RNA id: TCONS_00049960


Basic Information

Item Value
RNA id TCONS_00049960
length 3483
RNA type mRNA
GC content 0.42
exon number 4
gene id XLOC_025307
representative False

Chromosome Information

Item Value
chromosome id NC_007114.7
NCBI id CM002887.2
chromosome length 62628489
location 23697997 ~ 23771945 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CACAACTGCTCGGACCTTCTGTTTGGAGGGGAGTGAAATCTTGAAGGGCACTTGAAGACAACCCCCCTCCCTTTTCTACCATCTTCTATTCACCAAGTCATGCCACAAGAAAACTTTTTTGGCGAGGGATGTCCCATGAAGAATCTCTTGAAAATGTTAGCGCGAGTGAGAATCTTCACAGGACCAGAGATGGCAGCGTTTAAGTTCCTTCTCGTTATCAAGAAGCTGTATCCTTGCATAAAATCTAGAAGTGATAAAGGACAATATCTCGGTCAGCTTCCAAGAGGCCATTGGAAAGAGACCGTCACGTGACAACTGGTGCCAATGTTCTTCCAGAAGGTCGTCAGGACCCTGGTAGCCAGCAACTCGATTTTTGGAAATGCAGAAAACGACCTACTACGACAACTCGACACTTTTCGGAGGATACTCGTATCAGGGGGCAAACGGTTTTGGCTATGATGCCCCGGCACCAGCCTTCCAGAACTCAGCACATCTTGAGGGTGACTACCAAAGGTCTGCATGCTCCCTACAGTCGCTCGGCACCAGTGCACCCCCACAGCCTCAGCATGCCAAGACGAAAGAGCTTAATGGCAGCTGCATGCGGCCCAGTCTGCCACCTGAACACCATCCACCCCCCCAGGTTTCCCCTCCTCAGAACACTGTAAATGTTGCTGCCACGAATGCCACCCAGCAGCCAGGTGGcagtggtggtggtgggggggctGGCTCTGGGGGAACATCCAAATCATCATCCAAGTCATCCTCTATGGCCACAAACCCAACTCTCACGAAGCAAATCTTTCCTTGGATGAAGGAGTCACGTCAGAACACCAAGCAAAAAAACAGCTCCCCTAGTGCAAGCTCAGCTAATGCGGAGAGCAGCGGTGGTGAGAAAAGCCCTCCGGGTTCTGCAGCTTCCAAGAGAGCACGCACCGCTTACACCAGCGCACAGCTGGTGGAGCTCGAGAAGGAGTTTCACTTCAACCGATACCTGTGCCGGCCGAGGCGTGTGGAAATGGCCAATCTGCTAAACCTCAGTGAGCGGCAGATCAAGATTTGGTTCCAGAACAGGCGGATGAAGTACAAGAAAGATCAAAAGTCAAAAGGCATTGGTTCATCATCAGGGGGGCCTTCTCCTACAGGAAGTCCACCTCTTCCAATGCAGTCCTCAGCTGGTTTTATGAACTCTATGCACTCAATGGGCAGTTACGATGCTCCCTCTCCACCATCTTTTAACAAACCCCATCAAAATGCATACGCCATGTCAACAGCCTATCAGAACCCAATGAAAGGTTGCCCACCCCAACAGAAGTATGGAAACACACCACCGGATTATGACCCACACGGGCTACAGGGTAACAGTGGCAACTATGGGACACCAAACATGCAGGGTAGCCCTGTGTATGTAGGAGGTAACTATGTTGATGCCATGCCTGCCACTGGGCCTTCTATGTATGGCCTCAATCACCTACCACACCACCAGTCGGCAAGCATGGACTACAACGGTGCCACACAGATGTCAGCGAACCAGCACCATGGACCTTGTGACCCACATCCGACATACACGGATCTGTCTGCACACCATCCTTCTCAGGGTAGAATCCAAGAAGCACCCAAGTTGACTCATCTGTAGCAggtttggacaaaaaaaaaaaattaaaaagaagaaaaaaaatgaaaggaagaCAAAACAGACTAACCCATGGGGCGATGCAATGGGGTTGAAAAAGATGATCCAGTGGTTTCTTGCCATGACTAGGACACCGGTTTGTGTCAATGTTGTCCTTCCATTCATATGTGAACATCTCTGAATTTAGTATCCATAGGTCTaaaaacccctttaaaacaaTACATGTCATGAAAAGTGGCTTGTTTATGCCAAGGAATAGACTGTCTAGCTGTATGACCTCATTACATCATCCTAAATGTTTGTGTTTCTCACTCTTTGGAGGGAAGTACGatatagtaaatatataaacTTACTGGTGCAAGAAAACCACTGGATTGTTTTCGTCCACTACCCTTATTTCACatacctctttttttaaatgtatcaaaaacttcaattttttaaataacttgatCCCAAAACTGCAGCAGATTTGCACCATGTCTTTAGCAAGACAAGGTGATCAAGATATTCATCTGTTTAAATTGCGTTTTACACTATGCTACCTATCACTATTAATGAGAAGAAAATTGATTTTTGATATGGCTTTGACAGGGTAAAAAGAAGAGTTGAGAAAACTAGTAAAGTAAAGCTCATTTCCTCATTCTCAACTCACTTCCCCCTCCCTTCCCCTTATACTCCTTTCCCAGTTCTTGGGTTTGCCTACATTAGTCCAAACTAATATGAAAAGCCCACATTTTCTCATATCTTCATTTAACGTGGATACAGGGTATATTTGAACAAAATGCATGTCCGGGAAACCAAGCTATGGCGCAGACTTCTCTGTTTACGCCTACTGCGCTCTCGTCTGGGCATCATTGTTGCACTTAGAGTTTACATTAAATGGGTGAGGAAGAAAAGTAAATCTTATTTTGAATCGGAAGACCTTCAATCAGCGTCTTTCGCTAAGTGTGTTCAAGTGaacattcataaatatatatttatttgttatagcCAGTTTAAATACtttcttttttgtattatttatccCCATGTATTTATATcgataaaaatgtacttttttagtaTCTACCTGTTATAAAAAAGACGCTGTGTTCTTGTCATTGTAACAAATTAATTTTTAGTTCTTGTATTTTAGAAATATGTAGGTTTATGTTACCCTTGTATAAAAAATGTCTTGACTTGTACAGGGGGCACAAGAACGGAATCAAACCGTTCCCGCATAGTCGAGAATTAGACGGAATATAGCGAAACATTTTGAGAACTTCATTTGTCCTTTGTAACTACTTTTATTTCCTTGTTAAGAGTTGGTTGTTGAACAattctttaataaaatgttatgttATTCATTTGCACTCTAGAAGTTTATGAATTTACCAAGCAGACTCACACAATTTTATAGGCAAAGAGAGAAAAGGGTGGGGGTAGGGTTTCTATAGTCCTGTGAAAGCGTCCTCGAATCCGCGCCTGCAATAGTCACGTGAAGAGAGTCCAATAGAATCACTCTTTACTGAGTATGGAGTATTACTAAATATGGAATTAAAAGAAGTGATTATGCAAACCGAGATTTAAAGCAAAAATTGCATTTGCAACAAATGACTAAACATATTTTGGTAATTGCAATGGTAAAAAGAATAGCTGCGTTAATGTCTAAGATCATTCACCAActttagatttaatttaaacatgctAAACTATTTTCCGAGAGTGGAAAAAAGACGAAGCTTTTTAATGTTATGAGGTCAATTGATGCAACAAAAAAATCAGGACTACGTAAACACAAAAGCGTTTAAATATTAGATGAACAGTcaattaagaaaaataattacacacacacacacacacacgtgtgt

