RNA id: TCONS_00042312


Basic Information

Item Value
RNA id TCONS_00042312
length 5205
lncRNA type sense_over
GC content 0.40
exon number 3
gene id XLOC_020792
representative False

Chromosome Information

Item Value
chromosome id NC_007133.7
NCBI id CM002906.2
chromosome length 39133080
location 5701260 ~ 5724131 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

GCGAGTTGCGACCAGTGTTTCATATACAAAAATGGATGAAACGAATGAAAACAGAACTGATGAGTGTGTTGAGGATAGCagtgaggatgaagatgaaacgcTTGCTTCGGAGGAATCGTCAGACGAAAGTGCCGCTTCCAGCGCGGACTCTGGAGAGGAGATGTTCCTCGAGGCGATGGACCCCGTTTTGAATGGGTTTATAGATGACTCTGATGAGGATTGGTCTCCAGAGGTCACCCCACTAAAGAAGAAGAGAAAGGGTCCGTCTTCTGTTTCTCCATCCCCAGCAAAGTCTCGTAGAACTGCTTCACCTGGCTCTGCACGGAGTGCCAAAGGTAGGAAAGGCAGCGTGAGACGATCTTTACCATTTTCCTGCAGTATCCTAGAAAGCAAGTGGAAAAGTGTAGATGAGCCTGATATTGAGCCGCCTCAGCTATTGTTTAAACCCAAACGTACACCCGGTCCACAGTTGATATCCACTTCGTCATGCAGCGTTCTGCAGTATTTTCAGTTATTCTTTTCCAAATCAGTGATGCAGAAAATTGTAGATCATTCAAACATCTACGCCTCCATGCATACAAACGAAAAGAAGAAACCCTGGAAGAACATCACCATCAAAGACCTGAAATCATTCATAGCCATGGTGATTTACATGGGCATAGTGAAATGCTTCAATCTGACAGATTATTGGAAGAGGACAGACTTTTACAGTCTGCCCTATCCTGCAAGGATCATGTCTTGTAGAAAATTTCTTAGCATGTGTTGGGCTCTCCATCTTAGTAATCCCAAAGTGGATGCAGAAAATGACAAGAAGAAAGGAACACCTCAATACGACCGGCTGTGTAAGATCAAACCGCTGTACCAGGACATTAGAGATGCTTGTAAAGCTTCATTTCATCCTCATCAGAACATCTCCATCGATGAAAGAATGGTGGCGTCAAAGGCTAGACATGGCCTCATACAGTACATGAAAAATAAACCCACAAAATGGGGGTACAAACTGTTTGTGCTGGCAGATTCCCTCTGCGCCTACACGTGGGACTTCTTCATTTATGAGGGAAAGGTGAAAACGGAGCAGAGGAAAGGTATAAGTTATGATTCTGTCATGGCGCTGATTGATGAACGGGTGTTGGGCACTGGATACAAGCTGTTTGTCGACAACTTTTACACCAGTCCCACACTCTTCAGAGATCTGCTCAGCAAGAAGATCGGGGCTTGTGGCACGATTCGAGCGAATCGCATTGGCCACTCAAAGACTCCAGCTCCTCGTGGGAATATTCGCTGGTTTAGAGAAGACGGTCTGCTTTTTGTTGAGTGGAAGGACAAGAGAGACGTGCTGATGTGCTCCACCTTTCATAAAGCGTATAACGGAGACTATATAAAGCGGAATGTGAAAGGAAAAGGTGGCGTTTGGACTCCTCAGGATTTCCCCGTGCCAGCTGCTGTGTTGGACTACAACAAACACATGGGAGGAGTGGATGTGTCTGATGCACTAATCGGATATTACACAGTCCTCCATAAAACAAAGAAGTGGTATCGGTCCTTTTTCTACCACTTTGTGGACATCGCTGTCGTCAATGCCTTTATTCTGCACCAGCAGATGGCCAAGTCGAAGAACCAGAAGGCCATGACCCAGAAGGTCTTCCGCGAGACTCTGGTTGCAGAGCTTGCAGGAATAAGGGCTGGTTATCCTCCTGCACGCGAGGCTGCTATTGCTTCTACTGACAACCACCTGCCCAAGTACATCAAAGGCGACAGTACATTCGGAAGACGGAAATGCAAATTGTGCACCCATAAGACTCCAATCACGTGTGTAACGTGCCAGGTGCACTTGTGCTTTGTACCCAAGCGTGATTGTTACACTAAATGGCATGAATCCGGTAACTCTGATTCTGACACCGAGTAAAGTTGTCGAGTCCAAACTACTATCATTTATACTTTTATAAAACAGGCATGGTCAAAGTGCAAAAACACAAGAAATCCAAAGATCTATCAAAAGTGCAACATGAAACTACTAAGACATTCATTAAAGTAACACTTTTATTTGAAAATAGCCTAATTTTACAAGTCCACTAGAATTCAGTAGTTGagatttaccatttttgaatccattcagccaatctccacgTCTagcggaagcacttttagcttatgTAATCGAGGTCAGGTTGTAAACCTCACCCATCAGACCTCTAATAAGCagcagacgctagaggccatggtctttaggcTCTTGGTTATGCTGTGTTAACACTAGACGTTTGAACAAATCGCGATATCCATGCATAAATAGACGAGTGAACATTtagagtttactcgctttatttcAGATTCATTAGCGCACATTCacgtgtttatgtgctttatgaaggctgaaaaacagcgtcgattcgTTTGGAGCCTTGTCActagtccactagatcctttcagagatgcacccagctctgtgagttcataaactcctaaGTTCCAGAAACCgcacctggatgatggaggctttcagcagtgcttcagactgagccaccccagtttgatgaactgttgtccagtGTCGGCAGGAAGATTTCCCCCcggaacaccaacaacaggcgctacgtcataatcacgcccctataAGACAAAGCTCATGATTGGTTTACACAGCTTGGATGTCCGCTAAAGTTTACATTTTCCAACATGAGTGAAATGTGAGATAAGCCCATCAATCACGCAGCTTGCTCAACTCACGCCATTTCGTTCGCGGCAATTGTGTCATTTGCGTGtattgcgccgcaggatgtctattcgtgtctttgcattgacttgacaggtaaatcacttgcgcttgccACCGCTTtcgtgtctggtgtgaatgcagcattagaGCGACCGACTTCCATGCATtgagtcgctggttcaatcctagttcggagcgggttgggtggtgtaggacctgCGGGGTTgcacttagcttagcataaatcattgaattggattagaccattagcatctcatttaaaAATAGAGTTCCTATAATAAAGCTTGACTCCTGAAAGTTACTGTTTTCCAGGTCAATATGTCTAGAAACTTTTCTCTTATTCTTttataataatcaaggaactttgatGCGGTAAGCTAGAATTGCTCCCGGCAGACTTGGAAatcagctgaaatggtttataaaTGGTTGAACTCCTCgttttaactctaggggagttgtaaaaggGGACGTTCATtgtaaaaagtggagtgttccttttaGATGGTTGTTTCACCCAAAAACGAAACGCTTGTTATTAAATACCCACCCTTATGTTGTTCCAATCCCCAGAGACCTTCACTCTACTTCTCAAGTTTCAcctaaaataattcaataattctcATCCTCCATAGGCATTAAGGTTCAGTGGTTCAGTCGGATTATCAAGCTATAGGAATAATTTTGTGTGCATATAACAAAActaactttattcaacagtttcatcttctcagtgtcagtatattgcacaCATTCATTCAATAATGCATACCTTTCCCCAATGCACATGTGTCACTTCTTCTTCATGAAATAAAGCAAAAGAATCTTACGAAACATGTTATAGGTATGACACACATATCGCTAACATGAACGTGCgctctatactgacactgaggagttCTTCTCACTTTTAAATAAAGTTGCTAtcctagttttatttatttgaaatgtatattatttttattattttggataGGACGGTGAAGAGTACTGACAGGAAATCTTGTAGAGCAGAGAGAGAGGAATGATAGCCAAAATACCTTAAGCTTGGAATCGAACTGTCACCGTGAGCTAAAGCTGTGTAGTTAATCGAAATTcagtttcgattttggcttccGACAattgtggacaaaaaaaagtaaatcgaTATAAAACGATtattgtatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctataaactgctttaatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctataaactgctttaatctatctatctgtctgtctgtctgtctgtctgtctgtctgtctgtctgtctgtctgtctgtctgtctgtctgtctgtctatctatctatctatctatctatctataaactgctttaatctatatttatctatctatcatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatctatgcatccatccacgcatctatctgtctatctatctatctatgcatccatccacgcatctatctgtctatctatctatctatctacgcaTCTATCTGTCTacgcatccatccatccaataatcataattacaattttaACCAATATAATTGTGATTTgggatttttcccataatcaagaAGTCTTACCGTGAGCACCTCTGTGTTATATGTTGACACACTTAACCGCTAGGCTATTGGCACTGATactattttaatttcatgtgcgcaaaaaattattttcatagcCTGGGAATATTTAACTTGAACCACAGAAGGCATAAGGTCAGTTTTGTGAAagtttttggtatttttctggaTTTTAAACAACATGGACTTCATCAATATGCAATCTGAAGATTAATGAAGGCCTCAGGGGTTTTGAATCACATTAGGgcgagtaattaataatataactttaatttttgggtaaacaaaCACTTTAATGATATTTTAAGCTACTAACATGTATTAAAATATACCAAATATGTATGTAGAGTGGTTGGTTTTTATTACTCACACTTAATCTTTGTAAAGAAAtttatcaaatgtttttaatCTTACTTACTCGACAGTGCTGTGATCTGTAGACCTGAAGGGATGAAGTGTTTAACATTATCATCACAGTTTTATAGTCCACTTTTTTATACCTTTGTCTGTAATATGTTGAACTACTAACAATGCTGTGGCCGTGGCTTCAGTGGTGAATGAACACTGTCTTTAAACTACTGTGTATTATTAAATACTCATTTAAT

