RNA id: TCONS_00055162


Basic Information

Item Value
RNA id TCONS_00055162
length 2160
RNA type mRNA
GC content 0.54
exon number 10
gene id XLOC_028411
representative False

Chromosome Information

Item Value
chromosome id NC_007115.7
NCBI id CM002888.2
chromosome length 78093715
location 2041067 ~ 2059302 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CACCCGTTGGCGTCTCTTCTTCACGCGCAGTGAGAGCACCGAGGAGGAGGAGGGAAACAGAAAATGGCGGACGGTGTTGACCACATCGATATTTACGCGGATGTAGAAGAAGAATTTAACCAGGAGTCGGATTATCCTGTTCATGACCAGATTGACCTGTATGACGATGTCATCTCGCCATCTGCCAACAACGGGGACGCACCCGAGGACCGAGATTACCTGGATTCCCTTCCTGCACCTGGAGGCAACGAGGGCTCCAAAGGGGCTCCAGCTAATGTCGTCTACACCTACAATGGCAAACGGATCGCTCTGTACATCGGAAACCTCACATGGtgGACCACTGATGAAGATTTAACAGATGCCATTCGCTCAATAGGCATCAATGATGTGCTGGAGATCAAGTTTTTTGAGAACAGAGCAAATGGCCAGTCTAAAGGGTTTGCTCTGGTCTGCGTGGGATCAGATTCCTCTTCCAGGAAGCTCATGGATCTGTTGTCTAAACGGGAGCTGCATGGACAAAACCCCATCGTCACCCCTTGCAACAAACAGTCTCTCAGTCAGTTCGAGATGCAGTCACGAAAAAGCACACAGTCAGGACAGATGTCAGGAGAGGGGAAGGCTGGTCCTCCAGGCTCAGGATCTCGAGGTGGAGGATTCCCTCCTGGCAAAGGTCAGAGACGCTTTCCTGGCCCACCTGGACAAGGAGACCGCTTCCCTGGACCGGTTGGACCTGGCGGTCCTCCACCACACTTCCCAGGTATGCAGGGCCCACCACGTCTTCCCTCTGGCCCACCTGGGCCCCTGGGACCTCCAGGCCCCCCTCCACCTGGACAAGGTCTGCCTCCTCCCCTCGGCGGACCCCCTAACAGAGGAGACCGTCCTCCTCCACCTGTCTTGTTTCCTGGTCAGTTCGGGCAACCCCCAATGGGCCCGATGCCTCCTGGGCCTCCCCCACCAGGATACGGGCCTCCCCCAGGCCCCCCTCCACCTCAGCAGGGACCACCCCCTCCAGGACCCTTCCCTCCCCGTCCACCTGGGCCCTTAGGACCCCCGCTTGGCCTCGCACCCCCACCACACATGCAGGGACCCCCACCTGGAGGCCCACCGCCGGCTCCTCACGTCAACCCGGCCTTCTTCCCACCACCTGGAAACAACATGCCATCATCTGACGGCAGAGGACCCCCACCTGGAGACCCGTACGGCCGCCCACCTCCTTATGACAGAGACTTCCCTGGTGGCAGGGACATGGATGCGTCTCGCACTCCCCTGAGCGAAGCTGAGTTTGAGGAGATCATGAACCGGAACAGAGCGATTTCCAGCAGCGCTATTTCAAGGGCCGTTTCTGATGCCAGTGCAGCTGATTACGGCAGTGCTATAGAGACTCTGGTGACGGCCATCTCTCTGATCAAGCAGTCGAAGGTTTCTGCTGACGACCGCTGCAAAGTTCTCATCAGCTCACTGCAGGACTGCTTGCATGGAATCGAGTCCAAATCGTATGGCTCTGTGGCAGGCCGACGGGAGCGGTCCAGGGAGAGAGATCACAGTCGCTCTCGTGAGAAGAGCCGCCGGCACAAATCTCGCAGTCGAGACCGGCATGAGGATTACTACCGGGAGCGCAGCCGAGAGAGAGACCGCCATCGTGAGCGAGACAGAGACCGCGAGAGAGACAGAGAACGCGAGAGGGAATATCGCCACCGTTAATAGGAGAAGAAGCTGAAcgcaagaggaggaggaggagacgcCAGGAGCAACGAGGATTCatcgcgcacacacaaacaccgtCACGGAGAGCGCCGGACTCCGGACACACTAAAAAAAGTAGAGTTCTGTACAATACTATATACTCACTCTCTTAATTCCCTGCAGCtctttttattttgtacttttatttggAAGTAGCTGTGTGCTTAAGTCAGTTCAGCTTGTTTTGGCCAAGGAAGTGAATTATTTGCCTGCtcgttcaaaaaaagaaaaaaatacacacacacaactttcCGACTGCTATAATGTTGTAAATTGTCAGTTAGCTAGATTTGTTTTTATAGGATCCTTTCTTTCGTTTCGTGTTTCTTCCCTCATTTCCCCCCCTTCCCATTATCCATATAATGTTTGTAAGTGTCTTTTGGCTTGATTATTAAATAGAATCTGTGTTGTAATAAA

