RNA id: TCONS_00055110


Basic Information

Item Value
RNA id TCONS_00055110
length 657
lncRNA type retained_intron
GC content 0.51
exon number 4
gene id XLOC_028374
representative False

Chromosome Information

Item Value
chromosome id NC_007115.7
NCBI id CM002888.2
chromosome length 78093715
location 676710 ~ 685433 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CGCGAGTCGGCGTAACGTGTAGAGAAAGTTCGCTGTCAAAATCTGCGTTGATAATTGACAATAAAAATGAGTCGCTCTTACAACGATGAGCTCCAGTATCtggataaaatacacaaaaactgCTGGCGGATCAAGAAGGGTTTCGTGCCGAATATGCTGGTGGAAGGAGTGTTTTATGTCAATGACCCGCTGGAAAAGCTGATGTTCGAGGAGCTGAGAAACGCCTGTCGCGGAGGAGGGTTTGGAGGTTTCTTACCTGCGATGAAGCAGATTGGGAATGTGGCCGCTCTGCCAGGAATCGTGCACCGGTCGATCGGTTTACCGGACGTTCACTCAGGATACGGATTCGCTATCGGGAACATGGCAGCGTTCGACATGGAGAATCCGGACGCAGTCGTCTCTCCAGGTATGTGCTAATAATGTGCTTGTTCGTTATCCTGAGATATTTCATCATTAAatatccgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgttcaggcggTGTGGGTTTCGATATTAACTGTGGTGTTCGTCTGCTGCGCACAAACCTGGATGAGGGCGACGTTCAGCCGGTGAAGGAGCAGCTGGCACAGTCTCTCTTCGACCACATCCCTGTCGGAGTCGGCTCCAAGGGCGTCATTCCTATGGGTGCAAAG

Function

GO:

id name namespace
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation biological_process
GO:0006396 RNA processing biological_process
GO:0000971 tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate biological_process
GO:0008033 tRNA processing biological_process
GO:0072669 tRNA-splicing ligase complex cellular_component
GO:0005634 nucleus cellular_component
GO:0005737 cytoplasm cellular_component
GO:0008452 RNA ligase activity molecular_function
GO:0005525 GTP binding molecular_function
GO:0046872 metal ion binding molecular_function
GO:0003972 RNA ligase (ATP) activity molecular_function
GO:0000166 nucleotide binding molecular_function
GO:0016874 ligase activity molecular_function

KEGG:

id description
ko01501 beta-Lactam resistance
ko03016 Transfer RNA biogenesis

ZFIN:

id description
ZDB-GENE-040426-2096 Predicted to enable RNA ligase (ATP) activity. Predicted to be involved in tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate. Predicted to act upstream of or within tRNA processing. Predicted to be located in cytoplasm. Predicted to be part of tRNA-splicing ligase complex. Predicted to be active in nucleus. Orthologous to human RTCB (RNA 2',3'-cyclic phosphate and 5'-OH ligase).

Ensembl:

ensembl_id ENSDART00000169470

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00057975 lncRNA downstream 286142 393551 ~ 396819 (-) True XLOC_028373
TCONS_00055106 lncRNA downstream 352248 329771 ~ 330713 (-) True XLOC_028371
TCONS_00057305 lncRNA downstream 545204 134963 ~ 137757 (-) True XLOC_028364
TCONS_00057304 lncRNA downstream 563767 116322 ~ 119194 (-) True XLOC_028362
TCONS_00057974 lncRNA downstream 581584 99991 ~ 101377 (-) True XLOC_028360
TCONS_00055112 lncRNA upstream 16179 701612 ~ 734347 (-) True XLOC_028375
TCONS_00057306 lncRNA upstream 38397 723830 ~ 732484 (-) True XLOC_028376
TCONS_00055114 lncRNA upstream 65857 751290 ~ 753073 (-) True XLOC_028377
TCONS_00055116 lncRNA upstream 78963 764396 ~ 769820 (-) False XLOC_028378
TCONS_00055117 lncRNA upstream 83610 769043 ~ 769631 (-) False XLOC_028378
TCONS_00055107 mRNA downstream 292519 386435 ~ 390442 (-) False XLOC_028372
TCONS_00055108 mRNA downstream 292530 387143 ~ 390431 (-) True XLOC_028372
TCONS_00055105 mRNA downstream 352213 325028 ~ 330748 (-) False XLOC_028371
TCONS_00055104 mRNA downstream 395536 286425 ~ 287425 (-) True XLOC_028370
TCONS_00055103 mRNA downstream 405880 269443 ~ 277081 (-) True XLOC_028369
TCONS_00055113 mRNA upstream 52106 737539 ~ 760560 (-) False XLOC_028377
TCONS_00055115 mRNA upstream 78667 764100 ~ 779796 (-) False XLOC_028378
TCONS_00055119 mRNA upstream 98211 783644 ~ 797858 (-) False XLOC_028379
TCONS_00055120 mRNA upstream 99869 785302 ~ 789645 (-) False XLOC_028379
TCONS_00055121 mRNA upstream 101633 787066 ~ 797831 (-) True XLOC_028379
TCONS_00055123 other upstream 118714 804147 ~ 808453 (-) True XLOC_028380
TCONS_00055131 other upstream 251796 937229 ~ 948842 (-) True XLOC_028386
TCONS_00055166 other upstream 1375091 2060524 ~ 2162724 (-) False XLOC_028412
TCONS_00055185 other upstream 1989673 2675106 ~ 2686090 (-) False XLOC_028423
TCONS_00055220 other upstream 3807133 4492566 ~ 4496791 (-) True XLOC_028449

Expression Profile

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