RNA id: TCONS_00060794


Basic Information

Item Value
RNA id TCONS_00060794
length 727
lncRNA type retained_intron
GC content 0.39
exon number 2
gene id XLOC_031319
representative False

Chromosome Information

Item Value
chromosome id NC_007116.7
NCBI id CM002889.2
chromosome length 72500376
location 41639693 ~ 41645058 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

AAAGTTATGAAAGCAAACAAATATCCTTTAGGTTTTATAATCTATGATAAAGCTCAATGATAAAGTAAACCTCCTCTAGCACGAAGTGCTGTTTGAGCATGATTGCAAATGTGATCAGTTTTATACCGGAGTTCAGCAAACTAATTTATATTGAGTTGCATTTTAGACACAATGCTTTTTGAACTAATGAATGTGGTTGTAAGTTAAGGCAGAGTAcaatatttgtgtattttctAATAATAAATCAGGCACTTTGGATGAATTACTTGCATGAATGATTCGACGAGCCACTCATTAAGACACAGACTTCagtgtcatatttatatattaataaaataacttctATTAATATGATTCATGCAATCCCACAGAGACCAACTGAGCCTCGAGAATGATCACAGGAGAAGAACAACCAGTGAAATGAGCATGGCAAGTGTGGCCAGTTGCTCTACAATTCCACCAGAGGTGATCAGGCAGAAGGTGAAGAGACAGCTGACCAAACAACAGAAGGCGGCTCAGAGGAGACGTCTGCATAAGGGGGAAGCCAACCTGGTGACCAAGGAGAGGAGAGAGAACCAGAACAACATCAAGAGCAGTCTGGAGACTGCTTCCTTCTGGGGCTGAGGATCTACTCACTCAGCCTAATGGAGAAATGATCTCAGGACTGCTAACGgttttcacttgtgtgtgtatataaaattgattaataaaacatCTAAATCTGCAA

Function

GO:

id name namespace
GO:0044085 cellular component biogenesis biological_process
GO:0016070 RNA metabolic process biological_process
GO:0016072 rRNA metabolic process biological_process
GO:0071826 ribonucleoprotein complex subunit organization biological_process
GO:0022613 ribonucleoprotein complex biogenesis biological_process
GO:0022618 ribonucleoprotein complex assembly biological_process
GO:0065003 protein-containing complex assembly biological_process
GO:0071840 cellular component organization or biogenesis biological_process
GO:0034470 ncRNA processing biological_process
GO:0006364 rRNA processing biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0031290 retinal ganglion cell axon guidance biological_process
GO:0090305 nucleic acid phosphodiester bond hydrolysis biological_process
GO:0006396 RNA processing biological_process
GO:0030490 maturation of SSU-rRNA biological_process
GO:0006139 nucleobase-containing compound metabolic process biological_process
GO:0043933 protein-containing complex subunit organization biological_process
GO:0006725 cellular aromatic compound metabolic process biological_process
GO:1901360 organic cyclic compound metabolic process biological_process
GO:0010467 gene expression biological_process
GO:0044237 cellular metabolic process biological_process
GO:0006468 protein phosphorylation biological_process
GO:0044238 primary metabolic process biological_process
GO:0000460 maturation of 5.8S rRNA biological_process
GO:0042254 ribosome biogenesis biological_process
GO:0042255 ribosome assembly biological_process
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biological_process
GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biological_process
GO:0000469 cleavage involved in rRNA processing biological_process
GO:0000470 maturation of LSU-rRNA biological_process
GO:0042273 ribosomal large subunit biogenesis biological_process
GO:0042274 ribosomal small subunit biogenesis biological_process
GO:0000478 endonucleolytic cleavage involved in rRNA processing biological_process
GO:0000479 endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biological_process
GO:0043170 macromolecule metabolic process biological_process
GO:0034622 cellular protein-containing complex assembly biological_process
GO:0006807 nitrogen compound metabolic process biological_process
GO:0034641 cellular nitrogen compound metabolic process biological_process
GO:0016310 phosphorylation biological_process
GO:0034660 ncRNA metabolic process biological_process
GO:0046483 heterocycle metabolic process biological_process
GO:0090501 RNA phosphodiester bond hydrolysis biological_process
GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic biological_process
GO:0030684 preribosome cellular_component
GO:0030686 90S preribosome cellular_component
GO:0030687 preribosome, large subunit precursor cellular_component
GO:0032040 small-subunit processome cellular_component
GO:0030688 preribosome, small subunit precursor cellular_component
GO:0044422 obsolete organelle part cellular_component
GO:0044424 obsolete intracellular part cellular_component
GO:1990904 ribonucleoprotein complex cellular_component
GO:0044428 obsolete nuclear part cellular_component
GO:0070013 intracellular organelle lumen cellular_component
GO:0044446 obsolete intracellular organelle part cellular_component
GO:0044452 obsolete nucleolar part cellular_component
GO:0005829 cytosol cellular_component
GO:0032991 protein-containing complex cellular_component
GO:0005622 intracellular anatomical structure cellular_component
GO:0005634 nucleus cellular_component
GO:0031974 membrane-enclosed lumen cellular_component
GO:0031981 nuclear lumen cellular_component
GO:0043226 organelle cellular_component
GO:0043227 membrane-bounded organelle cellular_component
GO:0043228 non-membrane-bounded organelle cellular_component
GO:0043229 intracellular organelle cellular_component
GO:0043231 intracellular membrane-bounded organelle cellular_component
GO:0043232 intracellular non-membrane-bounded organelle cellular_component
GO:0043233 organelle lumen cellular_component
GO:0005730 nucleolus cellular_component
GO:0016740 transferase activity molecular_function
GO:0005524 ATP binding molecular_function
GO:0034511 U3 snoRNA binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0030515 snoRNA binding molecular_function
GO:0097159 organic cyclic compound binding molecular_function
GO:1901363 heterocyclic compound binding molecular_function
GO:0003723 RNA binding molecular_function
GO:0140098 catalytic activity, acting on RNA molecular_function
GO:0004672 protein kinase activity molecular_function
GO:0004674 protein serine/threonine kinase activity molecular_function
GO:0004386 helicase activity molecular_function
GO:0016301 kinase activity molecular_function

