RNA id: XM_007251890.3


Basic Information

Item Value
RNA id XM_007251890.3
length 2078
RNA type mRNA
GC content 0.47
exon number 3
gene id foxa1
representative True

Chromosome Information

Item Value
chromosome id NC_035905.1
NCBI id CM008308.1
chromosome length 42966623
location 23365431 ~ 23368635 (+)
genome version Astyanax_mexicanus-2.0_2017_mexican_tetra_Genome
species mexican tetra
(Astyanax mexicanus)

Sequence

GGCAAATGAGCCCGTGAAGTGGGCTGTACCGCTCTCTACGTAACAGCGAGGGGAAGATCTCCACAGCCCTCAGCTCACTGCGCTCCCAGCATTTCTTCAGTCCGCCCAAACCGCCGCGCAACCTCCCACCCCTGATTGGCGCACCATTCGCCGGAGCGCTTGGTGAAAACTTCTGTCTGAGAACTGCATGTTGACGACCTGTAGATTTCCACCATAATGCTAGGAGCAGTGAAAATGGAAGGACACGAAACTCCAGACTGGAGTAGTTATTACACCGATGCGCAAGAGGTGTACTCTCCCATGACAAACAGCAGCATGAACACTGGACTGAGCTCCATGAACAGTATGAACAGTTACATGAGTATGTCTACCAGTGGGAATATGACCTCTAGTTCCTTTAACATGTCTTATGCGAACCCTGCTCTCAGTGCTGGACTAAGCCCGGGGACTATGGCAGGGATGCAGTCGAGTGCAAGCAGCGCAATGAATGGAATGAGTGGCGGGGTATCATCCATGGGCACGGCACTCAGCCCCACCAACATGAATGCGATTTCAGCCCAGCACAGCTCCATGAATGCACTGAACCCCTACTCAAGCATCAGCCCCACTATGAGCCCCATGACATACGCTCAGCCCAGCCTCAACAGGGCACGGGACAACAAGACTTTCAGGAGAAGTTATCCTCATGCCAAGCCTCCATACTCCTACATCTCGCTCATCACCATGGCTATCCAGCAGTCACCCAGCAAGATGCTCACACTTAGTGAGATCTACCAGTGGATAATGGATCTTTTTCCATACTACCGTCAAAACCAACAAAGGTGGCAGAACTCCATCAGACACTCACTGTCTTTCAATGACTGTTTTGTCAAAGTGTCTAGGTCGCCCGACAAGCCAGGAAAAGGCTCTTACTGGACCCTGCATCCTGATTCTGGGAATATGTTTGAGAATGGCTGTTACCTCCGTAGACAGAAGCGCTTCAAATGTGACAGAAAGGTAGTAGGAAGTGGGAAAGGGCAAGATGGGAGAAAAGACCAGAATGGGTCAAGCTCGCCCTCGAGCGACAACTCAAACACAAAGACCGGGCACATGGACTCCAACTCCATAGCCAACGCAAACCAGTCCTCTAGCCCTCACAGCTTGGAGCACAGAAGCAGTACCACCAACTCTGAACTAAAGAGCAGCGGCCCACAGATACACCCCGTGGCCAGCTCAGCCACATCTCTCTCCTCTATCCCTTTGCCCCCGCACTCTATGGCCCATGAGTCTCAGCTGCACCTAAAGGGAGACCCCCATTACTCTTTCAACCACCCATTTTCCATCAATAATTTAATGTCCTCCTCGGAGCAACAGCACAAACTGGACTTGAAAGCTTACGAACAAGCATTGCAATATTCATCTTATGGCTCAGGTATGTCTTCCAGCCTGCCTCTAGGCAGTGCTTCCATGGCCGGGAGAGCCAGCATGGACCCCTCTGCTTTAGAGGCGTCTTACTACCAAGGTGTGTATTCAAGACCGGTTCTTAACACTTCTTAgttgcttctttttttgttgttgctgttcTTGTCATTATTTGCTGAACTCAGCCCTTGCTGAcagataaactttattttatttttgcatgcaCCCAGTGCATAAAGGACTGTTACtttaaagtataataatgtgtatgtgtataataaaatattgtaaagtgTTCCCCTGAATGATTGTATATCCCACCTATAAATCATTGCTAGTGTATTTAAGGCGATTTTAAGCTTGTAAAATAATGTTGTAATCCCCAAACGTGTAGACCCCTACCTACTATGATGTGTCCGTGTGTTACAATGTGCACGAATGAAGGTCAGTTATGGTCTTGTGGATCGCGCTgcaggtaaacaaacaaaaaaaaagaaaaagaaaaaaggtgaaGCACCTCTCTGCTGCAGATGTATTTGGATGTTGTCCTTTTACTCGTTCTTTTGGGTTTTATTTACCTCGTTTGAGAAGAACATTTCAATCCCAATTCTTGTACTGAAGTAAGTTAATCAAACGTGGAAATGCATTACGAATAAAACACGTATTTCTTAATCACG

