XLOC_028374 (rtcb)


Basic Information

Item Value
gene id XLOC_028374
gene name rtcb
gene type coding
species zebrafish (Danio rerio)
category of species model fish

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

Sequence

>TCONS_00055109
GAGAAAGTTCGCTGTCAAAATCTGCGTTGATAATTGACAATAAAAATGAGTCGCTCTTACAACGATGAGCTCCAGTATCtggataaaatacacaaaaactgCTGGCGGATCAAGAAGGGTTTCGTGCCGAATATGCTGGTGGAAGGAGTGTTTTATGTCAATGACCCGCTGGAAAAGCTGATGTTCGAGGAGCTGAGAAACGCCTGTCGCGGAGGAGGGTTTGGAGGTTTCTTACCTGCGATGAAGCAGATTGGGAATGTGGCCGCTCTGCCAGGAATCGTGCACCGGTCGATCGGTTTACCGGACGTTCACTCAGGATACGGATTCGCTATCGGGAACATGGCAGCGTTCGACATGGAGAATCCGGACGCAGTCGTCTCTCCAGgcggTGTGGGTTTCGATATTAACTGTGGTGTTCGTCTGCTGCGCACAAACCTGGATGAGGGCGACGTTCAGCCGGTGAAGGAGCAGCTGGCACAGTCTCTCTTCGACCACATCCCTGTCGGAGTCGGCTCCAAGGGCGTCATTCCTATGGGTGCAAAggacCTGGAGGAGGCGTTGGAGATGGGTGTGGACTGGTCTCTGAGGGAGGGATACGCCTGGGCGGAGGATAAAGAGCACTGTGAGGAGTACGGACGCATGCTGCAGGCCGACCCAAACAAAGTCTCCTCCAAAGCCAAGAAGAGAGGACTGCCACAGTTGGGAACTCTGGGTGCAGGAAACCACTACGCAGAGATTCAGGTGGTGGACGAGATCTACAATGATTACGCCGCCAAGAAGATGGGCATCGATCATAAAGGGCAGGTGTGTGTGATGATCCACAGCGGCAGCCGAGGACTCGGACATCAGGTGGCCACCGACGCCCTGGTGGCAATGGAGAAGGCCATGAAGCGCGACCGCATCACAGTGAACGACCGGCAGCTAGCGTGCGCGCGCATCACGTCAGAGGAGGGCCAGGATTATCTGAAGGGAATGGCGGCAGCAGGAAACTACGCCTGGGTCAACCGATCCTCCATGACCTTCCTCACACGACAGGCGTTCTCCAAAGTGTTCAGCACCACACCAGATGATCTGGACATGCACGTGATCTACGACGTCTCGCACAACATCGCCAAAGTGGAGGAGCACATGGTGGACGGCCGGCAGAAAACACTGCTGGTGCATAGGAAGGGCTCGACCAGAGCGTTTCCTCCACACCATCCACTCATACCTGTAGACTATCAGCTGACCGGTCAGCCAGTCCTGATTGGAGGAACCATGGGCACCTGCAGTTACGTGCTCACAGGCACAGAGCAGGGCATGACAGAGACGTTCGGCACCACATGTCACGGCGCTGGTCGAGCTTTATCCAGAGCCAAATCCAGACGCAACCTGGACTTCCAGGATGTTCTGGATAAACTGGCAGACATGGGCATCGCTATTAGGGTGGCGTCACCGAAGCTGGTGATGGAGGAGGCTCCTGAGTCCTACAAGAACGTGACAGACGTGGTGAACACATGCCATGATGCCGGCATCAGTAAAAAAGCCATCAAACTCAGACCCATCGCTGTGATTAAAGGTTAAACATCACAGCTGAAGAGCCGACATTCACACATTCTGCACTTACTACACCGGCTGAAGAGTCACCTGTGTTTGGTTTTGGGTGAAGGGTGCACAAGACATGTTtacgtcaaaataaaagtctccaTTATCA
>TCONS_00055110
CGCGAGTCGGCGTAACGTGTAGAGAAAGTTCGCTGTCAAAATCTGCGTTGATAATTGACAATAAAAATGAGTCGCTCTTACAACGATGAGCTCCAGTATCtggataaaatacacaaaaactgCTGGCGGATCAAGAAGGGTTTCGTGCCGAATATGCTGGTGGAAGGAGTGTTTTATGTCAATGACCCGCTGGAAAAGCTGATGTTCGAGGAGCTGAGAAACGCCTGTCGCGGAGGAGGGTTTGGAGGTTTCTTACCTGCGATGAAGCAGATTGGGAATGTGGCCGCTCTGCCAGGAATCGTGCACCGGTCGATCGGTTTACCGGACGTTCACTCAGGATACGGATTCGCTATCGGGAACATGGCAGCGTTCGACATGGAGAATCCGGACGCAGTCGTCTCTCCAGGTATGTGCTAATAATGTGCTTGTTCGTTATCCTGAGATATTTCATCATTAAatatccgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgttcaggcggTGTGGGTTTCGATATTAACTGTGGTGTTCGTCTGCTGCGCACAAACCTGGATGAGGGCGACGTTCAGCCGGTGAAGGAGCAGCTGGCACAGTCTCTCTTCGACCACATCCCTGTCGGAGTCGGCTCCAAGGGCGTCATTCCTATGGGTGCAAAG
>TCONS_00055111
ACGTGTAGAGAAAGTTCGCTGTCAAAATCTGCGTTGATAATTGACAATAAAAATGAGTCGCTCTTACAACGATGAGCTCCAGTATCtggataaaatacacaaaaactgCTGGCGGATCAAGAAGGGTTTCGTGCCGAATATGCTGGTAAAAGAGCTGTCAAAAACACACTAACTGAAAACATGTCGGCTTTACATTATCATCAAAATCAATGGTGTTTTATTAATTGGTGGAAGGAGTGTTTTATGTCAATGACCCGCTGGAAAAGCTGATGTTCGAGGAGCTGAGAAACGCCTGTCGCGGAGGAGGGTTTGGAGGTTTCTTACCTGCGATGAAGCAGATTGGGAATGTGGCCGCTCTGCCAGGAATCGTGCACCGGTCGATCGGTTTACCGGACGTTCACTCAGGATACGGATTCGCTATCGGGAACATGGCAGCGTTCGACATGGAGAATCCGGACGCAGTCGTCTCTCCAGgcggTGTGGGTTTCGATATTAACTGTGGTGTTCGTCTGCTGCGCACAAACCTGGATGAGGGCGACGT

