XLOC_013313 (rfx4)


Basic Information

Item Value
gene id XLOC_013313
gene name rfx4
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007129.7
NCBI id CM002902.2
chromosome length 51023478
location 15334117 ~ 15373620 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00026329
ACCCCACCCGCTCCTGCAACCCACACCCCCGCCTCCATCACCGCCGCCACCCTCTCCACGGACCTCACATCGTATGCATCTCTGCGACGGGCAGTTCTCTCGGAGAGACGGAGGGAACTGAGGAGGGGGAGTCCTGCACGGAGCCATTTTCTCAGAGGAGCCCCTGGAACGTGCATGGGAAGAGGATGCATTGTGGGCTGCTGGAAGAGCCTGACATGGATTCCACAGAGAGCTGGATTGAAAGATGTCTGAACGAAAGCGAGAGCAAGCGCTTCTCCAGCCACTCTTCTATTGGAAATATTTCCAACGACGAAAacGAAGAGAAGGAAAATAACCGAGCATCTAAGCCACATTCAACACCTGCTACATTACAATGGTTGGAGGAGAACTACGAGATCGCAGAGGGTGTGTGTATTCCTCGCAGCGCCCTGTACATGCACTACCTGGACTTTTGCGAAAAACTGGACTCACAGCCAGTCAATGCTGCAAGCTTCGGAAAGATAATAAGGCAACAGTTTCCTCAGTTGACCACGCGGAGATTAGGAACTAGAGGTCAATCAAAGTATCATTACTATGGCATCGCAGTGAAGGAGAGCTCCCAGTACTACGATGTGATGTACTCTAAAAAGGGTGCTGCGTGGGTGAACGAGACGGGCAAGAAAGAGGTCACCAAACAGACAGTAGCGTATTCACCGCGCTCCAAGCTGGGCACTCTCCTGCCAGACTTTCCAAATGTCAAAGACCTAAATCTGCCCGCCAGTCTGCCAGAGGAGAAGGTCTCGACCTTTATTATGATGTACAGAACTCACTGCCAGAGGATACTGGATACTGTCATACGCGCCAACTTCGATGAGGTTCAGAGCTTCCTGTTGCACTTTTGGCAGGGCATGCCGCCCCACATGCTCCCTGTCCTGGGCTCTTCTACAGTGGTCAACATAGTGGGTGTGTGTGACTCCATATTGTACAAGGCCATCTCAGGCGTCCTCATGCCCACCGTCCTACAAGCTCTGCCTGACAGCCTCACTCAGGTGATCAGGAAGTTTGCCAAGCAGCTGGACGAGTGGCTGAAGGTGGCTTTACATGACCTGCCCGAAAACCTGCGCAACATTAAGTTTGAATTGTCAAGAAGATTTTCTCAGATTCTCAAACGACAAACATCATTAAACCACCTCTGTCAGGCCTCTCGAACAGTGATCCACAGTGCAGACATCACCTTTCAGATGCTCGAGGACTGGAGGAACGTAGACCTCAACAGCATCACTAAACAAACTCTTTATACTATGGAAGACTCCAGAGAAGACCAGAGGAGACTCATCATCCAATTGTATCAAGAATTTGACAGACTGCTAGAGGACCAGTCTCCAATTGAAGCCTACATCGAGTGGCTGGACTCTATGGTGGAGAGATGTGTTGTGAGGGTGGCGGGGAAGAGACCCGGATCTCTGAAGAGGGTAGCTCAGCAGTTCCTGCTCATGTGGTCGTGTTTTGGGACAAGAGTTATCCGGGATATGACGCTGCATAGTGCACCAAGCTTTGGCTCGTTTCATCTGATTCACCTCATGTTTGATGACTATGTACTTTACCTGCTTGAATCTCTGCACTGCCAAGAGAGAGCCAATGAACTGATGAGGGCGATGAAAGGAGAGGGCGCACCAGCAGATACTGGAGAAGAGCTGATGCTGATGAGCTCCACTCCAACATCTACGTCACCTGCACCCTACTCTCCTGCCAAATCTGTTCACTCGGTGGGCGTACCGGCAGTAGGGTCCCCCAATTCAGCCCAGTCTCCGGAGTACACCAGCATATCGGCCACAACAGGAGCTGTTCAGTCATATACCTGGTCCCTTACATACACAGTGACAACTTCAGGCGGCAGCCCAACCGAGCCCGGATCCCAGCTGTCCTGCATGAGAGGCGGACCTGCGTTACACGGATCATCCTCTGCACACCGGATGCCAGTTTACCCACATCGGGATGAGCACGGGTACACTGGCAGCTATAATTACAGCAGCTACGCAAACCAGCACCATCATGCCATTCAGAGTCAATACTCCAGTTTAACCCATGAAGCAGGGCTGCCCACTCCTCTGCATTATTCCTCATACCACCGCACCTCCGCACAGtatCCGCTCAACAGTCAGATGTCCAGAATGGAGTCGTGTCTAATGAGCGGCTCTCCTCTCCTACACTCCAGTCCAGTGACCCCTCGATGGCCCGATGTGCCCTCTGCCAACAGCTGTTACTCCAGTCCCACCGTCCACGCATCCCGCTACTCCACCGGAGACATGTACTCGCCCCTTGCCCCACGCAGGAACTCTGAATACGAGCACGCACAACACTTTCCAGGATTCGCCTACATTAACGGGGAGGCCACGACCGGATGGGCAAAATGATAAACCAGCGGTGGTCCATATTTAACACATTACAGAGAATGTATCTGAGAATGGCAACGGTGTTTTATTGGTGTGGTCAGTGTTTACAGTGCAAAGCTGCCAATAAAAGTTGATTCGCAATCATTGTGAGAGAAAACGGGACATCCTAAAAAAACGACTGAATGatttaagttatttataaagTCTAAATTTGGTatacttttaataaaatatacattctaTGCACAGATTAACACAGAACGAACAGAACATGTTAAATTGCCCGTTAAATATTTTTCTCCCATATTAGAAAGAAAATGCTTAATTTGGCTTAATGCTTTAAAGAAGtgatgtatatatacagttgaagtcagaattattagtcgccctgtttattttttcctccaacttctgtttaacggagagaatacttttttaacacatttctaaacataatagttttaataactcatttaaaataactgatttattttatctttgccatgaacacagtacataatatttgactagatatttttaaagacacttctatacagctaaaagtgacatttaaaggcttaactaggttaattaggttaactaggcaggatagggtaattaggccagttattttataacgatggtttgttctgtagactatcggaaaaaataattttgaccttaaaatggttttaaaaattaaaaactgcttttattctagccg
>TCONS_00026330
CTGGATTGAAAGATGTCTGAACGAAAGCGAGAGCAAGCGCTTCTCCAGCCACTCTTCTATTGGAAATATTTCCAACGACGAAAacGAAGAGAAGGAAAATAACCGAGCATCTAAGCCACATTCAACACCTGCTACATTACAATGGTTGGAGGAGAACTACGAGATCGCAGAGGGTGTGTGTATTCCTCGCAGCGCCCTGTACATGCACTACCTGGACTTTTGCGAAAAACTGGACTCACAGCCAGTCAATGCTGCAAGCTTCGGAAAGgtactactgtatatatttaatctTTAATGATGGGTCATTACCTTATTAAAACAAGTCTAAGTTGaccctgaaaaaaaaagtaaaacatctgttactaaaaaaaaagcatgacatAACTGCATGTTTTATGAAGAGGAGACGCAGTCAGTGGTCTTTTCTTACACCTCTTCTGCAAACTCATAGCTGGACAATATAAACAATGAGCATGTTCACCCTTGTTCCCACAACCCCTCAACCCACCTACTCATACGGCCACCCCCCGACACCCTTATCCCGCTCCCCCGGGTCCCGTCGGAGGATATTGAAAAAAGAGAGGGGGCCTGGATTAATGTGTAATTAAAGGAAATTTGGAAGGGTGAGATGTT

