RNA id: TCONS_00003393


Basic Information

Item Value
RNA id TCONS_00003393
length 2300
lncRNA type inter_gene
GC content 0.34
exon number 2
gene id XLOC_001155
representative True

Chromosome Information

Item Value
chromosome id NC_007112.7
NCBI id CM002885.2
chromosome length 59578282
location 18933922 ~ 18936968 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

AATGATACAATTGTATTTTAATGGTAAGAATTAAAACAACCAATAAACAAACGCAAGAGAATTCATAAGCTCTCTTATTGGTTTCTGCAAAACAAAAGAATACGgggagagagaagaaaaaaaaaaaacataaatagtaAAACTGAGGTAACTGCTATTGTACCAAGcagggaaaaacaaaacaaaaaacctcCTATAACACAGAATGACGATGGTTAAGTAAGAGTAATGCACGTCTGTTTTTGCAAAGAATAAAGAATTCATAAGTTCGTGGTCGTCATGAATTCGATTATGACACTAAAGCGGACAACACTGGAGAATGGTTTAAAGGCATCTCTCATTAAGACACTGCAGGCTCTGAGACTAAAATCACACAAGTATATGACACTTTCTACACCAGTCATAGAGCCCACGTCATGCCACGCAGAGGCAGTTATATCCATTCATAATGACAACAATGCAGGACGTAAAACCATCATACagcatacataaaaacaaaccaacaaacaaacaaacaaacaccccCTTTTGGGTCGTAACGCATCTCAGGCATTCATTATAAAGTAACGCACATGGCTATGAATGGCTATAACAGCCTTATTGAGGCTGTATGAGTGGGTGCACTGGAAGGCAGTTTGAGtacagcaataaaaaaaagaagctaaCTGTATAGTGAGGGCAGTGACTAAACGACAAGAAACCGTTTACTAAAACCAGGAGCCTTTAGGGAATGATACTAACAACATTGCAATCTGTATTAGCCTTTTTTAGTCTGCAAACATTGCAAACAATATGATAACAACTCCTCTTTGAATGGGCATGTACGCATATTTTTGCTCTGATTACTACATTTTAAAGCATGCAAAatcaaataatgatttttttttttaaatcagagatAGCTGTGTTTATCTACTAGGTTAGCTGGTGAATGGATCACTTCTTAGGCAAAAACTGATATCTGATCTTGGGCTTAAAAATGATGAATTGCTATTTTTGGACACATAGGGTTAAGTTCATCTCAAAAtgaaatcctgtcatcatttgcAGACACTTACGTTGTTCTAATGTTTATTTGGAACACGAAGACATTTTAATCCAAGCAGATTTCTGCTCATATAttgacagttcactcaaaaacccAGACGCATTAGGAGATAAGttaatatcaatataaatggAGCCGTTTAATTTAAGTCTTTGAAGAAAACATGATCACTTTATACAATCAGCAGAAATAAATTAGACTTTTATTTGCATATAACTGTTGATCAGTAGACAATTCTGCAGCAATAAAATTTGGTCAAATTTGGAAGCACTaaaattaatgtgtgtgtgtgtgtgtgtgtcatgcgATATGCAAATAACCCCCTTCAAAAAAATCCCTTCATTGTATAATTTTTAAATCGAATAAAACGTTATATTTCCAGGTATGGATTATTGTTTTGACCGTTTCACGAATGGTTTATATTAAACTTTGAAATGTCAGAACTGAAAGCTttcatatttcattaaaaatatcctCTTATGAGTTTAAAAGAAGAAGGTCTTACAAGTGTGAAACAAcataagggagagtaaatgatgagcaaTTTACATTTCTGGACAATTAGACTTTTATTTGCATATAAACGTTAATCAGGAGACAATTTTGCAGCTTTAAAATTGGGTCAAATTAGGAACTGCTGAAATTAATGTGTGTCACGCGATATGCAAATAAcgcacaaaaatatttatttattgtataatgttcataaatttcaaaaatatataataaagccTTACATTTACAAGTATGGATTATTGTTTCGATTGCTTCACGAATGATTTAAAGCAAACATGTCAGAAATGAAAGCTTTCATATAGCATTAAATTTATCTTCTAATGTGTTTCAAACATGACAGAAGGTCTTACAGGTCTGAAACAACACAAGAATaatttaatgatgacagaatttacatgtCAGGACCAAACTAAACCCTAACAGCGAATATAACAGCCACCAACTCATAAAAATGGACACTATGGAGTTTTAAGTGCTAAAAGTGGTGATTTCTACATGATCAATCTGCAGGTCTGGCTAATAAATGgagtagcagtttttttttttatatgaagatAGCAAAAACGTGAAAGATTTCAAACAAAACTGGGAAAAAAATGAAGGCTGCAGCAGTATAAATCTATTAAGTAACTCAAAAATATTCCACTGCCCTCTAAACCAATCACATGTCATGTCAGTGCGCATCGTCAGCCAATCCCAGACGAGAATAAAAGTGAGAGTGAAAAGCCAGTGTTCT

