RNA id: TCONS_00020235


Basic Information

Item Value
RNA id TCONS_00020235
length 937
RNA type mRNA
GC content 0.45
exon number 6
gene id XLOC_010226
representative True

Chromosome Information

Item Value
chromosome id NC_007127.7
NCBI id CM002900.2
chromosome length 55266484
location 45922175 ~ 45930077 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

GCAGTGTCGTATAGAGTGTTCTGCGCATGCTCACAGCCGCTCACTCGCTTCTCACTCACAAGCAAGCATCATGGCGGACGTACTGGATCTTCATGAAGCGGGAGGCGAAGACTTTCCTATGGACGAGGATGGCGATGAGAGCATTCATAAGTTAAAAGAGAAAGCCAAGAAGAGGAAAGGTCGTGGATTTGGATCTGAGGAAGGAGCCAGATCTAGAGTCAGAGAGGACTATGACACAGTAGAACAGGATGGAGATGAGCCTGGACCACAGAGATCTGTTGAAGGATGGATTCTGTTTGTGACCGGTGTTCACGAGGAGGCAACAGAGGAGGATGTCCACGACAAGTTTGCAGAGTTTGGAGAAATCAAGAACTTGCATTTAAATTTGGACAGGAGAACCGGTTACCTTAAGGGCTATGCATTGGTGGAGTACGAGACCTACAAAGAAGCACAGGCTGCAATGGAGGGTCTGAATGGTCAAGAACTTATGGGACAACCAATCAGTGTTGACTGGTGCTTTGTAAGGGGACCCCCGAAGAGCAAGAGGAGGGGTGGAAGGAGGCGCAGCAGGAGTCCTGACAGACGGCGACGCTGATTTTACCCCTGTTTGCCTCCGGTGTCTGTTTCCCAGCCGCTGTGGGATCATTTTTCAACACAGTTTGGAGTCAGATTGAAGTGTATCTCTTTAAATAAAGGTTTTAGTGGGTTTTTTCCTCGTAATTGTTAGTTTTTCAGCATCTGCCTGGTGGCATTTTGTTAATGAAGTTGCTGACACGTACATGTTAAACCTGTTGGTATTTTCAACaccattttatttactttttttttgtacaaagtgGAAGTTCACTTTAAAATGTATGTGGATTGACATGTATTCACTCATTGAAACTCGTTGTTGTGAGTAGTGATCTGTATATTTCCAATAAATTAATTTGGA

Function

GO:

id name namespace
GO:0000381 regulation of alternative mRNA splicing, via spliceosome biological_process
GO:0006396 RNA processing biological_process
GO:0006397 mRNA processing biological_process
GO:0006417 regulation of translation biological_process
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay biological_process
GO:0051028 mRNA transport biological_process
GO:0008380 RNA splicing biological_process
GO:0005634 nucleus cellular_component
GO:0035145 exon-exon junction complex cellular_component
GO:0016607 nuclear speck cellular_component
GO:0005681 spliceosomal complex cellular_component
GO:0005737 cytoplasm cellular_component
GO:0071006 U2-type catalytic step 1 spliceosome cellular_component
GO:0003676 nucleic acid binding molecular_function
GO:0003723 RNA binding molecular_function
GO:0003729 mRNA binding molecular_function

KEGG:

id description
ko03040 Spliceosome
ko03013 Nucleocytoplasmic transport
ko03015 mRNA surveillance pathway
ko03019 Messenger RNA biogenesis
ko03041 Spliceosome

ZFIN:

id description
ZDB-GENE-050306-51 Predicted to enable mRNA binding activity. Predicted to be involved in RNA splicing and regulation of alternative mRNA splicing, via spliceosome. Predicted to act upstream of or within mRNA metabolic process; mRNA transport; and regulation of translation. Predicted to be located in nucleus. Predicted to be part of U2-type catalytic step 1 spliceosome and exon-exon junction complex. Human ortholog(s) of this gene implicated in thrombocytopenia-absent radius syndrome. Orthologous to human RBM8A (RNA binding motif protein 8A).

Ensembl:

ensembl_id ENSDART00000018253

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00022027 lncRNA upstream 109851 45787042 ~ 45812324 (+) False XLOC_010225
TCONS_00022028 lncRNA upstream 109851 45797162 ~ 45812324 (+) True XLOC_010225
TCONS_00022026 lncRNA upstream 440327 45455980 ~ 45481848 (+) False XLOC_010220
TCONS_00022025 lncRNA upstream 440327 45455980 ~ 45481848 (+) False XLOC_010220
TCONS_00020221 lncRNA upstream 648456 45217307 ~ 45273719 (+) True XLOC_010217
TCONS_00022029 lncRNA downstream 58354 45988431 ~ 45990842 (+) True XLOC_010228
TCONS_00022030 lncRNA downstream 155313 46085390 ~ 46104010 (+) True XLOC_010229
TCONS_00022031 lncRNA downstream 339647 46269724 ~ 46270888 (+) True XLOC_010232
TCONS_00021750 lncRNA downstream 346867 46276944 ~ 46282156 (+) True XLOC_010233
TCONS_00022032 lncRNA downstream 625317 46555394 ~ 46569152 (+) True XLOC_010240
TCONS_00020232 mRNA upstream 139568 45739277 ~ 45782607 (+) False XLOC_010224
TCONS_00020233 mRNA upstream 139616 45739419 ~ 45782559 (+) False XLOC_010224
TCONS_00020231 mRNA upstream 143511 45739193 ~ 45778664 (+) False XLOC_010224
TCONS_00020234 mRNA upstream 143511 45746549 ~ 45778664 (+) True XLOC_010224
TCONS_00020230 mRNA upstream 187962 45693413 ~ 45734213 (+) True XLOC_010223
TCONS_00020236 mRNA downstream 885 45930962 ~ 45980841 (+) False XLOC_010227
TCONS_00020237 mRNA downstream 964 45931041 ~ 45982657 (+) True XLOC_010227
TCONS_00020238 mRNA downstream 70879 46000956 ~ 46091600 (+) False XLOC_010229
TCONS_00020239 mRNA downstream 70904 46000981 ~ 46082219 (+) False XLOC_010229
TCONS_00020240 mRNA downstream 181772 46111849 ~ 46202705 (+) False XLOC_010230
TCONS_00020229 other upstream 255323 45666735 ~ 45666852 (+) True XLOC_010222
TCONS_00020228 other upstream 333845 45588214 ~ 45588330 (+) True XLOC_010221
TCONS_00020217 other upstream 1217021 44704372 ~ 44705154 (+) True XLOC_010213
TCONS_00020216 other upstream 1234240 44683065 ~ 44687935 (+) True XLOC_010212
TCONS_00020214 other upstream 1316735 44605326 ~ 44605440 (+) True XLOC_010211
TCONS_00020265 other downstream 1082264 47012341 ~ 47012457 (+) True XLOC_010251
TCONS_00020272 other downstream 2093216 48023293 ~ 48023408 (+) True XLOC_010259
TCONS_00020273 other downstream 2228232 48158309 ~ 48158423 (+) True XLOC_010260
TCONS_00020274 other downstream 2326936 48257013 ~ 48257130 (+) True XLOC_010261
TCONS_00020297 other downstream 3617694 49547771 ~ 49547886 (+) True XLOC_010272

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000027_01499088_01500312.mRNA True 2115 mRNA 0.35 4 CI01000027 1499040 ~ 1502028 (-)
mexican tetra (Astyanax mexicanus) TU468779 True 706 lncRNA 0.48 6 NW_019172945.1 815162 ~ 822832 (+)