LOC103030376 (raraa,rara,LOC108410801,LOC107678286,LOC107745620,LOC107716487)


Basic Information

Item Value
gene id LOC103030376
gene name raraa,rara,LOC108410801,LOC107678286,LOC107745620,LOC107716487
gene type coding
species mexican tetra (Astyanax mexicanus)
category of species ornamental fish

Chromosome Information

Item Value
chromosome id NC_035900.1
NCBI id CM008303.1
chromosome length 25652880
location 15224452 ~ 15383888 (+)
genome version Astyanax_mexicanus-2.0_2017_mexican_tetra_Genome

Sequence

>XM_007255152.3
tcgctcgtgCTGGTTTTCACACACGCAGCACGTGACTCCAATGGCCGCCGCTGCCTGTGGCGGAGCTGGGTTAGGACTCGGAGTGTCTCGGCGCTCCTGAATAACAGCAGCAACAGCCTGCAGCGGCGGCACACAGTCCTGCAGAGTCCTGCAGAGTCCCGCACAGTCCTGCAGAGCCCGCCGCCCTCAGCCCCGCGGCTTTATCCCGCCTGTACCAGGGGGGTCGCCTGTTCCCGTGCCGTTAGTCCCGGTCCGCGCAGCGGAGCAGCTCACCGTTACATCACCGAGCAGCCGCCGGTAGGAGGAGGAGTCAACAGGTCCAGtCTTGGACACTTGGACACAGTCATAGAATCAGTATTGTCTCAGGAGAGAGGCGGTTAAAGAGTGTTGGATTAATGAAACAGgtcCATCACCAGGCAGCATGGCCAGCAAGTAGCCTAAATGGTCACAGTGGTCACTCTATGGAATAACGAATCTTCTAGAAGCTTTACACGGAACGTTTCAGCACTGGGCTACTCTGTTGGTTTGGATTTTGTTGAGTTGACGTTTTAAGGAGATTCACCCTTCTGCTGTCCACCCCGTCCCTGAAGCCCCTCCCCTGAGGTGTCCCAATGGGGGCCAGAGCCCCGTGAGGCCTTCTTCCCAACGGCCGCATCGGTCTGTGTGTGTACGCGTTACCGTTGTGGCCGGTCCAGCAGTGACCGGTCCAGTGGTCATGTCCGGTAAGGGTAACCCGAGCCCTCACCTGAATGGCTTCCCCGTCCCGCACTTCTCCTACTTCTTCCCTCATGTGCTGGGGGGTCTGTCGCCCCCCGCCGTGCCTGCGCTGCCCATCAGCGGATACAGTACACCTTCTCCAGCCACCATCGAGACTCAGAGCACAAGTTCGGAGGAGATTGTCCCAAGTCCCCCCTCTCCACCCCCACCCCCGCGGGTCTACAAGCCATGCTTCGTCTGCCAGGACAAATCCTCTGGCTACCACTATGGCGTCAGCGCCTGCGAAGGCTGCAAGGGCTTCTTCCGCCGGAGCATCCAGAAAAATATGGTGTACACGTGCCACCGAGAGAAAAGCTGCATCATCAACAAGGTCACCCGCAACCGCTGCCAGTACTGTCGCCTGCAGAAGTGCCTGGAAGTGGGCATGTCCAAGGAGTcgGTGAGAAACGACAGgaataaaaagaagaaggaggagaaggagaagaaggtgGAGTGTTTAGAGAGCCCGACACTGACTCCTGATACGGAGCAGATGATCGACCGAGTCAGAAAAGCTCACCAGGATACCTTTCCATCACTGTGTCAACTGGGAAAATACACCACGAGTAACAGTTCAGAGCGGAGGGTCTCTCTGGACGTGGATCTGTGGGATAAGTTCAGTGAACTCTCCACTAAGTGCATCATCAAGACGGTGGAGTTCGCCAAGCAGCTGCCCGGATTCACCACGTTGTCCATCGCAGACCAGATCACACTCCTCAAAGCCGCCTGCCTCGACATACTGatTCTACGGATCTGTACGCGCTACACACCGGAACAGGACACAATGACGTTTTCAGACGGTCTGACGCTGAACCGGACACAGATGCACAACGCCGGCTTCGGGCCGCTCACCGACCTCGTATTCGCCTTCGCCAACCAGCTGCTCCCTCTGGAGATGGATGATGCTGAGACGGGCCTGCTGAGCGCCATCTGCCTGCTGTGTGGAGaccgGCAGGACCTGGAAGAGGCAGATAAAGTGGACGTCTTGCAGGAGCCACTGCTGGAGGCTCTGAAGCTGTATGTGAGGAGGAGAAgaccacacaaaccacacatgTTCCCCAAAATGCTGATGAAGATCACTGACCTGAGGAGCATCAGCGCCAAGGgaGCGGAGCGTGTGATCACTCTGAAGATGGAAATTCCTGGCTCCATGCCGCCTCTGATCCAGGAGATGCTGGAGAATTCCGAGGGTCTGGAGACCTCAGGCAGTGGAGCCTCGTCTCGTCCCGCCGGAGCTCCGCCTGGCAGCTGCAGTCCCTCCCTCTCCCCGAGCTCCGCCCAAAGCAGCCCACCGACACACTCGCCCTGA
>XM_007255155.3
ATGATGTATGAGGGTGTGGACGTAGTGGGTCTGAGCGCCAGCCCCAGCCCTAGCCCCTTCCTAATGGTGGATTACTACAGCCAGGCCAGGGCCGGCCATCACCCTTTCAGCAGTCATCACTGGAGCAGCTCCTCTCACTCCATCGAGACTCAGAGCACAAGTTCGGAGGAGATTGTCCCAAGTCCCCCCTCTCCACCCCCACCCCCGCGGGTCTACAAGCCATGCTTCGTCTGCCAGGACAAATCCTCTGGCTACCACTATGGCGTCAGCGCCTGCGAAGGCTGCAAGGGCTTCTTCCGCCGGAGCATCCAGAAAAATATGGTGTACACGTGCCACCGAGAGAAAAGCTGCATCATCAACAAGGTCACCCGCAACCGCTGCCAGTACTGTCGCCTGCAGAAGTGCCTGGAAGTGGGCATGTCCAAGGAGTcgGTGAGAAACGACAGgaataaaaagaagaaggaggagaaggagaagaaggtgGAGTGTTTAGAGAGCCCGACACTGACTCCTGATACGGAGCAGATGATCGACCGAGTCAGAAAAGCTCACCAGGATACCTTTCCATCACTGTGTCAACTGGGAAAATACACCACGAGTAACAGTTCAGAGCGGAGGGTCTCTCTGGACGTGGATCTGTGGGATAAGTTCAGTGAACTCTCCACTAAGTGCATCATCAAGACGGTGGAGTTCGCCAAGCAGCTGCCCGGATTCACCACGTTGTCCATCGCAGACCAGATCACACTCCTCAAAGCCGCCTGCCTCGACATACTGatTCTACGGATCTGTACGCGCTACACACCGGAACAGGACACAATGACGTTTTCAGACGGTCTGACGCTGAACCGGACACAGATGCACAACGCCGGCTTCGGGCCGCTCACCGACCTCGTATTCGCCTTCGCCAACCAGCTGCTCCCTCTGGAGATGGATGATGCTGAGACGGGCCTGCTGAGCGCCATCTGCCTGCTGTGTGGAGaccgGCAGGACCTGGAAGAGGCAGATAAAGTGGACGTCTTGCAGGAGCCACTGCTGGAGGCTCTGAAGCTGTATGTGAGGAGGAGAAgaccacacaaaccacacatgTTCCCCAAAATGCTGATGAAGATCACTGACCTGAGGAGCATCAGCGCCAAGGgaGCGGAGCGTGTGATCACTCTGAAGATGGAAATTCCTGGCTCCATGCCGCCTCTGATCCAGGAGATGCTGGAGAATTCCGAGGGTCTGGAGACCTCAGGCAGTGGAGCCTCGTCTCGTCCCGCCGGAGCTCCGCCTGGCAGCTGCAGTCCCTCCCTCTCCCCGAGCTCCGCCCAAAGCAGCCCACCGACACACTCGCCCTGA
>XM_015607336.2
ATGTCCGGTAAGGGTAACCCGAGCCCTCACCTGAATGGCTTCCCCGTCCCGCACTTCTCCTACTTCTTCCCTCATGTGCTGGGGGGTCTGTCGCCCCCCGCCGTGCCTGCGCTGCCCATCAGCGGATACAGTACACCTTCTCCAGCCACCATCGAGACTCAGAGCACAAGTTCGGAGGAGATTGTCCCAAGTCCCCCCTCTCCACCCCCACCCCCGCGGGTCTACAAGCCATGCTTCGTCTGCCAGGACAAATCCTCTGGCTACCACTATGGCGTCAGCGCCTGCGAAGGCTGCAAGGGCTTCTTCCGCCGGAGCATCCAGAAAAATATGGTGTACACGTGCCACCGAGAGAAAAGCTGCATCATCAACAAGGTCACCCGCAACCGCTGCCAGTACTGTCGCCTGCAGAAGTGCCTGGAAGTGGGCATGTCCAAGGAGTcgGTGAGAAACGACAGgaataaaaagaagaaggaggagaaggagaagaaggtgGAGTGTTTAGAGAGCCCGACACTGACTCCTGATACGGAGCAGATGATCGACCGAGTCAGAAAAGCTCACCAGGATACCTTTCCATCACTGTGTCAACTGGGAAAATACACCACGAGTAACAGTTCAGAGCGGAGGGTCTCTCTGGACGTGGATCTGTGGGATAAGTTCAGTGAACTCTCCACTAAGTGCATCATCAAGACGGTGGAGTTCGCCAAGCAGCTGCCCGGATTCACCACGTTGTCCATCGCAGACCAGATCACACTCCTCAAAGCCGCCTGCCTCGACATACTGatTCTACGGATCTGTACGCGCTACACACCGGAACAGGACACAATGACGTTTTCAGACGGTCTGACGCTGAACCGGACACAGATGCACAACGCCGGCTTCGGGCCGCTCACCGACCTCGTATTCGCCTTCGCCAACCAGCTGCTCCCTCTGGAGATGGATGATGCTGAGACGGGCCTGCTGAGCGCCATCTGCCTGCTGTGTGGAGaccgGCAGGACCTGGAAGAGGCAGATAAAGTGGACGTCTTGCAGGAGCCACTGCTGGAGGCTCTGAAGCTGTATGTGAGGAGGAGAAgaccacacaaaccacacatgTTCCCCAAAATGCTGATGAAGATCACTGACCTGAGGAGCATCAGCGCCAAGGgaGCGGAGCGTGTGATCACTCTGAAGATGGAAATTCCTGGCTCCATGCCGCCTCTGATCCAGGAGATGCTGGAGAATTCCGAGGGTCTGGAGACCTCAGGCAGTGGAGCCTCGTCTCGTCCCGCCGGAGCTCCGCCTGGCAGCTGCAGTCCCTCCCTCTCCCCGAGCTCCGCCCAAAGCAGCCCACCGACACACTCGCCCTGACCAACGCTGTCGCCGCGGCAACAACCGCCTACCGACTACTGTGTCCCCTCAAACACACCCCACACATGCTGACTGGCCTGAGCCAGACCGGagtggagcttttttttttcccccatttccTCCCTCCTGCTCTCCCTCTGTCCTCCTCCTGGCCGGCGCCATgtccttcatctctctctttctatccctcTCAGTTTCTCCCTCTTCTCTGTCTGCTCACGTGAGAGATGGAAGGCTGAAAGGCTTATCCAGTGGACGGAGGGAGGAGTGCCCGGCATCGCTGGACGGAAGCAGGAGCAAGAGGGAAAGTGTGGGTGTGAGGACAAAATGGCAATTCTAGGGGTCCAAGAACCCCAAGAGTGCAAAGACCTGCAAAgaggagaagtgtgtgtgtgtgtgtgtgtgtgtgaaaggacTAAGAGGACAAACAGCATACAGACTCTGAGAatccagtgtgaatttttcttctgttttgttttagtttttttttttctttttttctttttttgttcttctcaCTCCGACACCTCAGGCCTGGACTTCAGATGAATGAATGATTGCACTGGCCTGACCTTTTCCAACTTCCAAGAGACAGatgttttttacaaaatatatataaatataaatatatagagagaaagaagcaAGAATGATTGTGATCCAGTTGAAaatagaagaaaacaaaaacaagtggACATGTGGAGAGTAGATGCAGTTGAATTTCttcactgatgtttttttttttctctttttatgacCATTagagtaaaaggaaaaaaagaatgaagagaacattttgttgtttattgcagactgataatgatgattatgatgatgtttttcatggaaacaaaaacatttggaaaaaaaaatatttacactcaCATAAATTGTGCACAGAAGAAATTACATAAACCGTGGtcgaaaaaaaacaacaaagggCTTTGTTGAGTTTTTGTCCTGGTATTACTTGtctatatttgtaattttaGCATTATAATAGAACTAAATATAGGAAGTGTGGTCAGGTATTGTTTAAGgttttaaacaaaacactggtgttacataaaaaaaattccaaGGACcctgaagtgtgttcaggtaaatctGGCATGTTTTTATCTTTGTGGCGGTAGaaacaggtgcaccactgactgaataaaaccatgacaacagt