Function

GO:

id name namespace
GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway biological_process
GO:0001704 formation of primary germ layer biological_process
GO:0048729 tissue morphogenesis biological_process
GO:0001706 endoderm formation biological_process
GO:0045995 regulation of embryonic development 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:0022603 regulation of anatomical structure morphogenesis biological_process
GO:0007492 endoderm development biological_process
GO:0080090 regulation of primary metabolic process biological_process
GO:0002009 morphogenesis of an epithelium 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:0043011 myeloid dendritic cell differentiation biological_process
GO:0051171 regulation of nitrogen compound metabolic process biological_process
GO:0006366 transcription by RNA polymerase II biological_process
GO:0036342 post-anal tail morphogenesis biological_process
GO:0002030 inhibitory G protein-coupled receptor phosphorylation biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0001773 myeloid dendritic cell activation biological_process
GO:0035295 tube development biological_process
GO:0009058 biosynthetic process biological_process
GO:0009059 macromolecule biosynthetic process biological_process
GO:0043049 otic placode formation biological_process
GO:1901576 organic substance biosynthetic process biological_process
GO:0009887 animal organ morphogenesis biological_process
GO:0009888 tissue development 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:0060429 epithelium development biological_process
GO:0031326 regulation of cellular biosynthetic process biological_process
GO:0006139 nucleobase-containing compound metabolic process biological_process
GO:0090092 regulation of transmembrane receptor protein serine/threonine kinase signaling pathway biological_process
GO:1903224 regulation of endodermal cell differentiation biological_process
GO:0009653 anatomical structure morphogenesis biological_process
GO:0051252 regulation of RNA metabolic process biological_process
GO:0006725 cellular aromatic 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:0048598 embryonic morphogenesis biological_process
GO:0010468 regulation of gene expression biological_process
GO:1904323 regulation of inhibitory G protein-coupled receptor phosphorylation biological_process
GO:1904325 positive regulation of inhibitory G protein-coupled receptor phosphorylation biological_process
GO:0044249 cellular biosynthetic process biological_process
GO:0009953 dorsal/ventral pattern formation biological_process
GO:0051281 positive regulation of release of sequestered calcium ion into cytosol biological_process
GO:0044271 cellular nitrogen compound biosynthetic process biological_process
GO:0007369 gastrulation biological_process
GO:0048646 anatomical structure formation involved in morphogenesis biological_process
GO:0060255 regulation of macromolecule metabolic process biological_process
GO:0003002 regionalization biological_process
GO:0007389 pattern specification process biological_process
GO:0010524 positive regulation of calcium ion transport into cytosol biological_process
GO:2001141 regulation of RNA biosynthetic process biological_process