Function

GO:

id name namespace
GO:0001704 formation of primary germ layer biological_process
GO:0048729 tissue morphogenesis biological_process
GO:0001706 endoderm formation biological_process
GO:0019219 regulation of nucleobase-containing compound metabolic process biological_process
GO:0001711 endodermal cell fate commitment biological_process
GO:0019222 regulation of metabolic process biological_process
GO:0001714 endodermal cell fate specification biological_process
GO:0016070 RNA metabolic process biological_process
GO:0007492 endoderm development 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:0065007 biological regulation 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:0048785 hatching gland development biological_process
GO:0003401 axis elongation 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:0009887 animal organ morphogenesis 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:1903224 regulation of endodermal cell differentiation biological_process
GO:0010453 regulation of cell fate commitment 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:0044238 primary metabolic process biological_process
GO:0010470 regulation of gastrulation biological_process
GO:2000027 regulation of animal organ morphogenesis biological_process
GO:0044249 cellular biosynthetic process biological_process
GO:0044260 cellular macromolecule metabolic process biological_process
GO:0044271 cellular nitrogen compound biosynthetic process biological_process
GO:0048332 mesoderm morphogenesis biological_process
GO:0060255 regulation of macromolecule metabolic process biological_process
GO:0043170 macromolecule metabolic process biological_process
GO:0003002 regionalization biological_process
GO:0050789 regulation of biological process biological_process
GO:0050794 regulation of cellular process biological_process
GO:0060795 cell fate commitment involved in formation of primary germ layer biological_process
GO:2001141 regulation of RNA biosynthetic 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:0035987 endodermal cell differentiation biological_process
GO:2000112 regulation of cellular macromolecule biosynthetic process biological_process
GO:0042659 regulation of cell fate specification biological_process
GO:0046483 heterocycle metabolic process biological_process
GO:0042663 regulation of endodermal cell fate specification biological_process
GO:0005634 nucleus cellular_component
GO:0043226 organelle cellular_component
GO:0043227 membrane-bounded organelle cellular_component
GO:0043229 intracellular organelle cellular_component
GO:0043231 intracellular membrane-bounded organelle cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0005488 binding 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_00041936 lncRNA downstream 70179 5624373 ~ 5631081 (-) False XLOC_020788
TCONS_00041937 lncRNA downstream 70250 5625625 ~ 5631010 (-) True XLOC_020788
TCONS_00041935 lncRNA downstream 238145 5453243 ~ 5463115 (-) True XLOC_020784
TCONS_00042311 lncRNA downstream 385671 5312971 ~ 5315589 (-) True XLOC_020781
TCONS_00042310 lncRNA downstream 385678 5312971 ~ 5315582 (-) False XLOC_020781
TCONS_00042313 lncRNA upstream 9535 5723328 ~ 5825199 (-) True XLOC_020793
TCONS_00042314 lncRNA upstream 146347 5860140 ~ 5872245 (-) False XLOC_020798
TCONS_00042315 lncRNA upstream 146347 5860140 ~ 5872272 (-) True XLOC_020798
TCONS_00042316 lncRNA upstream 176054 5889847 ~ 5894546 (-) False XLOC_020799
TCONS_00042317 lncRNA upstream 178953 5892746 ~ 5894628 (-) False XLOC_020799
TCONS_00040985 mRNA downstream 18766 5667371 ~ 5682494 (-) True XLOC_020791
TCONS_00040984 mRNA downstream 37906 5657022 ~ 5663354 (-) True XLOC_020790
TCONS_00040983 mRNA downstream 39471 5655756 ~ 5661789 (-) False XLOC_020790
TCONS_00040982 mRNA downstream 45580 5632029 ~ 5655680 (-) True XLOC_020789
TCONS_00040981 mRNA downstream 148253 5549734 ~ 5553007 (-) True XLOC_020787
TCONS_00040988 mRNA upstream 6027 5719820 ~ 5724131 (-) True XLOC_020792
TCONS_00040989 mRNA upstream 28380 5742173 ~ 5744491 (-) False XLOC_020794
TCONS_00040990 mRNA upstream 28433 5742226 ~ 5752009 (-) True XLOC_020794
TCONS_00040994 mRNA upstream 44297 5758090 ~ 5822147 (-) True XLOC_020796
TCONS_00040995 mRNA upstream 121900 5835693 ~ 5839686 (-) True XLOC_020797
TCONS_00040947 other downstream 801966 4819410 ~ 4899294 (-) False XLOC_020764
TCONS_00040949 other downstream 801966 4827956 ~ 4899294 (-) False XLOC_020764
TCONS_00040955 other downstream 802144 4898586 ~ 4899116 (-) True XLOC_020764
TCONS_00040930 other downstream 1388142 4311803 ~ 4313118 (-) True XLOC_020752
TCONS_00040924 other downstream 2020535 3595268 ~ 3680725 (-) True XLOC_020748
TCONS_00040991 other upstream 31510 5745303 ~ 5748548 (-) False XLOC_020795
TCONS_00040992 other upstream 32412 5746205 ~ 5749448 (-) False XLOC_020795
TCONS_00040993 other upstream 33808 5747601 ~ 5749450 (-) True XLOC_020795
TCONS_00040996 other upstream 157242 5871035 ~ 5894497 (-) False XLOC_020799
TCONS_00040997 other upstream 179676 5893469 ~ 5894628 (-) True XLOC_020799

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000030_10646148_10649874.mRNA True 2258 mRNA 0.45 3 CI01000030 10645873 ~ 10649937 (+)