RNA id: TCONS_00040879


Basic Information

Item Value
RNA id TCONS_00040879
length 962
lncRNA type retained_intron
GC content 0.49
exon number 3
gene id XLOC_020670
representative True

Chromosome Information

Item Value
chromosome id NC_007133.7
NCBI id CM002906.2
chromosome length 39133080
location 613265 ~ 622967 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CGTCCGCGTTTCCGCGCTGCGCCATTTCGGAGCAGACCCGTGCCAggaatcaaacacacacacacggccagAAATACGCGATAATTACGATTGAACCATGCATCGCGACTGCCCCCTGGACTGCAAGGTTTACGTTGGGAATCTGGGGAATAATGGGAATAAGTCTGAGCTGGAGAGGGCGTTTGGCTACTACGGACCTCTGAGGAGCGTCTGGGTGGCCAGAAACCCTCCTGGTTTTGCGTTTGTTGAGTTTGAAGACCCTCGTGATGCCACAGACGCCGTCAGAGAGCTGGACGGGCGGACCCTCTGTGGTTGCCGAGTGAGGGTTGAATTGTCCAATGGCGAGAAGCGGACTCGTAGCCGGGGTCCACCTCCTTCTTGGAACCGCCGCCCACGGGATGACTACCGCCGCCGCAGCAGCCCGCCCCAGAGGCGCAGGTAAACCTGTCCTCCGCTCACCTGTCTCTCTGTAGCTTGTGTTTCAGAGCAAACTAATGTGCTTCTGCCCCGTCCGCCAGTCCTGGAGGCCACTGCTCCGCCGGTGCCACGGGTCCCGGTCCGATGAGCGTCTGCCGGACATCTTTAGCTCCTCCATCTTCATTGTCATTGATAACCATTCAATAATGATTTGACTGGGCTTCTCAAATTCGATAGACAGTCATGATTGTTTGGTGTAAAAGCGGATGAGTACTCAATTAAATGCTAATCTCATAGCAATGTACCTGGGCTACATTTCACTTCAGAATCAAAGATATTTTGGGGTAAAACTTTGCAATAAGGTTCCCTTTAATAATATTACCTTACCGCTAAAGCATTCACTAATATATTACTAAAAACAAAAGTTGtatgtaattgtttttattaagctAACACTATTTAGCAAGAAATGCTTTGTTTAAACGGTGGCTAATATTAGCATGAACCTCTACATGTCAATACTTCAGTGTTAAATGTTGGGACTT

Function

GO:

id name namespace
GO:0000381 regulation of alternative mRNA splicing, via spliceosome biological_process
GO:0045292 mRNA cis splicing, via spliceosome biological_process
GO:0005634 nucleus cellular_component
GO:0016607 nuclear speck cellular_component
GO:0003676 nucleic acid binding molecular_function
GO:0003723 RNA binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-071005-2 Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be active in nuclear speck. Orthologous to human SRSF3 (serine and arginine rich splicing factor 3).

Ensembl:

ensembl_id ENSDART00000134828

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00040876 lncRNA downstream 921 613298 ~ 616609 (-) False XLOC_020670
TCONS_00042233 lncRNA downstream 221630 392619 ~ 395900 (-) False XLOC_020664
TCONS_00042232 lncRNA downstream 221630 392619 ~ 395900 (-) False XLOC_020664
TCONS_00042231 lncRNA downstream 221630 392619 ~ 395900 (-) True XLOC_020664
TCONS_00042230 lncRNA downstream 222792 392619 ~ 394738 (-) False XLOC_020664
TCONS_00042234 lncRNA upstream 38293 659917 ~ 697504 (-) True XLOC_020672
TCONS_00042235 lncRNA upstream 78589 700213 ~ 704907 (-) True XLOC_020673
TCONS_00042236 lncRNA upstream 111620 733244 ~ 735244 (-) True XLOC_020675
TCONS_00042237 lncRNA upstream 117676 739300 ~ 760886 (-) True XLOC_020676
TCONS_00042238 lncRNA upstream 396721 1018345 ~ 1022428 (-) False XLOC_020684
TCONS_00040871 mRNA downstream 9718 603719 ~ 607812 (-) True XLOC_020669
TCONS_00040870 mRNA downstream 11463 603382 ~ 606067 (-) False XLOC_020669
TCONS_00040869 mRNA downstream 17514 591809 ~ 600016 (-) True XLOC_020668
TCONS_00040868 mRNA downstream 59565 550828 ~ 557965 (-) True XLOC_020667
TCONS_00040867 mRNA downstream 69770 539681 ~ 547760 (-) True XLOC_020666
TCONS_00040880 mRNA upstream 19718 641342 ~ 651719 (-) True XLOC_020671
TCONS_00040881 mRNA upstream 89135 710759 ~ 718615 (-) True XLOC_020674
TCONS_00040882 mRNA upstream 148377 770001 ~ 775776 (-) False XLOC_020677
TCONS_00040883 mRNA upstream 148377 770001 ~ 784110 (-) True XLOC_020677
TCONS_00040884 mRNA upstream 191224 812848 ~ 817479 (-) False XLOC_020678
TCONS_00040857 other downstream 270116 344918 ~ 347414 (-) False XLOC_020658
TCONS_00040885 other upstream 191296 812920 ~ 817407 (-) True XLOC_020678
TCONS_00040895 other upstream 536445 1158069 ~ 1159749 (-) False XLOC_020686
TCONS_00040899 other upstream 608282 1229906 ~ 1230022 (-) True XLOC_020689
TCONS_00040924 other upstream 2973644 3595268 ~ 3680725 (-) True XLOC_020748
TCONS_00040930 other upstream 3690179 4311803 ~ 4313118 (-) True XLOC_020752

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) TU218900 True 384 lncRNA 0.41 1 CI01000043 5160068 ~ 5160451 (-)
grasscarp (Ctenopharyngodon idella) TU432362 False 101 TUCP 0.47 1 CI01000186 411820 ~ 411920 (+)
tiger barb (Puntius tetrazona) TU218900 True 2790 TUCP 0.49 5 NC_056720.1 783863 ~ 788153 (-)