GO:0032774 RNA biosynthetic process biological_process
GO:1903587 regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis biological_process
GO:1903589 positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis 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:0097028 dendritic cell differentiation biological_process
GO:0009790 embryo development biological_process
GO:0001702 gastrulation with mouth forming second biological_process
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0060182 apelin receptor activity 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: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_00001837 lncRNA downstream 122435 18810891 ~ 18811487 (-) False XLOC_001153
TCONS_00001839 lncRNA downstream 122438 18810894 ~ 18811484 (-) True XLOC_001153
TCONS_00001840 lncRNA downstream 122439 18810891 ~ 18811483 (-) False XLOC_001153
TCONS_00003392 lncRNA downstream 695982 18233995 ~ 18237940 (-) False XLOC_001144
TCONS_00003391 lncRNA downstream 695982 18233995 ~ 18237940 (-) False XLOC_001144
TCONS_00002942 lncRNA upstream 5431 18942399 ~ 18945609 (-) False XLOC_001156
TCONS_00003394 lncRNA upstream 6154 18943122 ~ 18946851 (-) False XLOC_001156
TCONS_00002943 lncRNA upstream 7495 18944463 ~ 18945315 (-) False XLOC_001156
TCONS_00002944 lncRNA upstream 8399 18945367 ~ 18946858 (-) True XLOC_001156
TCONS_00002945 lncRNA upstream 153451 19090419 ~ 19091229 (-) True XLOC_001158
TCONS_00001841 mRNA downstream 84893 18841462 ~ 18849029 (-) False XLOC_001154
TCONS_00001842 mRNA downstream 84967 18841636 ~ 18848955 (-) True XLOC_001154
TCONS_00001838 mRNA downstream 122405 18810891 ~ 18811517 (-) False XLOC_001153
TCONS_00001835 mRNA downstream 130003 18779168 ~ 18803919 (-) True XLOC_001152
TCONS_00001832 mRNA downstream 161681 18645348 ~ 18772241 (-) False XLOC_001151
TCONS_00001843 mRNA upstream 137358 19074326 ~ 19079957 (-) True XLOC_001157
TCONS_00001844 mRNA upstream 185952 19122920 ~ 19237612 (-) False XLOC_001160
TCONS_00001846 mRNA upstream 186642 19123610 ~ 19215336 (-) False XLOC_001160
TCONS_00001845 mRNA upstream 186642 19123610 ~ 19215336 (-) False XLOC_001160
TCONS_00001847 mRNA upstream 268229 19205197 ~ 19233890 (-) False XLOC_001160
TCONS_00001836 other downstream 122438 18810891 ~ 18811484 (-) False XLOC_001153
TCONS_00001833 other downstream 181458 18716178 ~ 18752464 (-) False XLOC_001151
TCONS_00001834 other downstream 192304 18726359 ~ 18741618 (-) True XLOC_001151
TCONS_00001826 other downstream 318948 18605635 ~ 18614974 (-) True XLOC_001150
TCONS_00001824 other downstream 346724 18584948 ~ 18587198 (-) True XLOC_001149
TCONS_00001850 other upstream 424237 19361205 ~ 19366174 (-) False XLOC_001163
TCONS_00001851 other upstream 432029 19368997 ~ 19402815 (-) True XLOC_001163
TCONS_00001874 other upstream 906266 19843234 ~ 19845380 (-) True XLOC_001174
TCONS_00001878 other upstream 1544141 20481109 ~ 20553129 (-) False XLOC_001178
TCONS_00001883 other upstream 1902514 20839482 ~ 20878076 (-) False XLOC_001182

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
tiger barb (Puntius tetrazona) TU247932 True 312 lncRNA 0.40 2 NC_056723.1 8212221 ~ 8212605 (+)
mexican tetra (Astyanax mexicanus) TU247932 True 1054 lncRNA 0.43 2 NC_035917.1 6478227 ~ 6498006 (+)