RNA id: TCONS_00001085


Basic Information

Item Value
RNA id TCONS_00001085
length 1629
RNA type mRNA
GC content 0.52
exon number 4
gene id XLOC_000639
representative False

Chromosome Information

Item Value
chromosome id NC_007112.7
NCBI id CM002885.2
chromosome length 59578282
location 50921266 ~ 50929957 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

AATCTCAATCCGTCAGCATTGCTTATCAGCGATAATATTACGTTTGGATACAAGGATCCTCTTTAGACAGCGCATATGCGTGGACTTTAAGCAAATTGGGAACTTGTTGTGAAGTTTGGCTAATTTGTTTTTGGCTAATCAGCTGGAGTCGCCTTCCTCTCAAAAGTAAAAAGGTGTTTCTTGGCTTTGTGGATTTTCAGTTTACGGATCTCAAAGAAAATATCACAGAAGATCAAGACAAAAAGGTGTCTCCCTGGAGCTCAACAATGATGTCATACCTCAAGCAGGCCCCGTATGCCATGAACGGGCTGGGGCTCGGCGGGGCAACCATGGACCTCCTGCATCCCTCTGTGGGATATCCCACGAATCCTCGTAAACAAAGAAGAGAGAGGACGACATTTACACGCACTCAGCTGGACATCTTGGAGAGTCTGTTCGCTAAAACCCGCTATCCTGACATTTTCATGCGCGAGGAGGTCGCCCTGAAGATTAATTTGCCCGAGTCAAGAGTGCAGGTTTGGTTTAAAAACAGAAGAGCAAAGTGtcgccagcagcagcagcagagcaGCACCAACTCAAAGATCCGTCCAGCAAAGAAGAAACCGTCTCCGTCCCGCGAGAGCCCGGGGTCTGAGAGCAGCGGCCACTTCACTCCCCCTGCCgtctcttcatcatcctcatcctcgTCTTCATCCTCGGGCTCCAACCCGTCTGCTCTTAGCGGAGTTGGTCTGATCAGCAGCTCGTCCTCAGGAACACCTGTCCCGTCCATCTGGAGTCCCGCACCAGTCTCTCCAGTCCCCGCACCCCCCTCCCTCCCTGATATCTCGCCTCCAGCCAGCGCATCCTGCATGCAGAGGGCTATGTCTAGTGGAGGGGGGACCACTGGCGTCCCGTCGTACCCCATGCCCTACAATCAGGCTCCCAGCTACGCCCAGGGCTACCCGACCTCAAACGCTGCTTCTTATTTCGGAGGCATGGACTGCGGATCCTACTTGGCACCCATGACCGGCCACGCCCACCATCACCCGCATGCCCATCACTCACAGCTGAGCACCGCCGCTGCAGTCTCAGGACACCATCATCCTCACCATATTGGGCAGAGCAGCGGGCACCACCCTCATCACCAGGGGTACGGTGGCACCGCGCTGCCTTTCAGCTCTTCAGACTGTCTGGATTACAAAGAGCAAGTGGCGTCATCATGGAAACTCAACTTCAGCTCTGCGGCGGCCGACTGCTTGGACTATAAAGACCAGGCCGCCTGGCGCTTTCAGGTTTTGTAAGAATGTTTCCCCCgatgtttacttgtttgtttttcttcCCGAACAAGTGTGTTTTCCTCACCATTTGGGAAAAAGCAGTGACTGTTTTGGGCCAGCTTTTTTTCCAGAGCTTACCAAAGTGTGTTTCTAAATGGAGGCGGGTTCTCCGTGGCCCCTCAGTCGGACTGAGTTGAAAGCGAGGGCTGCATTTGACGTGACGCACTCAAGGAATGGTGTTTTGAAACTATGAAggcaataataattttatatataactcTTTCCGTTGGCGAAGGTGGCCTACAGCTCATGTGAGATGTTACACACTAATTTGCATTCAtgttcatttaataaatataaagctGAAAAT

Function

GO:

id name namespace
GO:0021549 cerebellum development biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0003406 retinal pigment epithelium development biological_process
GO:0007275 multicellular organism development biological_process
GO:0030901 midbrain development biological_process
GO:0030902 hindbrain development biological_process
GO:0030917 midbrain-hindbrain boundary development biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-980526-27 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 brain development and retinal pigment epithelium development. Predicted to be active in nucleus. Is expressed in several structures, including anterior neural keel; axis; brain; immature eye; and neural plate. Orthologous to human OTX1 (orthodenticle homeobox 1).

