RNA id: TCONS_00020138


Basic Information

Item Value
RNA id TCONS_00020138
length 2194
RNA type mRNA
GC content 0.49
exon number 6
gene id XLOC_010153
representative False

Chromosome Information

Item Value
chromosome id NC_007127.7
NCBI id CM002900.2
chromosome length 55266484
location 40131464 ~ 40339027 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

AGTTACCAGACGAGCACACGAGCTGAGAGCAGGCGAGAGATAGTGAATTGCTCAACCGTGAAACTGTGAGCTATCGAGACTGAATAGAGAAAAGCGACGCTATTTACAAATCAGGTTTCACTGAAAAGTTCTTCGAGATGCTGTGATGAGGATGACGCGAGGACCTCCTACACGTCAAGCtcaataaataaagtaaccttCACACCTGGACGTGTCGTGCTGGATCACAGAGGGGAATACATACAGTCATTCGGGAAGACAATCCAACTTTTTTCTCACCATGCCAATTTAATTTGCTCGCCTCCTCCCCATCTTTACGTTTTGCGCTGGATGGAGAACTAGCACTTTTTCACTGTTTCCATGGAATGAGTGGCTCTCTCTTTGGATATCTCACAGTGGCACATATGTGGATTGCCTCCAATATGTTACTGCCGAATCGGCCCAGGTGCATATGGGCCATTGAAAATTCTCTTTCTTTTGCGCGTGAGCACAACTGGGGCTTCTGCCCGGTTTAGGAATAACATATTGAGTATTGCACACATCACAGTGCGATAAGCGACATTGAAATTGACAAGACAAGCATCATTCCCCTGATTACTATGCAATTGCAACTGATCTCCATTGTTTTGATCTTGCATTTTATGGAATACACAAACTGTCAGCATCACGGCTCCAGGCACCGGGGAAACAAACAGGTATCAGGCGTGAGCTCCCAGGGCTGCCAGGGAGGCTGTCAGACCTGCTCGGTTTACAATGGCTGTCTGACCTGCAAACCCAAGCTTTTTATTCACCTGGAGAGGGACGGGATGAGGCAGATCGGAGTGTGCCTGGCCTCCTGCCCCAATGGTTTCTACGGCACACGTTCCCCCGACAGGAACGACTGCATAAAGTGTGGGTCAGAGTGCGACTCGTGCTTTAACAGGAACTTTTGCCTGCGCTGCAGAGCAGGATCCTACTTGCACAAGGGCAAGTGCATGGAGAGCTGTCCAGATGGGCTGGTGCCGAGCGATACCAAGAAAGAGTGTGTTGCTGCATGTCCAGCGCTCTGTGACTTGTGTCAGAACAGTGACACGTGTACGAGGTGTGTGTCGGGACACTTCCTTCATGCAGGGCAATGCCATCATGTCTGTCCTGATGAATTTGAGCCAAATGACTCAATGGAGTGCATTCCGACAGTGCACTGTGAAGTGAGCGAGTGGAGCGAGTGGGGCACCTGCTCGCGCTCGGGAAAAACCTGTGGCTTCAAATGGGGTGAAGAAACAAGGACCCGGAAGGTCCTACAGAATCCTTCTCCAATGGGGAGCCCATGCCCTCCAACTTCTGAAAAGAGGGAATGCTTTGTCAAAAAGAAGAGATGTAAGCCGCCGAAAGGCCAGCGGCGAGGAGAGAAGAAAAAACGCTTTAACCTGCAAGAGAAAGTGACTGCAGAGGCCCGTCGAGAGAGGAAGAGGGAACGAGAGAAGGAGACAATCGACCGAGAGGAATCCGAAAGCAGGAACAAAACAGAACAGCGCCGCCGCAGGGACCAGAGCAGAGACGCTGGAACAGTATAGACAGATGCTGCTCCTCATTGCTCCTCTGCCTTTCTTTCCTCTATCAGTCCATGTCACCCCCTCACCCTCTTATCCCCTCGCCGAGGGGGTGTTGCTGCTACCTGTATAATTTAAACgtatactgtatatgcacatGAGAGAGGGGCGCATTGCAGACAGTGAGGACCTTCACCCCCTCGGGCCCCGTCTGGTGCTGGATTGAGGCTGAACTGTGTAACAGGGGCCAGGAATGTCCTAAGATCCGTGgaatggtttatttttttaaacgggGTCCAGGTACAGCACTGCATCGTGGTTTGAATGTAGGTTTTTAAGACATTAAAGTAGAGTTTTTGTATAAACGTCTGTATTTTTTTGGAGGAGGGCGGGGGTtgagtaaattaaaattaaatgagcaTGCTTACCGTCGCCACGGACAGCCTGAGACTGCATGTGGATGGGTGTATGAACTGGCTTTCTTCATACTGGATGAGCGACAACAATCTTCGCCGCAACAGTGTATTAACTTTTCGTTCCATTCTCTCTCCAAACAAAGTGTTGATTTGCCTGTCTGTATAAACAGGATCCGAGCTTTCCATCGAAGCCATCTGACCAGAAATCAAAAGCACCTGtatgtcaaataaacaaataccaaGTTTGTA