Function

GO:

id name namespace
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:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0048704 embryonic skeletal system morphogenesis 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

KEGG: NA

ZFIN:

id description
ZDB-GENE-990415-104 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anterior/posterior pattern specification; embryonic skeletal system morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in several structures, including ectoderm; hindbrain neural keel; nervous system; neural crest; and pharyngeal arch. Orthologous to human HOXB3 (homeobox B3).

Ensembl:

ensembl_id ENSDART00000174580

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00049952 lncRNA upstream 29940 23694156 ~ 23696208 (+) True XLOC_025306
TCONS_00052661 lncRNA upstream 57951 23665161 ~ 23668197 (+) False XLOC_025301
TCONS_00052662 lncRNA upstream 57951 23666387 ~ 23668197 (+) True XLOC_025301
TCONS_00052660 lncRNA upstream 109347 23604478 ~ 23616801 (+) True XLOC_025299
TCONS_00052659 lncRNA upstream 201761 23518137 ~ 23524387 (+) True XLOC_025298
TCONS_00052663 lncRNA downstream 180536 23930446 ~ 23967966 (+) False XLOC_025313
TCONS_00049968 lncRNA downstream 184982 23934892 ~ 23967966 (+) False XLOC_025313
TCONS_00052664 lncRNA downstream 185031 23934941 ~ 23965038 (+) False XLOC_025313
TCONS_00052665 lncRNA downstream 185054 23934964 ~ 23962671 (+) True XLOC_025313
TCONS_00052666 lncRNA downstream 371291 24121201 ~ 24133485 (+) True XLOC_025317
TCONS_00049959 mRNA upstream 2166 23721808 ~ 23723982 (+) True XLOC_025310
TCONS_00049957 mRNA upstream 2549 23710839 ~ 23723599 (+) False XLOC_025310
TCONS_00049956 mRNA upstream 16053 23707691 ~ 23710095 (+) True XLOC_025309
TCONS_00049955 mRNA upstream 20402 23703704 ~ 23705746 (+) True XLOC_025308
TCONS_00049949 mRNA upstream 30168 23691847 ~ 23695980 (+) False XLOC_025306
TCONS_00049966 mRNA downstream 2240 23752150 ~ 23754831 (+) True XLOC_025312
TCONS_00049967 mRNA downstream 18988 23768898 ~ 23771142 (+) True XLOC_025307
TCONS_00049969 mRNA downstream 300133 24050043 ~ 24065393 (+) False XLOC_025314
TCONS_00049970 mRNA downstream 310544 24060454 ~ 24071582 (+) False XLOC_025314
TCONS_00049971 mRNA downstream 312838 24062748 ~ 24070047 (+) True XLOC_025314
TCONS_00049958 other upstream 5403 23720651 ~ 23720745 (+) True XLOC_025311
TCONS_00049951 other upstream 30135 23694156 ~ 23696013 (+) False XLOC_025306
TCONS_00049946 other upstream 52693 23673377 ~ 23673455 (+) True XLOC_025303
TCONS_00049938 other upstream 486690 23235668 ~ 23239458 (+) True XLOC_025294
TCONS_00049913 other upstream 1157042 22568987 ~ 22569106 (+) True XLOC_025283
TCONS_00049974 other downstream 345250 24095160 ~ 24101082 (+) True XLOC_025315
TCONS_00049975 other downstream 346047 24095957 ~ 24096036 (+) True XLOC_025316
TCONS_00049977 other downstream 384647 24134557 ~ 24137908 (+) True XLOC_025318
TCONS_00050021 other downstream 1376546 25126456 ~ 25132231 (+) True XLOC_025346
TCONS_00050056 other downstream 2394855 26144765 ~ 26151560 (+) False XLOC_025372

Expression Profile

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