Ensembl:

ensembl_id ENSDART00000006538

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00003158 lncRNA upstream 112818 50733156 ~ 50808448 (+) True XLOC_000637
TCONS_00003157 lncRNA upstream 389572 50528134 ~ 50531694 (+) True XLOC_000633
TCONS_00003155 lncRNA upstream 528477 50389319 ~ 50392789 (+) False XLOC_000632
TCONS_00003156 lncRNA upstream 528477 50389366 ~ 50392789 (+) True XLOC_000632
TCONS_00003154 lncRNA upstream 998393 49920790 ~ 49922873 (+) True XLOC_000628
TCONS_00003159 lncRNA downstream 13635 50943592 ~ 50953558 (+) True XLOC_000640
TCONS_00001091 lncRNA downstream 47597 50977554 ~ 50983939 (+) False XLOC_000641
TCONS_00003160 lncRNA downstream 85901 51015858 ~ 51018551 (+) True XLOC_000643
TCONS_00001095 lncRNA downstream 109601 51039558 ~ 51042332 (+) True XLOC_000644
TCONS_00001098 lncRNA downstream 136859 51066816 ~ 51073128 (+) True XLOC_000645
TCONS_00001083 mRNA upstream 229728 50639416 ~ 50691538 (+) True XLOC_000636
TCONS_00001082 mRNA upstream 284045 50613868 ~ 50637221 (+) True XLOC_000635
TCONS_00001081 mRNA upstream 364236 50538839 ~ 50557030 (+) True XLOC_000634
TCONS_00001080 mRNA upstream 601612 50293938 ~ 50319654 (+) True XLOC_000631
TCONS_00001078 mRNA upstream 733509 50085640 ~ 50187757 (+) False XLOC_000630
TCONS_00001087 mRNA downstream 38951 50968908 ~ 50983855 (+) False XLOC_000641
TCONS_00001088 mRNA downstream 38951 50968908 ~ 50990889 (+) False XLOC_000641
TCONS_00001089 mRNA downstream 47018 50976975 ~ 50990886 (+) False XLOC_000641
TCONS_00001090 mRNA downstream 47119 50977076 ~ 50977997 (+) False XLOC_000641
TCONS_00001092 mRNA downstream 57578 50987535 ~ 50988174 (+) True XLOC_000641
TCONS_00001084 other upstream 66788 50854364 ~ 50854478 (+) True XLOC_000638
TCONS_00001079 other upstream 789257 50131158 ~ 50132009 (+) True XLOC_000630
TCONS_00001068 other upstream 1205444 49699903 ~ 49715822 (+) False XLOC_000626
TCONS_00001057 other upstream 1330443 49590701 ~ 49590823 (+) True XLOC_000623
TCONS_00001054 other upstream 1448941 49464741 ~ 49472325 (+) True XLOC_000620
TCONS_00001097 other downstream 136825 51066782 ~ 51073107 (+) False XLOC_000645
TCONS_00001111 other downstream 535511 51465468 ~ 51465582 (+) True XLOC_000651
TCONS_00001119 other downstream 753562 51683519 ~ 51683618 (+) True XLOC_000655
TCONS_00001126 other downstream 1200207 52130164 ~ 52135502 (+) False XLOC_000662
TCONS_00001154 other downstream 2069875 52999832 ~ 53061197 (+) False XLOC_000682

Expression Profile

//

Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000301_00987966_00990310.mRNA True 2656 mRNA 0.46 3 CI01000301 986699 ~ 990691 (+)