RNA id: TCONS_00049956


Basic Information

Item Value
RNA id TCONS_00049956
length 1790
RNA type mRNA
GC content 0.42
exon number 2
gene id XLOC_025309
representative True

Chromosome Information

Item Value
chromosome id NC_007114.7
NCBI id CM002887.2
chromosome length 62628489
location 23707691 ~ 23710095 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CAGTGCATTGCTATAATTCATTAATACATCATAAATCGTGAAGCACAGCGTTATAACGACCAAGATCTACAAATCAAGCCCTCTAAAACAACCTAAATGAGCTCTTACTTTGTAAACTCGTTCTCAGGGCGCTACCCAAATGGCCCTGACTATCAGTTACTAAATTATGGAACTAGCAGCAGCGCTATGAACGCTTCGTACAGGGACTCCGGCACCATGCATTCAGGCTCTTACGGCTACAACTACAATGGAATGGACCTAAGCGTCAATCGTTCAACCAGCACTGGCCACTTTGGGGCGGTTGGGGACAACTCCCGGGTCTTCCAGTCTCCAGCTCCGGAGACGCGATTCCGGCAGCCATCAAGCTGCTCGCTCGCGTCTCCGGAGCCGCTGCCTTGTTCCAACAGCGAAAGCCTTGGACCCAAAGGCTCTTCGCCCCCTTCCGACCAAAGCACCACCACTGCGGGTAATAATCTCAACAGCAACACACATTTTACAGAAATCGACGAGGCCAGTGCTTCATCGGAGACCGAGGAGGCGTCTCACAGAGCGAACAACTCTGCACCCCGGACACAACAGAAGCAAGAGACCACGGCAACCTCCACTACCTCGGCGACGTCCGATGGCCAAGCTCCCCAAATATTCCCTTGGATGAGGAAACTACATATTAGCCATGATATGACTGGACCAGACGGCAAAAGGGCCCGAACTGCATATACCCGCTATCAGACGCTAGAGCTGGAAAAAGAGTTCCATTTCAATAGATACCTCACCCGAAGAAGGAGGATAGAGATAGCCCACGCTCTATGCCTCTCAGAGCGTCAAATTAAGATATGGTTCCAAAACCGGCGGATGAAATGGAAAAAGGACAATAAACTGAAGAGCATGAGTCTGGCTACCGCAGGTAGCGCTTTCCAACCATAGTTGTATCCCAAGACCTGCTACGTGGTGTGCAAAAAATTACGCGGAAAATGAGATGAAAAAGAGATCTCAAAACATTACCTACAGAGTACTGTACATCGCGGCACCTTTCGGCATGTTATGGATGTTTTAGGCATTTTAAAATTCTACTGTGGTACTGCTATAATGAAACAAAAATTAGTGTTCATATGTTGTTCTTTTATGGTGACTTTAATTTTGGCAAGTAAATAAAACTGAAGGGAAAGAAGCTATCAATATAACGCTTGTTGTTCTTGTTACAAATATTGTTTATGTGTCAAGTGCTATGTTAATGCTTTCTTGAGAGTTAGCATGTGAGCTCTTAAATGTTATAACTTATTTACCTATACACGTGTATAACTACCTTTTGAGTTTACAGCTTAGAAACGCATCTGCCCTTGTATGAAGTGAAGCTCTAGTTTAGAGGTGACTGCAGTAAATTTAGCAGAAGCCTATGTTTCATGGTCCTCTGTTTAATCAATGTCTAAATAATCACAATCGATTTGTCATGTGTTCACAatcttctattattattattattttttttttgaaaaaaaaaaaataattaaatggtgtaaatagaCCTCGCTAGATTCTTGTACTCGTTCATACGTGTGTATAGTTGTATTccaaatatataattgtatattacTGGATCATGTTTATGTTCCAAAAAAGGTTGTATATATTGAACATTTTTATTGTGATCAGTTGGCTATTTGTAGTGGGCAGAATAAACGGCAATGTGGAAAAAAGTCATGTCAATCTGCCTGTTAGCATTTTGCCAAAATgctttttgtatttgtttgtagtTTAACTTGGAGTAAAAAATAAAGTTCCTCATATTCAAA

Function

GO:

id name namespace
GO:0001708 cell fate specification biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0007275 multicellular organism development biological_process
GO:0009952 anterior/posterior pattern specification biological_process
GO:0007420 brain 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
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-980526-70 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 cell fate specification. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; mesenchyme; mesoderm; neural tube; and somite. Orthologous to human HOXB5 (homeobox B5).