Function

symbol description
rfx4 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within ventral midline development. Predicted to be located in nucleus. Is expressed in central nervous system and neural rod. Orthologous to human RFX4 (regulatory factor X4).

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:0021914 negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning biological_process
GO:0007418 ventral midline development biological_process
GO:0005634 nucleus cellular_component
GO:0003677 DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function

KEGG:

id description
ko03000 Transcription factors

ZFIN:

id description
ZDB-GENE-040909-2 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within ventral midline development. Predicted to be located in nucleus. Is expressed in central nervous system and neural rod. Orthologous to human RFX4 (regulatory factor X4).

Ensembl:

ensembl_id ENSDARG00000026395

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00026329 False 3096 mRNA 0.47 18 15334117 15373620
TCONS_00026330 True 633 lncRNA 0.44 3 15367500 15370455

Neighbor

gene id symbol gene type direction distance location
XLOC_013312 ric8b coding downstream 4646 15287065 ~ 15329471 (-)
XLOC_013311 tmem263 coding downstream 64845 15259388 ~ 15269272 (-)
XLOC_013310 NA coding downstream 142305 15188017 ~ 15191812 (-)
XLOC_013309 mterf2 coding downstream 178155 15147931 ~ 15155962 (-)
XLOC_013307 btbd11b coding downstream 229259 14956165 ~ 15104858 (-)
XLOC_013314 polr3b coding upstream 8409 15382029 ~ 15420168 (-)
XLOC_013315 endouc coding upstream 85698 15459318 ~ 15467446 (-)
XLOC_013316 ppfibp1b coding upstream 95395 15469015 ~ 15551456 (-)
XLOC_013317 si:ch211-245j22.3 coding upstream 180761 15554381 ~ 15559817 (-)
XLOC_013318 arntl2 coding upstream 196007 15569627 ~ 15610856 (-)
XLOC_013384 BX323829.1 misc upstream 4168482 19542102 ~ 19542231 (-)
XLOC_013308 BX649610.1 non-coding downstream 297848 15036151 ~ 15036269 (-)
XLOC_013300 NA non-coding downstream 568234 14763903 ~ 14765883 (-)
XLOC_013294 BX950204.1 non-coding downstream 1789750 13544250 ~ 13544367 (-)
XLOC_013293 BX890576.1 non-coding downstream 1855895 13477102 ~ 13478222 (-)
XLOC_013319 BX928740.1 non-coding upstream 214467 15588087 ~ 15588201 (-)
XLOC_013321 CR854977.1 non-coding upstream 502042 15875662 ~ 15875780 (-)
XLOC_013323 NA non-coding upstream 565641 15939261 ~ 15970573 (-)
XLOC_013324 NA non-coding upstream 617834 15991454 ~ 16018087 (-)
XLOC_013327 NA non-coding upstream 851170 16224790 ~ 16307937 (-)

Expression


Co-expression Network