KEGG:

id description
ko00230 Purine metabolism
ko00240 Pyrimidine metabolism
ko03020 RNA polymerase
ko03008 Ribosome biogenesis in eukaryotes
ko04623 Cytosolic DNA-sensing pathway
ko05169 Epstein-Barr virus infection
ko05016 Huntington disease
ko01001 Protein kinases
ko03009 Ribosome biogenesis

ZFIN:

id description
ZDB-GENE-040426-2913 Predicted to enable protein kinase activity. Predicted to be involved in maturation of SSU-rRNA. Predicted to act upstream of or within protein phosphorylation and ribosome biogenesis. Predicted to be part of preribosome, small subunit precursor. Predicted to be active in cytosol and nucleus. Orthologous to human RIOK2 (RIO kinase 2).

Ensembl:

ensembl_id ENSDART00000137974

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00060790 lncRNA downstream 144890 41491802 ~ 41494803 (-) True XLOC_031315
TCONS_00061544 lncRNA downstream 165433 41464093 ~ 41474260 (-) True XLOC_031314
TCONS_00061543 lncRNA downstream 809860 40810788 ~ 40829833 (-) True XLOC_031306
TCONS_00060769 lncRNA downstream 925701 40584818 ~ 40713992 (-) False XLOC_031304
TCONS_00060771 lncRNA downstream 925806 40600199 ~ 40713887 (-) True XLOC_031304
TCONS_00062060 lncRNA upstream 444426 42085004 ~ 42091969 (-) True XLOC_031330
TCONS_00062061 lncRNA upstream 630457 42271035 ~ 42272962 (-) False XLOC_031334
TCONS_00060824 lncRNA upstream 630457 42271035 ~ 42273074 (-) False XLOC_031334
TCONS_00062062 lncRNA upstream 700047 42340625 ~ 42342427 (-) True XLOC_031337
TCONS_00062063 lncRNA upstream 705332 42345910 ~ 42347490 (-) True XLOC_031338
TCONS_00060793 mRNA downstream 1654 41582643 ~ 41638039 (-) True XLOC_031318
TCONS_00060792 mRNA downstream 78819 41542436 ~ 41560874 (-) True XLOC_031317
TCONS_00060791 mRNA downstream 108064 41521043 ~ 41531629 (-) True XLOC_031316
TCONS_00060788 mRNA downstream 144862 41485277 ~ 41494831 (-) False XLOC_031315
TCONS_00060787 mRNA downstream 332143 41260478 ~ 41307550 (-) True XLOC_031313
TCONS_00060797 mRNA upstream 4901 41645479 ~ 41709234 (-) True XLOC_031320
TCONS_00060798 mRNA upstream 159504 41800082 ~ 41804398 (-) True XLOC_031321
TCONS_00060799 mRNA upstream 186380 41826958 ~ 41831646 (-) False XLOC_031322
TCONS_00060800 mRNA upstream 187042 41827620 ~ 41841892 (-) False XLOC_031322
TCONS_00060801 mRNA upstream 188862 41829440 ~ 41845116 (-) False XLOC_031322
TCONS_00060789 other downstream 151714 41485282 ~ 41487979 (-) False XLOC_031315
TCONS_00060786 other downstream 456441 41183136 ~ 41183252 (-) True XLOC_031312
TCONS_00060785 other downstream 496925 41133345 ~ 41142768 (-) True XLOC_031311
TCONS_00060783 other downstream 496927 41124755 ~ 41142766 (-) False XLOC_031311
TCONS_00060796 other upstream 1727 41642305 ~ 41643920 (-) True XLOC_031319
TCONS_00060805 other upstream 212860 41853438 ~ 41855394 (-) True XLOC_031323
TCONS_00060822 other upstream 611631 42252209 ~ 42253313 (-) True XLOC_031333
TCONS_00060825 other upstream 631393 42271971 ~ 42272030 (-) False XLOC_031334
TCONS_00060826 other upstream 631496 42272074 ~ 42272162 (-) True XLOC_031334

Expression Profile

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