Ensembl:

ensembl_id ENSDART00000025449

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00049952 lncRNA upstream 11483 23694156 ~ 23696208 (+) True XLOC_025306
TCONS_00052661 lncRNA upstream 39494 23665161 ~ 23668197 (+) False XLOC_025301
TCONS_00052662 lncRNA upstream 39494 23666387 ~ 23668197 (+) True XLOC_025301
TCONS_00052660 lncRNA upstream 90890 23604478 ~ 23616801 (+) True XLOC_025299
TCONS_00052659 lncRNA upstream 183304 23518137 ~ 23524387 (+) True XLOC_025298
TCONS_00052663 lncRNA downstream 220351 23930446 ~ 23967966 (+) False XLOC_025313
TCONS_00049968 lncRNA downstream 224797 23934892 ~ 23967966 (+) False XLOC_025313
TCONS_00052664 lncRNA downstream 224846 23934941 ~ 23965038 (+) False XLOC_025313
TCONS_00052665 lncRNA downstream 224869 23934964 ~ 23962671 (+) True XLOC_025313
TCONS_00052666 lncRNA downstream 411106 24121201 ~ 24133485 (+) True XLOC_025317
TCONS_00049955 mRNA upstream 1945 23703704 ~ 23705746 (+) True XLOC_025308
TCONS_00049949 mRNA upstream 11711 23691847 ~ 23695980 (+) False XLOC_025306
TCONS_00049950 mRNA upstream 11825 23692462 ~ 23695866 (+) False XLOC_025306
TCONS_00049948 mRNA upstream 17210 23687909 ~ 23690481 (+) True XLOC_025305
TCONS_00049947 mRNA upstream 25255 23677351 ~ 23682436 (+) True XLOC_025304
TCONS_00049957 mRNA downstream 744 23710839 ~ 23723599 (+) False XLOC_025310
TCONS_00049959 mRNA downstream 11713 23721808 ~ 23723982 (+) True XLOC_025310
TCONS_00049960 mRNA downstream 16053 23726148 ~ 23749910 (+) False XLOC_025307
TCONS_00049961 mRNA downstream 21014 23731109 ~ 23746474 (+) False XLOC_025307
TCONS_00049962 mRNA downstream 27700 23737795 ~ 23749910 (+) False XLOC_025307
TCONS_00049951 other upstream 11678 23694156 ~ 23696013 (+) False XLOC_025306
TCONS_00049946 other upstream 34236 23673377 ~ 23673455 (+) True XLOC_025303
TCONS_00049938 other upstream 468233 23235668 ~ 23239458 (+) True XLOC_025294
TCONS_00049913 other upstream 1138585 22568987 ~ 22569106 (+) True XLOC_025283
TCONS_00049893 other upstream 1646603 22059313 ~ 22061088 (+) False XLOC_025275
TCONS_00049958 other downstream 10556 23720651 ~ 23720745 (+) True XLOC_025311
TCONS_00049974 other downstream 385065 24095160 ~ 24101082 (+) True XLOC_025315
TCONS_00049975 other downstream 385862 24095957 ~ 24096036 (+) True XLOC_025316
TCONS_00049977 other downstream 424462 24134557 ~ 24137908 (+) True XLOC_025318
TCONS_00050021 other downstream 1416361 25126456 ~ 25132231 (+) True XLOC_025346

Expression Profile

//

Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000034_01666303_01667765.mRNA True 1202 mRNA 0.48 2 CI01000034 1666064 ~ 1667900 (-)
bowfin (Amia calva) AMCG00016671 False 1066 mRNA 0.56 2 CM030122.1 27265887 ~ 27272025 (-)