RNA id: TCONS_00017760


Basic Information

Item Value
RNA id TCONS_00017760
length 696
lncRNA type retained_intron
GC content 0.40
exon number 5
gene id XLOC_009008
representative True

Chromosome Information

Item Value
chromosome id NC_007126.7
NCBI id CM002899.2
chromosome length 48040578
location 5898410 ~ 5901982 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

GATAGAACATTTAAGCTTGCTTCAGTGTTTCCTAGACCTGTTTTTTTACTCTTTACTAATCGGTGCTGAAGCTGCTGTAATTTATTTCCTATTTTTGTTCTAAAAGCACACACGCTTTAAGCAGCCATGCCTAAAAGGAGCAAAGCTAACAATGACACTGAAGCAGCTGGGGTAAGTTTGCCTCTTTTACTGTGGCATTTAACACATTCTTGAACACAACTGTTACAAGTTTGTCTTGTTTTCTTAATTTCTTGTTTTCTCCACATAAACAGCCCAAGAGACGGTCTGAGAGACTTCAGGGTAAACCACAAACGCCAAAGTCTGAGCCCAAGCCAAAGAAAGCACCTGCACGAGGAAAGAAGGCCAAGGATGTAGAAAAGGCCAAACCAGAAGAGAAGAAAGAGGACGCAAAGCCAGAAGCCGAGGAGAAAACTCCAGCGGAGAACGGAGAGACCAAAGCTGATGAAaacAACGGAGAGGCAGGAGGTGACGACGAAAAAGCTGAATAACGTTAATATCATTTCACCAGAGCTCCCATACCTCTTTTCTTGTACAATACAGAGGAATATTTTTATTgactattttctaaaaaaaaaaaaggttttgttttagtAGTTCAAAAATTAGAAGCTCGTTTTATAGACGATGTTCAAGAGAAAAGCCTTAGAAGAGAGATTCCATCTTTTCCCACTCCAG

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: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: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: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: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:0032991 protein-containing complex 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: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

KEGG:

id description
ko00230 Purine metabolism
ko00240 Pyrimidine metabolism
ko03020 RNA polymerase
ko03230 Viral genome structure
ko04623 Cytosolic DNA-sensing pathway
ko05164 Influenza A
ko05169 Epstein-Barr virus infection
ko05016 Huntington disease
ko03200 Viral proteins

ZFIN:

id description
ZDB-GENE-131120-172 Predicted to enable nucleosomal DNA binding activity. Predicted to be located in chromatin and nucleus.

Ensembl:

ensembl_id ENSDART00000155971

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00017753 lncRNA downstream 101268 5794963 ~ 5797918 (-) True XLOC_009005
TCONS_00017751 lncRNA downstream 107855 5787186 ~ 5791331 (-) False XLOC_009005
TCONS_00018811 lncRNA downstream 681480 5215808 ~ 5217706 (-) True XLOC_008989
TCONS_00018810 lncRNA downstream 696019 5202251 ~ 5203167 (-) True XLOC_008986
TCONS_00017703 lncRNA downstream 1413319 4445060 ~ 4485867 (-) True XLOC_008974
TCONS_00017775 lncRNA upstream 1066903 6968381 ~ 6976921 (-) False XLOC_009014
TCONS_00017779 lncRNA upstream 1130619 7032097 ~ 7034722 (-) True XLOC_009016
TCONS_00019120 lncRNA upstream 1162990 7064468 ~ 7065313 (-) True XLOC_009017
TCONS_00019121 lncRNA upstream 2448551 8350029 ~ 8394601 (-) True XLOC_009023
TCONS_00019122 lncRNA upstream 2698113 8599591 ~ 8602094 (-) True XLOC_009025
TCONS_00017756 mRNA downstream 4062 5887848 ~ 5895124 (-) True XLOC_009007
TCONS_00017755 mRNA downstream 6536 5828994 ~ 5892650 (-) False XLOC_009007
TCONS_00017754 mRNA downstream 84180 5803458 ~ 5815006 (-) True XLOC_009006
TCONS_00017749 mRNA downstream 100003 5784212 ~ 5799183 (-) False XLOC_009005
TCONS_00017761 mRNA upstream 236945 6138423 ~ 6247775 (-) False XLOC_009009
TCONS_00017762 mRNA upstream 238220 6139698 ~ 6404443 (-) True XLOC_009009
TCONS_00017763 mRNA upstream 613486 6514964 ~ 6615555 (-) False XLOC_009010
TCONS_00017764 mRNA upstream 613922 6515400 ~ 6650993 (-) True XLOC_009010
TCONS_00017765 mRNA upstream 936561 6838039 ~ 6863317 (-) False XLOC_009011
TCONS_00017752 other downstream 103771 5789338 ~ 5795415 (-) False XLOC_009005
TCONS_00017735 other downstream 516006 5383062 ~ 5383180 (-) True XLOC_008997
TCONS_00017702 other downstream 1416956 4435465 ~ 4482230 (-) False XLOC_008974
TCONS_00017700 other downstream 1417039 4426494 ~ 4482147 (-) False XLOC_008974
TCONS_00017694 other downstream 1533914 4365158 ~ 4365272 (-) True XLOC_008973
TCONS_00017769 other upstream 1025540 6927018 ~ 6946091 (-) False XLOC_009012
TCONS_00017770 other upstream 1037410 6938888 ~ 6940927 (-) True XLOC_009012
TCONS_00017772 other upstream 1047193 6948671 ~ 6966239 (-) False XLOC_009013
TCONS_00017773 other upstream 1047415 6948893 ~ 6966245 (-) False XLOC_009013
TCONS_00017778 other upstream 1107344 7008822 ~ 7008938 (-) True XLOC_009015

Expression Profile

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