Function

symbol description
rtcb 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).

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 ENSDARG00000101047

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00055109 False 1693 mRNA 0.54 12 676710 685412
TCONS_00055110 False 657 lncRNA 0.51 4 682961 685433
TCONS_00055111 True 541 nonsense_mediated_decay 0.48 5 683052 685419

Neighbor

gene id symbol gene type direction distance location
XLOC_028373 NA coding downstream 279891 393551 ~ 396819 (-)
XLOC_028372 dynlt1 coding downstream 286268 386435 ~ 390442 (-)
XLOC_028371 mrps10 coding downstream 345962 325028 ~ 330748 (-)
XLOC_028370 echdc3 coding downstream 389285 286425 ~ 287425 (-)
XLOC_028369 si:ch73-252i11.1 coding downstream 399629 269443 ~ 277081 (-)
XLOC_028375 CU855889.2 coding upstream 16179 701612 ~ 734347 (-)
XLOC_028376 NA coding upstream 38397 723830 ~ 732484 (-)
XLOC_028377 agbl5 coding upstream 52106 737539 ~ 760560 (-)
XLOC_028378 tmem214 coding upstream 78667 764100 ~ 779796 (-)
XLOC_028379 mapre3b coding upstream 98211 783644 ~ 797858 (-)
XLOC_028362 NA non-coding downstream 557516 116322 ~ 119194 (-)
XLOC_028360 NA non-coding downstream 575333 99991 ~ 101377 (-)
XLOC_028359 NA non-coding downstream 602102 73430 ~ 74608 (-)
XLOC_028358 NA non-coding downstream 604052 71463 ~ 72658 (-)
XLOC_028383 NA non-coding upstream 214529 899962 ~ 904022 (-)
XLOC_028385 NA non-coding upstream 234319 919752 ~ 921761 (-)
XLOC_028389 NA non-coding upstream 325527 1010960 ~ 1013095 (-)

Expression


Co-expression Network