Function

symbol description
raraa Enables nuclear receptor activity. Involved in hindbrain morphogenesis and response to retinoic acid. Acts upstream of or within liver development. Predicted to be located in nucleus. Is expressed in several structures, including endoderm; gonad; mesoderm; nervous system; and neural keel. Human ortholog(s) of this gene implicated in acute promyelocytic leukemia; lung carcinoma (multiple); and syndromic microphthalmia 12. Orthologous to several human genes including RARA (retinoic acid receptor alpha).
rara Enables several functions, including DNA binding activity; nuclear receptor activity; and protein kinase B binding activity. Involved in several processes, including cellular response to estrogen stimulus; regulation of gene expression; and regulation of leukocyte differentiation. Located in several cellular components, including actin cytoskeleton; chromatin; and nuclear lumen. Part of protein-containing complex. Implicated in acute promyelocytic leukemia. Biomarker of mood disorder.

NR:

description
PREDICTED: retinoic acid receptor alpha isoform X1

GO:

id name namespace
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0021575 hindbrain morphogenesis biological_process
GO:0043401 steroid hormone mediated signaling pathway biological_process
GO:0001889 liver development biological_process
GO:0048384 retinoic acid receptor signaling pathway biological_process
GO:0032526 response to retinoic acid biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003707 steroid hormone receptor activity molecular_function
GO:0008270 zinc ion binding molecular_function

KEGG:

id description
K08527 RARA, NR1B1; retinoic acid receptor alpha

RNA

RNA id representative length rna type GC content exon number start site end site
XM_007255152.3 False 2065 mRNA 0.58 10 15224452 15382711
XM_007255155.3 False 1341 mRNA 0.57 8 15348632 15382711
XM_015607336.2 True 2527 mRNA 0.50 8 15319767 15383888

Neighbor

gene id symbol gene type direction distance location
gjd3 gjd3 coding upstream 88549 15134302 ~ 15135903 (+)
top2a top2a coding upstream 91199 15116824 ~ 15133253 (+)
LOC103032173 NA coding upstream 188498 15032389 ~ 15035954 (+)
LOC103032486 lrrc3c,lrrc3ca,LOC107598050,LOC107716457,LOC107660473,LOC107678436 coding upstream 233153 14967880 ~ 14991299 (+)
get4 get4 coding upstream 390105 14823653 ~ 14834347 (+)
LOC103029630 NA coding downstream 9127 15393015 ~ 15406356 (+)
LOC103029312 NA coding downstream 23597 15407485 ~ 15423095 (+)
LOC103028270 mpp2,LOC108410806,LOC108273574 coding downstream 57679 15441567 ~ 15520594 (+)
LOC103033971 NA coding downstream 237423 15621311 ~ 15672444 (+)
LOC103023844 LOC108443155,LOC106596407,LOC107689097 coding downstream 424317 15808205 ~ 15811853 (+)
G36532 NA non-coding upstream 24379 15199822 ~ 15200073 (+)
G36524 NA non-coding upstream 43374 15177106 ~ 15181078 (+)
LOC111192405 NA non-coding upstream 72324 15150171 ~ 15152128 (+)
G36512 NA non-coding upstream 134076 15086356 ~ 15090376 (+)
G36511 med24,LOC107598039,LOC107660474 non-coding upstream 140512 15081564 ~ 15083940 (+)
G36582 psmc5,LOC102777430,LOC107684752 non-coding downstream 157226 15541114 ~ 15547526 (+)
G36584 NA non-coding downstream 224204 15608092 ~ 15679320 (+)
G36618 NA non-coding downstream 364886 15748774 ~ 15774590 (+)
G36708 NA non-coding downstream 488660 15872548 ~ 15879307 (+)
G36706 NA non-coding downstream 490526 15874414 ~ 15875884 (+)
G36439 LOC103041415 other upstream 433619 14789380 ~ 14790833 (+)
LOC107197918 NA other upstream 656540 14564925 ~ 14567912 (+)
G36371 NA other upstream 760813 14463137 ~ 14463639 (+)
LOC103039668 LOC108435045 other upstream 1703750 13502246 ~ 13520702 (+)
G35995 NA other upstream 2521396 12702305 ~ 12703056 (+)
LOC103028998 pyyb,LOC103028998,LOC108410797,LOC107745683,LOC107569181,LOC107684781,LOC107695522,LOC107753323,LOC107560546 other downstream 48941 15432829 ~ 15440157 (+)
cabcoco1 NA other downstream 829902 16213790 ~ 16233839 (+)
sun1 NA other downstream 1616494 17000382 ~ 17040957 (+)
phf5a phf5a,PHF5A,LOC107584099,LOC102780084,LOC106609350 other downstream 1817609 17201497 ~ 17205033 (+)
cby1 cby1 other downstream 1848932 17232820 ~ 17234559 (+)

Expression


Co-expression Network