Function

GO:

id name namespace
GO:0110104 mRNA alternative polyadenylation biological_process
GO:0046833 positive regulation of RNA export from nucleus biological_process
GO:1990120 messenger ribonucleoprotein complex assembly biological_process
GO:0006397 mRNA processing biological_process
GO:0051290 protein heterotetramerization biological_process
GO:0042382 paraspeckles cellular_component
GO:0005849 mRNA cleavage factor complex cellular_component
GO:0035061 interchromatin granule cellular_component
GO:0005634 nucleus cellular_component
GO:0016607 nuclear speck cellular_component
GO:0005726 perichromatin fibrils cellular_component
GO:0005737 cytoplasm cellular_component
GO:0003676 nucleic acid binding molecular_function
GO:0003723 RNA binding molecular_function
GO:0003729 mRNA binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-030131-5277 Predicted to enable mRNA binding activity. Predicted to be involved in mRNA alternative polyadenylation; positive regulation of RNA export from nucleus; and protein-containing complex assembly. Predicted to act upstream of or within mRNA processing. Located in paraspeckles. Is expressed in several structures, including blastomere; central nervous system; digestive system; eye; and yolk. Orthologous to human CPSF6 (cleavage and polyadenylation specific factor 6).

Ensembl:

ensembl_id ENSDART00000129521

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00057986 lncRNA downstream 66075 1942033 ~ 1979057 (-) False XLOC_028408
TCONS_00057985 lncRNA downstream 66145 1916275 ~ 1978987 (-) False XLOC_028408
TCONS_00057987 lncRNA downstream 70068 1974147 ~ 1975064 (-) True XLOC_028408
TCONS_00057308 lncRNA downstream 128566 1915786 ~ 1916566 (-) False XLOC_028408
TCONS_00057984 lncRNA downstream 189361 1848660 ~ 1855771 (-) True XLOC_028406
TCONS_00057309 lncRNA upstream 332776 2392072 ~ 2397407 (-) False XLOC_028417
TCONS_00057988 lncRNA upstream 386461 2445757 ~ 2479720 (-) False XLOC_028418
TCONS_00057989 lncRNA upstream 388543 2447839 ~ 2479720 (-) True XLOC_028418
TCONS_00057310 lncRNA upstream 604872 2664168 ~ 2666870 (-) True XLOC_028422
TCONS_00057990 lncRNA upstream 1191478 3250774 ~ 3257564 (-) True XLOC_028427
TCONS_00055158 mRNA downstream 8512 1988460 ~ 2036620 (-) False XLOC_028410
TCONS_00055159 mRNA downstream 30726 1989489 ~ 2014406 (-) True XLOC_028410
TCONS_00055157 mRNA downstream 115108 1921011 ~ 1930024 (-) True XLOC_028409
TCONS_00055156 mRNA downstream 130904 1880180 ~ 1914228 (-) True XLOC_028407
TCONS_00055155 mRNA downstream 136953 1878573 ~ 1908179 (-) False XLOC_028407
TCONS_00055167 mRNA upstream 87995 2147291 ~ 2168805 (-) False XLOC_028412
TCONS_00055168 mRNA upstream 92083 2151379 ~ 2162688 (-) False XLOC_028412
TCONS_00055169 mRNA upstream 98565 2157861 ~ 2196798 (-) False XLOC_028412
TCONS_00055170 mRNA upstream 101566 2160862 ~ 2196928 (-) True XLOC_028412
TCONS_00055171 mRNA upstream 151021 2210317 ~ 2219705 (-) True XLOC_028413
TCONS_00055131 other downstream 1096290 937229 ~ 948842 (-) True XLOC_028386
TCONS_00055123 other downstream 1236679 804147 ~ 808453 (-) True XLOC_028380
TCONS_00055111 other downstream 1359713 683052 ~ 685419 (-) True XLOC_028374
TCONS_00055166 other upstream 1228 2060524 ~ 2162724 (-) False XLOC_028412
TCONS_00055185 other upstream 615810 2675106 ~ 2686090 (-) False XLOC_028423
TCONS_00055220 other upstream 2433270 4492566 ~ 4496791 (-) True XLOC_028449
TCONS_00055225 other upstream 2486913 4546209 ~ 4570805 (-) True XLOC_028452
TCONS_00055239 other upstream 2871115 4930411 ~ 4932524 (-) True XLOC_028460

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) TU307541 True 1201 lncRNA 0.59 6 CI01000066 2120288 ~ 2123706 (+)