RNA id: TCONS_00028828


Basic Information

Item Value
RNA id TCONS_00028828
length 2665
RNA type mRNA
GC content 0.45
exon number 13
gene id XLOC_014586
representative False

Chromosome Information

Item Value
chromosome id NC_007130.7
NCBI id CM002903.2
chromosome length 48449771
location 10299002 ~ 10324573 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CTTGAATTGGGTTAAACCTTCACTCCGGGCCTTTAGGGGTCGCATGTCATCAGTGTTTTTGTTCAGCGAGTTTTTACCGTGAGGAAAAGATGAGCGCATCCGCCAACGCGGAATAAGCGGTTAGCCCCTTTGGTCAAAACGAGCTACACTTAACCTCAATCAATAAGGACTATTAGCTCAATTTGAGTATCAGGAAATACATCTAAACGGCTAATCGTTATAACGAAATGGTTAAATCTTAAACATTATCGACGCAAGCCTTTTATTCGTGCTCCGCAGTGGTTCCGTTTAGCATTAGCTGCTAACAACCTTCTCAAGCAAAGCGTTTATTTCAACCTCTGCGCAAATAACGTTATAGGTGTATTTCGGCAAAGTCTTTATGCTTGtgttaaatttttaaaacatctGCGTTTTATAGTTGGTCTCCTGTAATAGCGTGTGACGGGAATAAAGCTATCTAAGGAAAACGGCGTGTTAGCTGAAGTTTGATCAAAACACCAGGATGTCTGATTTTGATGAATTTGAGAGACAGCTGTCTGAAAATAAACAAGGTGACAGTCTAAACGGTCATGAGAGGGACAAGGAGAACCGGCACCGGCGACGCAGTCCGTCCCGCAGCCGCAGTCGAGAACGGAAGAGAAGGAGCAGAGAGAGGAGAAGCAGGGAGCGCCGCGGTGACAGCAAGGAACGCCGACACAGACGCAGCGATCATACACAGAACCACCCCCAAGAAAATGTCAGCCGTTCACCTCACCgggagaaaaagaagaaaattaaGAAGTACTGGGATGTCCCTCCTCCAGGCTTTGAGCATATTACTCCAATGCAGTATAAGGCAATGCAAGCTGCTGGTCAAATCCCCGCTACCGCTTTGCTGCCCACCATGACGCCAGACGGCCTGGCAGTAACGCCGACCCCGGTGCCTGTAGTAGGCAGTCAGATGACTCGCCAGGCTCGCAGACTTTACGTTGGCAACATCCCATTTGGCATCACAGAGGAATCTATGATGGACTTCTTCAATGCTCAGATGAGATTGGGTGGTCTGACTCAGGCCCCTGGAAACCCTGTCCTCGCCGTCCAGATTAACCAGGATAAGAACTTTGCTTTCCTTGAGTTCCGATCAGTGGATGAGACCACGCAGGCCATGGCATTCGATGGCATCATCTTCCAGGCACAGAGCTTAAAGATTCGCAGACCGCATGACTATCAGCCATTACCTGGCATGAGCGAGAACCCCAGCGTTTATGTGCCAGGTGTGGTGTCTACTGTTGTACCAGACTCTATTCACAAGCTGTTCATTGGAGGTTTACCAAACTATCTCAATGACGACCAGGTTAAAGAGTTGTTGACCTCTTTTGGACCTCTCAAAGCCTTCAATCTGGTTAAGGACAGTGCTACCGGCCTGTCAAAGGGTTATGCTTTCTGTGAATATGTGGATGTTAACGTCAATGATCAGGCTATTGCAGGATTGAATGGCATGCAGTTGGCAGATAAGAAGCTGCTGGTTCAGAGGGCAAGTGTTGGAGCCAAGAATGCCACAATGACGAGTATAAACGAGACTCCAGTGACGTTGCAAGTGCCTGGCCTCACATCCAACCCCATGATCCAGATGGGCGGTATTCCCACTGAGGTCCTGTGTCTGATGAACATGGTGGCTCCAGAGGAGCTTATCGACGATGAGGAGTACGAGGAGATCGTGGAGGACGTCAAAGAGGAGTGCTCTAAATATGGCCAGGTCAAGAGCATAGAAATTCCCAGACCCGTCGATGGCCTTGATATACCTGGAACTGGCAAGATCTTTGTGGAGTTCACCTCTGTTTACGACTCCCAGAAGGCCATGCAGGGCTTAACGGGGAGAAAGTTCGCCAACAGGGTGGTGGTGACCAAGTACTGCGATCCAGACGCTTATCATCGCCGAGACTTCTGGTAGAGTGCTGAGCTCATTTCGTAAAAAGAAATCGAATTGGAGGCAGTGATGATGAAGAGGggggaacatttttttttgtactcttaaaaaaaaaaaaaaaaaaaagaagccaaaaggtgaatgttgtgttttttttgttttgaggcTTAAATTAAAAGATGATTCGTGAGCAATTGTGGGAGGGTTTTTTGCTTTTCGTTTGTATTTTAAGAACATTAGCGAGAGCTATTCTGCTATACTGATGATACCTAATCtgttaataaaattattactattttttaattgtatactgaaacaaatgtaaaatagtgATCGTTGACCATCAGAGAAGACCAACTATCGACGCCCCAACCAATCCTGGAGGTTTATTGCTAATCATTCAAATGAAGATGTCCCTTACTTGGTTTTTATCTCTTTTTATTCCTCTTTTGAATCGATCCCACTGACTGATCCTTCTCAAAAGTCCTCGCTCTTCTCTGTTGGTCAAATCTCCCTCCCATTTTGTAGCTTTTTGCAGTTCATATCTCAAGGTATTAGATAGTCTCagatcttcttcttttttttttgtctggttttGTTCTTATACATACTTGGTCTCTTCCATGCATATCACCAGCTCATTAGAAGGTGATGACATTTGTCCAGTGTGGCACCTGTTTTTCAGTTTCTGTATGCgtgatgtttttgttttctcaGTATAATAGGCCACTTTTGATAATAAAACTCTTGGAAGTTTGA

