAAAAGTCTGAAGGTTTATCCAGTCAGAGAAGTTCGCTGCTCAACAGCCATCTGCAGTGGCTGCTGGATAATTACGAGACAGCAGAGGGCGTGAGTCTGCCGCGCTCCACCCTCTACAATCACTACCTGCGCCACTGTCAGGAGCAGAAGCTGGACCCTGTCAATGCTGCGTCCTTCGGGAAGCTCATCCGCTCCATCTTCATGGGGCTGCGCACACGCCGCCTGGGGAcacgagGGAACTCAAAGTATCATTATTACGGGATTCGTGTGAAGCCGGACTCTCCTCTGAACCGCTTGCAGGAGGACATGCAGTACATGGCACTGAGACAGCAGCCCGTCCAGCAGAAGCAGAGATTTAAGCCTGTGCAGAAGATGGACGGAGTTTCGGGAGATAACTTCAGCAGCGCTGGACAGCACACACCCAATGCTGCAGAGCAGACCTTCATCGCTCAGAGCCAACATCATCAGCAGTTCCTGGATGGCTCCAGAGCTCTGCCGGAGTTTGTTGAACTGGATCTTGGAGAGGCAGTGGACGGCGTCGGCCCAGAGGATGTCAAAGCCCTTCAGACGCTCTACAGAGAACACTGCGAGGCCATCCTGGATGTAGTGGTGAACCTGCAGTTCAATCTGATCGAGAACCTGTGGCAGACGTTCTGGCGCTATTCTGCCTCCAGCTCTGTAGAGGGCGTCACAATCACAGAAAACAGTGGTTTGAGTGAGATCGAGGGCCGTCTGCCGCGGGCCAGGCTGATTCTGCTGTGCCGACATGAGGCCGTGCACAAGTGGATGAACACCTGCGATCACCTGATGTACCAGGCCCTCGTGGAGATCCTCATCCCGGACGTCCTGAGACCCATTCCTAGTGCCTTGACTCAAGCCATCCGTAACTTTGCCAAAAGCCTTGAGGGCTGGCTCACCAATGCCATGAGCAGCATTCCCCCGAGGATGATCAATACCAAGGTTTCCGCTGTTAGTGCCTTCGCTCAGACCCTCCGCAGATACACGTCCCTGAATCATCTGGCGCAGGCGGCTCGCGCAGTCCTGCAGAACACCTCGCAGATCAACCAGATGCTCAGCGATCTCAACCGGGTCGACTTCGCCAATGTGCAGGAGCAGGCCTCATGGGTGTGCCAGTGTGAAGAGGGTGTCGTCCAGCGCCTCGAGCAGGATTTTAAGGCCACCCTGCAGCAGCAGAGCTCACTGGAGCAGTGGGCCGCCTGGCTGGATAACGTGGTCACCCAGATACTGAAGCCGTACGAGGACAAGCCCACCCTGCCCAAAGCTGCACGCCAGTTCCTGCTCAAGTGGTCCTTCTACAGCTCTATGGTCATCAGAGATCTGACCCTCCGCAGCGCTGCCAGCTTCGGCTCGTTCCACCTGATCCGGCTGCTGTACGACGAGTACATGTTCTACCTGGTGGAGCATCGCGTCGCCCAGGCAACAGGAGAGACGGCCATCGGAGTCATGGGCGAGTTtcaggacctgaacaccatgtcaCCTGCCAACATCGACAAAGATGAGGTGAGCGAGATGGACAGCGATCTGGACGAGGAGATGGAGGAGGCGGACGAGCCACTGGCCAAGCGGGAGAAGGTGGAGGCGGACGTGATCCAGGTGCTGCAGGTAGGGGCGATGGAGGATGGCAGCAGCGCGGTGGTGGGCATCGTCCAGCCGAGCATGATCAACTCTCTGCCCCCGACCACCAACAATCACAGCGAACACATCCTCAGCACCGGAACCAGCACTATCCGCCATGTGGGAAACACCTACGCCTCCGTCTAAACATCTGCAGCACCACTACCATCTCCACCAACCCGCAACACATCCCTTTTCATCACAGAATCTACACGTGATGCTTCGTCCAATGGTGGGATCATCTGCAAACTCCCACATTGCTGATTGTAGAAGTGGAACGCCCTgatgctaacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacactgaatccACGCCACCGGATCTATCAGGGAAATGTTGATGattctggaaaaaaataaactaccATTTGCCTAGTGGATAT
>TCONS_00004661