Function

GO:

id name namespace
GO:0016070 RNA metabolic process biological_process
GO:0016071 mRNA metabolic process biological_process
GO:0035282 segmentation biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0000375 RNA splicing, via transesterification reactions biological_process
GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile biological_process
GO:0006396 RNA processing biological_process
GO:0006397 mRNA processing biological_process
GO:0000398 mRNA splicing, via spliceosome biological_process
GO:0006139 nucleobase-containing compound metabolic process 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:0044238 primary metabolic process biological_process
GO:0071704 organic substance metabolic process biological_process
GO:0043170 macromolecule metabolic process biological_process
GO:0006807 nitrogen compound metabolic process biological_process
GO:0034641 cellular nitrogen compound metabolic process biological_process
GO:0046483 heterocycle metabolic process biological_process
GO:0008380 RNA splicing biological_process
GO:0071013 catalytic step 2 spliceosome 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:0044451 obsolete nucleoplasm part cellular_component
GO:0044464 obsolete cell part cellular_component
GO:0000974 Prp19 complex cellular_component
GO:0030532 small nuclear ribonucleoprotein complex cellular_component
GO:0032991 protein-containing complex cellular_component
GO:0005622 intracellular anatomical structure cellular_component
GO:0005623 obsolete cell cellular_component
GO:0005634 nucleus cellular_component
GO:0005654 nucleoplasm cellular_component
GO:0016607 nuclear speck cellular_component
GO:0005681 spliceosomal complex cellular_component
GO:0005684 U2-type spliceosomal complex cellular_component
GO:0031974 membrane-enclosed lumen cellular_component
GO:0097525 spliceosomal snRNP complex cellular_component
GO:0031981 nuclear lumen cellular_component
GO:0043226 organelle cellular_component
GO:0043227 membrane-bounded organelle cellular_component
GO:0043229 intracellular organelle cellular_component
GO:0043231 intracellular membrane-bounded organelle cellular_component
GO:0043233 organelle lumen cellular_component
GO:0008139 nuclear localization sequence binding molecular_function
GO:0017069 snRNA binding molecular_function
GO:0003676 nucleic acid 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:0061608 nuclear import signal receptor activity molecular_function

KEGG:

id description
ko00230 Purine metabolism
ko00240 Pyrimidine metabolism
ko03020 RNA polymerase
ko03230 Viral genome structure
ko05164 Influenza A
ko03200 Viral proteins

ZFIN:

id description
ZDB-GENE-030131-9814 Predicted to enable heparin binding activity. Acts upstream of or within negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification; negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation; and posterior lateral line neuromast development. Predicted to be located in extracellular region. Is expressed in several structures, including digestive system; endoderm; forebrain neural keel; nervous system; and presumptive telencephalon. Orthologous to human RSPO3 (R-spondin 3).

Ensembl:

ensembl_id ENSDART00000058578

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00020133 lncRNA upstream 147374 40131464 ~ 40153682 (+) False XLOC_010153
TCONS_00020135 lncRNA upstream 147374 40131580 ~ 40153682 (+) False XLOC_010153
TCONS_00022006 lncRNA upstream 186249 40082902 ~ 40114807 (+) True XLOC_010152
TCONS_00022004 lncRNA upstream 219000 40077311 ~ 40082056 (+) False XLOC_010151
TCONS_00020143 lncRNA downstream 7457 40346484 ~ 40354078 (+) False XLOC_010157
TCONS_00020153 lncRNA downstream 241473 40580500 ~ 40583150 (+) True XLOC_010161
TCONS_00022007 lncRNA downstream 534214 40873241 ~ 40893518 (+) True XLOC_010162
TCONS_00021742 lncRNA downstream 602710 40941737 ~ 40945757 (+) False XLOC_010163
TCONS_00021743 lncRNA downstream 602725 40941752 ~ 40943109 (+) False XLOC_010163
TCONS_00020137 mRNA upstream 80136 40217043 ~ 40220920 (+) True XLOC_010155
TCONS_00020128 mRNA upstream 226911 40043673 ~ 40074145 (+) False XLOC_010150
TCONS_00020129 mRNA upstream 226914 40043707 ~ 40074142 (+) False XLOC_010150
TCONS_00020127 mRNA upstream 269277 40024883 ~ 40031779 (+) True XLOC_010149
TCONS_00020123 mRNA upstream 717388 39485608 ~ 39583668 (+) True XLOC_010141
TCONS_00020140 mRNA downstream 1195 40340222 ~ 40345372 (+) False XLOC_010156
TCONS_00020141 mRNA downstream 1496 40340523 ~ 40344211 (+) True XLOC_010156
TCONS_00020145 mRNA downstream 124338 40463365 ~ 40464426 (+) True XLOC_010158
TCONS_00020146 mRNA downstream 169855 40508882 ~ 40541981 (+) True XLOC_010159
TCONS_00020147 mRNA downstream 221595 40560622 ~ 40569769 (+) False XLOC_010160
TCONS_00020136 other upstream 117197 40183743 ~ 40183859 (+) True XLOC_010154
TCONS_00020126 other upstream 289065 40011869 ~ 40011991 (+) True XLOC_010148
TCONS_00020117 other upstream 1142874 39147002 ~ 39158182 (+) False XLOC_010137
TCONS_00020107 other upstream 1904261 38394413 ~ 38396795 (+) True XLOC_010132
TCONS_00020102 other upstream 1948778 38350723 ~ 38352278 (+) False XLOC_010130
TCONS_00020142 other downstream 7420 40346447 ~ 40347376 (+) False XLOC_010157
TCONS_00020144 other downstream 7568 40346595 ~ 40348954 (+) True XLOC_010157
TCONS_00020150 other downstream 237652 40576679 ~ 40585776 (+) False XLOC_010161
TCONS_00020157 other downstream 703283 41042310 ~ 41054232 (+) False XLOC_010166
TCONS_00020166 other downstream 1207736 41546763 ~ 41548437 (+) True XLOC_010175

Expression Profile

//

Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000016_00601605_00607255.mRNA True 1910 mRNA 0.43 6 CI01000016 600622 ~ 607255 (-)