RNA id: TCONS_00000730


Basic Information

Item Value
RNA id TCONS_00000730
length 726
RNA type mRNA
GC content 0.40
exon number 4
gene id XLOC_000426
representative True

Chromosome Information

Item Value
chromosome id NC_007112.7
NCBI id CM002885.2
chromosome length 59578282
location 36194761 ~ 36204000 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CGCTCAGTCGAAACGTGCGGTTAACGTTGCTAAACGACATAGGTAAATAACGTTAAATGTTGTATGCTTTAATATAAGAATGCATTCGACGTTAGTGGGGTTTTAAAAAACTGCAGCACTGTAGTTACCTTGCTAGATATACGATGACACGTTTATTAAGTGATACGTTGGGTTGGAATGCTAGCATGCTAAATTAGCCGCTTATCGATAACGTTCACCGGCAATTTCCAAACAAATAAGGTTAAACCTCTTCTGGAAACCCCTTATGTGGTTTAAAATAAACGTCTTTActaaaATGAGTCTCCGAAAGCAGACACCAAGTGATTTCCTGAAGCAGATCATTGGGAGGCCAGTGGTGGTGAAACTGAACTCTGGTGTCGATTACAGAGGAGTCCTGGCCTGCCTTGACGGCTACATGAATATTGCGGTGGAACAGACAGAGGAATATGTCAACGGCCAACTGAAGAACAAGTATGGAGATGCATTTCTCAGAGGAAACAATGTGTTATACATCAGCACCCAGAAGAGGAAGATGTGAAGCTGCTTTACTTATTTCTTCATGCGTTGTTAGAGAAGTCAATTGTTTACTGTTAATATTCATAAATCCTTTGTTAGCTGATGATGATGTCTAAgtttgttaaatgttttgtaaCACACATTTGCTGTCCTGCAGAACGAAGCAGTAGCATTTGTTTTCCAACAATAAATTGTGTTCATGTTTCCCTG

Function

GO:

id name namespace
GO:0006397 mRNA processing biological_process
GO:0000398 mRNA splicing, via spliceosome biological_process
GO:0030490 maturation of SSU-rRNA biological_process
GO:0008380 RNA splicing biological_process
GO:0046540 U4/U6 x U5 tri-snRNP complex cellular_component
GO:0000932 P-body cellular_component
GO:0005634 nucleus cellular_component
GO:0005681 spliceosomal complex cellular_component
GO:0005688 U6 snRNP cellular_component
GO:0005730 nucleolus cellular_component
GO:0005732 small nucleolar ribonucleoprotein complex cellular_component
GO:0003723 RNA binding molecular_function

KEGG:

id description
ko03040 Spliceosome
ko03018 RNA degradation
ko03019 Messenger RNA biogenesis
ko03041 Spliceosome

ZFIN:

id description
ZDB-GENE-040625-50 Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome and maturation of SSU-rRNA. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of U4/U6 x U5 tri-snRNP complex; U6 snRNP; and sno(s)RNA-containing ribonucleoprotein complex. Predicted to be active in P-body and nucleolus. Orthologous to human LSM6 (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated).

Ensembl:

ensembl_id ENSDART00000147458

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00000727 lncRNA upstream 200572 35993297 ~ 35994209 (+) True XLOC_000424
TCONS_00003089 lncRNA upstream 231719 35956461 ~ 35963062 (+) False XLOC_000423
TCONS_00000721 lncRNA upstream 231719 35956461 ~ 35963062 (+) False XLOC_000423
TCONS_00000722 lncRNA upstream 234726 35956493 ~ 35960055 (+) False XLOC_000423
TCONS_00003088 lncRNA upstream 296344 35896392 ~ 35898437 (+) True XLOC_000421
TCONS_00002855 lncRNA downstream 447081 36651080 ~ 36657815 (+) False XLOC_000428
TCONS_00002856 lncRNA downstream 762001 36966000 ~ 36966282 (+) True XLOC_000431
TCONS_00000757 lncRNA downstream 1008237 37212236 ~ 37259712 (+) False XLOC_000433
TCONS_00000758 lncRNA downstream 1080576 37284575 ~ 37292181 (+) True XLOC_000433
TCONS_00000764 lncRNA downstream 1200991 37404990 ~ 37417631 (+) True XLOC_000435
TCONS_00000724 mRNA upstream 192007 35985813 ~ 36002774 (+) False XLOC_000424
TCONS_00000725 mRNA upstream 196384 35985893 ~ 35998397 (+) False XLOC_000424
TCONS_00000726 mRNA upstream 204401 35985919 ~ 35990380 (+) False XLOC_000424
TCONS_00000720 mRNA upstream 224522 35956435 ~ 35970259 (+) False XLOC_000423
TCONS_00000723 mRNA upstream 231521 35956529 ~ 35963260 (+) True XLOC_000423
TCONS_00000731 mRNA downstream 232937 36436936 ~ 36440301 (+) False XLOC_000427
TCONS_00000732 mRNA downstream 233586 36437585 ~ 36438731 (+) True XLOC_000427
TCONS_00000733 mRNA downstream 408661 36612660 ~ 36701206 (+) False XLOC_000428
TCONS_00000734 mRNA downstream 447060 36651059 ~ 36701206 (+) False XLOC_000428
TCONS_00000736 mRNA downstream 461556 36665555 ~ 36674695 (+) False XLOC_000428
TCONS_00000728 other upstream 40404 36154261 ~ 36154377 (+) True XLOC_000425
TCONS_00000717 other upstream 391697 35790892 ~ 35803084 (+) True XLOC_000419
TCONS_00000714 other upstream 679508 35494904 ~ 35515273 (+) False XLOC_000418
TCONS_00000704 other upstream 1488311 34695514 ~ 34706470 (+) False XLOC_000411
TCONS_00000699 other upstream 1506139 34685445 ~ 34688642 (+) False XLOC_000410
TCONS_00000735 other downstream 461544 36665543 ~ 36690899 (+) False XLOC_000428
TCONS_00000740 other downstream 524298 36728297 ~ 36746569 (+) True XLOC_000429
TCONS_00000744 other downstream 919643 37123642 ~ 37123772 (+) True XLOC_000432
TCONS_00000769 other downstream 1792460 37996459 ~ 37996577 (+) True XLOC_000440
TCONS_00000777 other downstream 2158349 38362348 ~ 38374799 (+) False XLOC_000445

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000049_04473766_04475768.mRNA False 945 mRNA 0.38 4 CI01000049 4473662 ~ 4476249 (+)
rainbow trout (Oncorhynchus mykiss) TU1045265 True 451 TUCP 0.41 4 NC_048574.1 67947503 ~ 67949276 (-)
striped catfish (Pangasianodon hypophthalmus) TU48528 False 442 TUCP 0.51 4 NC_047597.1 5225030 ~ 5227923 (-)
tiger barb (Puntius tetrazona) TU48528 True 1026 lncRNA 0.43 2 NC_056703.1 3388301 ~ 3389487 (+)
mexican tetra (Astyanax mexicanus) TU289611 False 497 TUCP 0.43 4 NC_035921.1 2678107 ~ 2685804 (-)