GGCGCCATGCAGACCCCAGAGGCAGGCGCTGACTCCACCGTGTCCACCGTGCCCCTCCAGACCAGCGTGCCTGTGCAGCCTGCGGTcagtggccagcaggtggcgtctCAGGTGCCCGTCCAGCAGCAGGCGCAGACTGTTCAACAGGTCCAGCATGTGTATCAAGCACAGGTTCAGTATGTGCAGGAGGAAAACAACAGCGTTTACACCAACGGAACCATACGGGCGTACTCGTACTCGGAGCCACAGCTCTACAACCAGAACAGCAGCGGGAACTACTTCGACACGCAGGGCGGCGGAGGCAGCGCGGCACAGGTCAGCACCGTAGTGTCCACTCACAGCATGGCCAACAACGGCAACGGCACCGGCGCTCTGGCTATGGGGCTCACCGGAGGCCAGATCATCAGCAGCTCAGGAGCTTATCTGATTGGAGGAAACTCCATGGATGGCTCCGCCCCTCACGGCGCCGCACAGACCACCAGAGCCTCCCCTGCTACGATTGAAATGGCGATTGAGACGCTCCAAAAGTCTGAAGGTTTATCCAGTCAGAGAAGTTCGCTGCTCAACAGCCATCTGCAGTGGCTGCTGGATAATTACGAGACAGCAGAGGGCGTGAGTCTGCCGCGCTCCACCCTCTACAATCACTACCTGCGCCACTGTCAGGAGCAGAAGCTGGACCCTGTCAATGCTGCGTCCTTCGGGAAGCTCATCCGCTCCATCTTCATGGGGCTGCGCACACGCCGCCTGGGGAcacgagGGAACTCAAAGTATCATTATTACGGGATTCGTGTGAAGCCGGACTCTCCTCTGAACCGCTTGCAGGAGGACATGCAGTACATGGCACTGAGACAGCAGCCCGTCCAGCAGAAGCAGAGATTTAAGCCTGTGCAGAAGATGGACGGAGTTTCGGGAGATAACTTCAGCAGCGCTGGACAGCACACACCCAATGCTGCAGAGCAGACCTTCATCGCTCAGAGCCAACATCATCAGCAGTTCCTGGATGGCTCCAGAGCTCTGCCGGAGTTTGTTGAACTGGATCTTGGAGAGGCAGTGGACGGCGTCGGCCCAGAGGATGTCAAAGCCCTTCAGACGCTCTACAGAGAACACTGCGAGGCCATCCTGGATGTAGTGGTGAACCTGCAGTTCAATCTGATCGAGAACCTGTGGCAGACGTTCTGGCGCTATTCTGCCTCCAGCTCTGTAGAGGGCGTCACAATCACAGAAAACAGTGGTTTGAGTGAGATCGAGGGCCGTCTGCCGCGGGCCAGGCTGATTCTGCTGTGCCGACATGAGGCCGTGCACAAGTGGATGAACACCTGCGATCACCTGATGTACCAGGCCCTCGTGGAGATCCTCATCCCGGACGTCCTGAGACCCATTCCTAGTGCCTTGACTCAAGCCATCCGTAACTTTGCCAAAAGCCTTGAGGGCTGGCTCACCAATGCCATGAGCAGCATTCCCCCGAGGATGATCAATACCAAGGTTTCCGCTGTTAGTGCCTTCGCTCAGACCCTCCGCAGATACACGTCCCTGAATCATCTGGCGCAGGCGGCTCGCGCAGTCCTGCAGAACACCTCGCAGATCAACCAGATGCTCAGCGATCTCAACCGGGTCGACTTCGCCAATGTGCAGGAGCAGGCCTCATGGGTGTGCCAGTGTGAAGAGGGTGTCGTCCAGCGCCTCGAGCAGGATTTTAAGGCCACCCTGCAGCAGCAGAGCTCACTGGAGCAGTGGGCCGCCTGGCTGGATAACGTGGTCACCCAGATACTGAAGCCGTACGAGGACAAGCCCACCCTGCCCAAAGCTGCACGCCAGTTCCTGCTCAAGTGGTCCTTCTACAGCTCTATGGTCATCAGAGATCTGACCCTCCGCAGCGCTGCCAGCTTCGGCTCGTTCCACCTGATCCGGCTGCTGTACGACGAGTACATGTTCTACCTGGTGGAGCATCGCGTCGCCCAGGCAACAGGAGAGACGGCCATCGGAGTCATGGGCGAGTTtcaggacctgaacaccatgtcaCCTGCCAACATCGACAAAGATGAGGTGAGCGAGATGGACAGCGATCTGGACGAGGAGATGGAGGAGGCGGACGAGCCACTGGCCAAGCGGGAGAAGGTGGAGGCGGACGTGATCCAGGTGCTGCAGGTAGGGGCGATGGAGGATGGCAGCAGCGCGGTGGTGGGCATCGTCCAGCCGAGCATGATCAACTCTCTGCCCCCGACCACCAACAATCACAGCGAACACATCCTCAGCACCGGAACCAGCACTATCCGCCATGTGGGAAACACCTACGCCTCCGTCTAAACATCTGCAGCACCACTACCATCT