Function

GO:

id name namespace
GO:0006397 mRNA processing biological_process
GO:0008380 RNA splicing biological_process
GO:0089701 U2AF complex cellular_component
GO:0005634 nucleus cellular_component
GO:0016607 nuclear speck cellular_component
GO:0000243 commitment complex cellular_component
GO:0071004 U2-type prespliceosome cellular_component
GO:0008187 poly-pyrimidine tract binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003723 RNA binding molecular_function
GO:0030628 pre-mRNA 3'-splice site binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-040426-1881 Predicted to enable poly-pyrimidine tract binding activity and pre-mRNA 3'-splice site binding activity. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of U2-type prespliceosome; U2AF complex; and commitment complex. Predicted to be active in nuclear speck. Orthologous to human U2AF2 (U2 small nuclear RNA auxiliary factor 2).

Ensembl:

ensembl_id ENSDART00000023571

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00029757 lncRNA downstream 392063 9904324 ~ 9906939 (-) True XLOC_014578
TCONS_00028805 lncRNA downstream 615494 9676517 ~ 9683508 (-) True XLOC_014572
TCONS_00030166 lncRNA downstream 689490 9594867 ~ 9609512 (-) False XLOC_014570
TCONS_00030167 lncRNA downstream 689627 9605861 ~ 9609375 (-) True XLOC_014570
TCONS_00030165 lncRNA downstream 838673 9457546 ~ 9460329 (-) True XLOC_014566
TCONS_00028866 lncRNA upstream 534804 10859122 ~ 10860449 (-) False XLOC_014603
TCONS_00028865 lncRNA upstream 534876 10859194 ~ 10864799 (-) False XLOC_014603
TCONS_00028870 lncRNA upstream 551415 10875733 ~ 10876830 (-) False XLOC_014603
TCONS_00030168 lncRNA upstream 895443 11219761 ~ 11227568 (-) True XLOC_014612
TCONS_00028909 lncRNA upstream 1810473 12134791 ~ 12138739 (-) False XLOC_014624
TCONS_00028827 mRNA downstream 3829 10255223 ~ 10295173 (-) True XLOC_014585
TCONS_00028826 mRNA downstream 12774 10252052 ~ 10286228 (-) False XLOC_014585
TCONS_00028824 mRNA downstream 55854 10217598 ~ 10243148 (-) False XLOC_014584
TCONS_00028823 mRNA downstream 84737 10206515 ~ 10214265 (-) True XLOC_014583
TCONS_00028822 mRNA downstream 84738 10201170 ~ 10214264 (-) False XLOC_014583
TCONS_00028836 mRNA upstream 1042 10325360 ~ 10330778 (-) False XLOC_014587
TCONS_00028837 mRNA upstream 1049 10325367 ~ 10330831 (-) False XLOC_014587
TCONS_00028838 mRNA upstream 1824 10326142 ~ 10330826 (-) True XLOC_014587
TCONS_00028839 mRNA upstream 32027 10356345 ~ 10360188 (-) False XLOC_014588
TCONS_00028840 mRNA upstream 32028 10356346 ~ 10373630 (-) True XLOC_014588
TCONS_00028825 other downstream 56891 10238453 ~ 10242111 (-) True XLOC_014584
TCONS_00028819 other downstream 175655 10123233 ~ 10123347 (-) True XLOC_014581
TCONS_00028818 other downstream 286388 10012498 ~ 10012614 (-) True XLOC_014580
TCONS_00028791 other downstream 1446347 8852540 ~ 8852655 (-) True XLOC_014556
TCONS_00028774 other downstream 2473469 7825395 ~ 7825533 (-) True XLOC_014543
TCONS_00028853 other upstream 312051 10636369 ~ 10646822 (-) False XLOC_014597
TCONS_00028860 other upstream 367848 10692166 ~ 10730478 (-) False XLOC_014599
TCONS_00028862 other upstream 381141 10705459 ~ 10705475 (-) True XLOC_014600
TCONS_00028867 other upstream 534899 10859217 ~ 10860466 (-) False XLOC_014603
TCONS_00028885 other upstream 868931 11193249 ~ 11193363 (-) True XLOC_014611

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000321_03749658_03759359.mRNA True 1629 mRNA 0.49 11 CI01000321 3749658 ~ 3759645 (+)
bowfin (Amia calva) AMCG00001960 False 1260 mRNA 0.60 13 PESF01000029.1 40587 ~ 48320 (+)