Function

GO:

id name namespace
GO:0000122 negative regulation of transcription by RNA polymerase II biological_process
GO:0048319 axial mesoderm morphogenesis biological_process
GO:0007389 pattern specification process biological_process
GO:0048665 neuron fate specification biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0051090 regulation of DNA-binding transcription factor activity biological_process
GO:0009790 embryo development biological_process
GO:0005667 transcription regulator complex cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0008134 transcription factor binding molecular_function
GO:0003690 double-stranded DNA binding molecular_function
GO:0019904 protein domain specific binding molecular_function
GO:0008301 DNA binding, bending molecular_function

KEGG:

id description
K09387 FOXA1, HNF3A; forkhead box protein A1, hepatocyte nuclear factor 3-alpha

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TU111319 lncRNA upstream 138521 23225765 ~ 23226910 (+) True G82606
TU111308 lncRNA upstream 156632 23208495 ~ 23208799 (+) True G82596
TU111297 lncRNA upstream 159987 23204815 ~ 23205444 (+) True G82588
TU111288 lncRNA upstream 171141 23127953 ~ 23194290 (+) True G82579
TU111497 lncRNA downstream 104569 23473204 ~ 23473455 (+) True G82748
TU111516 lncRNA downstream 130084 23498719 ~ 23499013 (+) True G82754
TU111515 lncRNA downstream 130401 23499036 ~ 23552919 (+) True G82753
TU111526 lncRNA downstream 212513 23581148 ~ 23581751 (+) True G82763
TU111529 lncRNA downstream 221865 23590500 ~ 23590893 (+) True G82766
XM_007251888.3 mRNA upstream 53065 23309045 ~ 23312366 (+) True clec14a
XM_007240480.3 mRNA upstream 97569 23250660 ~ 23267862 (+) True sec23a
XM_007240478.3 mRNA upstream 116582 23242171 ~ 23248849 (+) True srp54
XM_015603404.2 mRNA upstream 116582 23242171 ~ 23248849 (+) False srp54
XM_007253775.3 mRNA upstream 210846 22857844 ~ 23154585 (+) True npas3
XM_007251896.3 mRNA downstream 85366 23454001 ~ 23473086 (+) True tyro3
XM_007251893.3 mRNA downstream 106624 23475259 ~ 23498557 (+) True LOC103028567
XM_022672964.1 mRNA downstream 137021 23505656 ~ 23549535 (+) True LOC103030470
XM_022672965.1 mRNA downstream 138143 23506778 ~ 23549535 (+) False LOC103030470
XM_007251901.3 mRNA downstream 138143 23506778 ~ 23549342 (+) False LOC103030470
TU111323 other upstream 134113 23230430 ~ 23231318 (+) True G82609
TU111179 other upstream 1007296 22357644 ~ 22358135 (+) True G82488
TU110179 other upstream 3691793 19673127 ~ 19673638 (+) True G81763
TU110177 other upstream 3699384 19665736 ~ 19666047 (+) True G81761
TU110107 other upstream 4434677 18930238 ~ 18930754 (+) True G81704
TU111569 other downstream 506804 23875439 ~ 23877767 (+) False timm9
TU111570 other downstream 506804 23875439 ~ 23877767 (+) True timm9
TU111581 other downstream 541047 23909682 ~ 23920698 (+) True G82811
TU111651 other downstream 770754 24139389 ~ 24142232 (+) True G82853
trnal-uaa_1 other downstream 937976 24306611 ~ 24306693 (+) True trnal-uaa_1

Expression Profile