Function

symbol description
rfx3 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including cilium-dependent cell motility; epithelial cilium movement involved in determination of left/right asymmetry; and regulation of insulin secretion. Predicted to act upstream of or within cell differentiation. Predicted to be located in nucleus. Orthologous to human RFX3 (regulatory factor X3).

GO:

id name namespace
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0030154 cell differentiation biological_process
GO:0031018 endocrine pancreas development biological_process
GO:0007275 multicellular organism development biological_process
GO:0050796 regulation of insulin secretion biological_process
GO:0060285 cilium-dependent cell motility biological_process
GO:0060287 epithelial cilium movement involved in determination of left/right asymmetry biological_process
GO:0005634 nucleus cellular_component
GO:0003677 DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000976 transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-061103-253 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including cilium-dependent cell motility; epithelial cilium movement involved in determination of left/right asymmetry; and regulation of insulin secretion. Predicted to act upstream of or within cell differentiation. Predicted to be located in nucleus. Orthologous to human RFX3 (regulatory factor X3).

Ensembl:

ensembl_id ENSDARG00000014550

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00004660 False 2779 mRNA 0.57 17 600164 641609
TCONS_00004661 True 2328 mRNA 0.59 16 600425 625441

Neighbor

gene id symbol gene type direction distance location
XLOC_002492 NA coding downstream 51963 546202 ~ 548201 (-)
XLOC_002491 NA coding downstream 178511 415997 ~ 421653 (-)
XLOC_002490 CU929346.1 coding downstream 226589 360237 ~ 373575 (-)
XLOC_002489 NA coding downstream 241457 356555 ~ 358707 (-)
XLOC_002488 NA coding downstream 245507 354093 ~ 354657 (-)
XLOC_002494 glis3 coding upstream 2965 644574 ~ 690170 (-)
XLOC_002495 NA coding upstream 15442 657051 ~ 657406 (-)
XLOC_002496 bmpr1bb coding upstream 441352 1082961 ~ 1180314 (-)
XLOC_002497 pdlim5b coding upstream 546044 1187653 ~ 1276046 (-)
XLOC_002498 opn4xa coding upstream 652854 1294463 ~ 1320114 (-)
XLOC_002487 CABZ01049604.1 non-coding downstream 260137 339912 ~ 340027 (-)
XLOC_002499 NA non-coding upstream 781632 1423241 ~ 1433140 (-)
XLOC_002501 CABZ01066320.2 non-coding upstream 899654 1541263 ~ 1544095 (-)
XLOC_002502 CABZ01066320.1 non-coding upstream 902554 1544163 ~ 1552789 (-)
XLOC_002504 NA non-coding upstream 1024733 1666342 ~ 1667630 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
bowfin (Amia calva) AMCG00010095 rfx3,LOC106568181 coding CM030129.1 CM030129.1 14376602 ~ 14396883 (+)