RNA id: TCONS_00013739


Basic Information

Item Value
RNA id TCONS_00013739
length 2011
lncRNA type inter_gene
GC content 0.39
exon number 2
gene id XLOC_006400
representative True

Chromosome Information

Item Value
chromosome id NC_007124.7
NCBI id CM002897.2
chromosome length 52186027
location 5360309 ~ 5365910 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CTCGAAACCCGTCaccaactcctctctgcatctcaggtTTGCCGATGTATgcggcgagctactggacaagctggtaacagtgggaaagccatccacatgcaGCTTCTGTGCAAGCTCACTTTGGAGTTCCAGAGAAAGATGTCTCCAGGGTTGCCAAAACCCCAGGCCTCAAAGCCAAACAGCAAAGTTGGGAATGTCCCGGCAGACATGTCAACAGGAGTGAAGAAGGCCCACCACACTGACCTTCTGATGACAGCATTACTGCAATTCATTACGTTTACAAGCTGCAATTACGGTCGGAGCGTTTCACTCACCCTTTTTGTTCTCCTTTCTGTTTCCTACTGTCTGTTGGTTCCTGAAAACTGGGTGAAGTCTGACCAATGTGGCAGACCAGTGTCAGCTAGAATTCACTCAcactctttatttttttctttatatgaaaCCTGAAATATTCTTGAGTCTGGATACTGTGTTGCTCTTCATATCCTTCGACAGAAGGATACTCACTTCTGATTTCTCCAATGCTTTTTCAAAGTCTTGGCACATGCAGCTTTACTTAATGTGGatctgcaacccaggctcattctgaatatgtacccctatatacatttctggagagtgcaaaatatgtcccaggaactACATTTTTTCACCAGCGTCCACTGTGTAccctttttcagatttcaaatttctcttgcaagtgccattaaTGTCTGCTGTTCtcctgtaaatccaccagaggccgctgtttactGGCTGACTGACTGTGCAACTGACCAATCACCCCACCTCCTTACCTAAACGCAATcgattgtgttttaaaaagcacccacCTACCACCTtccaaacccaaccgacagtttttaatccagaaaaagaaaagccctcacggcagcctgattttttaccatgttttcagatctaaCCATGTTCTCATGCTgatattcacttgtttatttatttttgctgtttgtttttgttttatctgctttctgaaactgttctttGTTGAACTTGAATCCTGTCGTCACtgtcaactccactctgcgtctcatacatggcgagccactgggcaaactggtaacagcggaaaagctgtcaAAATGGATGTAATGGGTCAGCTGTTagcacaaaaagaaacagaagaagTCGGTAATACCACcccgtagtgtttgttttaaagatgaaatgcagccagatgtagctctggctacataatttgcactcttcagaaatgtatacaaggctacgttttcacaatgagtctGTAATTCACAGATCTGTGTCTCAGTAAATttctgtgcactgtaaaaaataaaaaatcctgggttccacacaattgatttgttataagacaaaacaaatgaactaagttaacttattattttaaaggaaaattaagtggattgaacataaaacaattaaccaCACAAAAAACTTAACCATTGTGTTTCAGCTCAAACTTtgagtgtttgaatgtgtgtacAGACCGGTGTACAGTTAATtgctgtgtaaatgcatttataacACCTCTGAGTGGTAGCAAACAATCAAATGCCACTTCAGAAGTGCTTCATGTCACCTTTGAGGTGTAAATAAggcatgattttttttaaaatagagcaGGAAATAAAAGTTCTACTTATTTACGCTCAATGAATGATGAACATCGAAGACTAACAACAGGCATTTAAaaattacactgttaaaaaatgtgtggaacccagcattttttatcaGTGTAGTTTTTAATCGCATGTTGTTAGTCTGACTAGAATCAAATCCTCAATGCATTAAAATGACATTgatctttcagaaaaaaaattcagtaaGATTGTTTCTTAATATTGTATTCAGTCCAAATCTTTCTTTAAGCTTGTATTCAAATCTGCCTTCATCTAATCAGCAACTGATCCACAGAACCAAGTACCACTATTTCTTTTTTGACTGATTTTACTTTAACCTACTTTGTAATAGTGTGAAAAATGATGTCTCTCAGTTTATAAGTGTA

Function

GO:

id name namespace
GO:0021521 ventral spinal cord interneuron specification biological_process
GO:0019219 regulation of nucleobase-containing compound metabolic process biological_process
GO:0019222 regulation of metabolic process biological_process
GO:0016070 RNA metabolic process biological_process
GO:0080090 regulation of primary metabolic process biological_process
GO:0018130 heterocycle biosynthetic process biological_process
GO:0006351 transcription, DNA-templated biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0051171 regulation of nitrogen compound metabolic process biological_process
GO:0006366 transcription by RNA polymerase II biological_process
GO:0030154 cell differentiation biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0009058 biosynthetic process biological_process
GO:0009059 macromolecule biosynthetic process biological_process
GO:1901576 organic substance biosynthetic process biological_process
GO:0009889 regulation of biosynthetic process biological_process
GO:0097659 nucleic acid-templated transcription biological_process
GO:0031323 regulation of cellular metabolic process biological_process
GO:0031326 regulation of cellular biosynthetic process biological_process
GO:0006139 nucleobase-containing compound metabolic process biological_process
GO:0051252 regulation of RNA metabolic process biological_process
GO:0006725 cellular aromatic compound metabolic process biological_process
GO:1901360 organic cyclic compound metabolic process biological_process
GO:1903506 regulation of nucleic acid-templated transcription biological_process
GO:1901362 organic cyclic compound biosynthetic process biological_process
GO:0010467 gene expression biological_process
GO:0010468 regulation of gene expression biological_process
GO:0048869 cellular developmental process biological_process
GO:0044249 cellular biosynthetic process biological_process
GO:0044271 cellular nitrogen compound biosynthetic process biological_process
GO:0060255 regulation of macromolecule metabolic process biological_process
GO:0048663 neuron fate commitment biological_process
GO:0048665 neuron fate specification biological_process
GO:2001141 regulation of RNA biosynthetic process biological_process
GO:0032502 developmental process biological_process
GO:0032774 RNA biosynthetic process biological_process
GO:0034641 cellular nitrogen compound metabolic process biological_process
GO:0019438 aromatic compound biosynthetic process biological_process
GO:0010556 regulation of macromolecule biosynthetic process biological_process
GO:0034645 cellular macromolecule biosynthetic process biological_process
GO:0034654 nucleobase-containing compound biosynthetic process biological_process
GO:2000112 regulation of cellular macromolecule biosynthetic process biological_process
GO:0046483 heterocycle metabolic process biological_process
GO:0060573 cell fate specification involved in pattern specification biological_process
GO:0060579 ventral spinal cord interneuron fate commitment biological_process
GO:0060581 cell fate commitment involved in pattern specification biological_process
GO:0021511 spinal cord patterning biological_process
GO:0021513 spinal cord dorsal/ventral patterning biological_process
GO:0021517 ventral spinal cord development biological_process
GO:0043292 contractile fiber cellular_component
GO:0044449 obsolete contractile fiber part cellular_component
GO:0015629 actin cytoskeleton cellular_component
GO:0005634 nucleus cellular_component
GO:0030016 myofibril cellular_component
GO:0030017 sarcomere cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003690 double-stranded DNA binding molecular_function
GO:0097159 organic cyclic compound binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000976 transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function
GO:1901363 heterocyclic compound binding molecular_function
GO:0140110 transcription regulator activity molecular_function
GO:0001067 regulatory region nucleic acid binding molecular_function
GO:1990837 sequence-specific double-stranded DNA binding molecular_function

KEGG:

id description
ko03230 Viral genome structure
ko05164 Influenza A
ko03200 Viral proteins

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00013457 lncRNA downstream 103006 5255308 ~ 5257303 (-) True XLOC_006399
TCONS_00013734 lncRNA downstream 640916 4717790 ~ 4719393 (-) True XLOC_006394
TCONS_00012406 lncRNA downstream 646203 4712421 ~ 4714106 (-) True XLOC_006393
TCONS_00012401 lncRNA downstream 912656 4445578 ~ 4447653 (-) True XLOC_006390
TCONS_00012400 lncRNA downstream 913102 4445553 ~ 4447207 (-) False XLOC_006390
TCONS_00013740 lncRNA upstream 24587 5390497 ~ 5395920 (-) True XLOC_006401
TCONS_00013741 lncRNA upstream 98244 5464154 ~ 5471589 (-) True XLOC_006402
TCONS_00013458 lncRNA upstream 115077 5480987 ~ 5487505 (-) False XLOC_006403
TCONS_00013459 lncRNA upstream 118921 5484831 ~ 5487613 (-) False XLOC_006403
TCONS_00013460 lncRNA upstream 119050 5484960 ~ 5486643 (-) True XLOC_006403
TCONS_00012417 mRNA downstream 103006 5243167 ~ 5257303 (-) False XLOC_006399
TCONS_00012418 mRNA downstream 107750 5247389 ~ 5252559 (-) False XLOC_006399
TCONS_00012416 mRNA downstream 280798 5069552 ~ 5079511 (-) True XLOC_006398
TCONS_00012415 mRNA downstream 294770 5049595 ~ 5065539 (-) True XLOC_006397
TCONS_00012414 mRNA downstream 295828 5043738 ~ 5064481 (-) False XLOC_006397
TCONS_00012419 mRNA upstream 124641 5490551 ~ 5569562 (-) False XLOC_006404
TCONS_00012420 mRNA upstream 125165 5491075 ~ 5568928 (-) False XLOC_006404
TCONS_00012423 mRNA upstream 504734 5870644 ~ 5937034 (-) True XLOC_006407
TCONS_00012424 mRNA upstream 580697 5946607 ~ 5978433 (-) False XLOC_006408
TCONS_00012425 mRNA upstream 587838 5953748 ~ 5965423 (-) True XLOC_006408
TCONS_00012410 other downstream 367924 4976175 ~ 4992385 (-) False XLOC_006396
TCONS_00012397 other downstream 1051643 4307685 ~ 4308666 (-) True XLOC_006386
TCONS_00012394 other downstream 1136354 4218329 ~ 4223955 (-) False XLOC_006384
TCONS_00012381 other downstream 2117051 3198438 ~ 3243258 (-) True XLOC_006376
TCONS_00012378 other downstream 2305372 3054823 ~ 3054937 (-) True XLOC_006374
TCONS_00012432 other upstream 882077 6247987 ~ 6252514 (-) True XLOC_006414
TCONS_00012435 other upstream 922634 6288544 ~ 6320158 (-) False XLOC_006416
TCONS_00012458 other upstream 3283801 8649711 ~ 8650051 (-) True XLOC_006434
TCONS_00012459 other upstream 3289209 8655119 ~ 8655447 (-) True XLOC_006435
TCONS_00012477 other upstream 3637217 9003127 ~ 9009241 (-) False XLOC_006442

Expression Profile

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