RNA id: TCONS_00008329


Basic Information

Item Value
RNA id TCONS_00008329
length 3534
RNA type mRNA
GC content 0.40
exon number 12
gene id XLOC_004403
representative False

Chromosome Information

Item Value
chromosome id NC_007122.7
NCBI id CM002895.2
chromosome length 45484837
location 44878571 ~ 44898129 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

agttctAATAAACTTTCGACCACAGCTGTATCACTTTTTTATTAAGctccaaaacattcattcattcattcatttaatcattcattcattcattttcttgtcagcttagtaacttttttaatccggggtagccacagcgcaatgaaccgccaacttagccagcacatttttacgcagcggatgcccttccagccgcaacccatctctgggaaaagctCCAAAACAGTGTATacaatataaacataaacatgcaGTAACAAATaggcaaaatatttatatttaacaatcaaaaacatacaaaaacgggGAGAAACAACTAAACACAGagacagctgtatcccttttttattttttattttttcagctgTATCCTTTCTAGCGACGCCAGGACTCTTGTGTGACGTCACTGCGCGTCTCCTGCTTTGTGCGTCACCGGTGCGACACACGCGGCTCTCTACGCGCACAGTCGCGCTTTCATATTTTAACTCGTAATTTACACCGAAATCCGTCACAATTATGGCCACCGCCGTCGTTCCCGTGAGGAAGAGGATCCTGAAGGAGGAAGACATGACGAAGATTGAGTTTGAGACGAGTGAAGAAGTGGACGTGACGCCGACGTTTGACACGATGGGCCTGAGGGAGGATTTACTGCGCGGGATCTACGCATACGGTTTTGAGAAGCCATCGGCCATCCAGCAGAGAGCCATCAAACAGATCATCAAGGGCAGAGACGTCATCGCACAGTCACAGTCTGGAACTGGTAAAACAGCCACCTTCTGTGTCTCAGTGCTGCAGTGTCTGGATATACAGGTACGAGAGACTCAAGCGTTGATTTTGGCTCCAACCAGAGAGTTAGCAGGACAGATCCAGAAGGTTTTACTGGCTCTGGGCGACTACATGAACGTTCAGTGTCACGCGTGTATCGGCGGCACAAATGTCGGTGAAGACATCCGGAAGCTGGATTACGGTCAGCACGTGGTGGCAGGAACGCCTGGACGAGTGTTCGACATGATCCGCAGGAGGAGTTTAAGGACTCGCGCCATCAAGATGCTGGTGTTGGATGAAGCCGATGAGATGCTCAACAAGGGTTTTAAGGAACAGATTTACGACGTGTACCGATACCTGCCGCCGGCCACTCAGGTGTGTCTGATCAGCGCCACACTGCCACACGAGATCCTGGAGATGACCAACAAGTTCATGACCGACCCCATCCGCATCCTGGTCAAACGtgatGAGTTGACTCTGGAGGGCATTAAGCAGTTCTTCGTGGCCGTGGAGCGCGAGGAGTGGAAGTTCGACACTCTGTGTGATCTGTACGACACGCTGACCATCACACAGGCCGTCATCTTCTGCAACACCAAACGCAAGgtgGACTGGCTGACAGAGAAAATGAGGGAGGCAAATTTCACCGTATCCTCGATGCACGGAGACATGCCTCAGAAAGAGCGAGAGTCCATTATGAAGGAGTTCAGATCTGGAgccagTCGAGTGTTGATCTCCACAGACGTTTGGGCCAGAGGTCTGGATGTGCCGCAGGTTTCCCTCATCATTAACTACGATCTTCCCAACAACAGAGAGCTGTACATCCACAGGATTGGTCGATCGGGTCGTTACGGCAGGAAGGGTGTGGCCATCAACTTTGTGAAGAATGACGACATCCGTATCCTGCGTGATATCGAGCAGTACTACTCCACACAGATCGATGAAATGCCCATGAACGTGGCTGATCTGATCTGAGAACAGAGATTATCCCAGAACAGTTCTGCTTTCCTCTGCATCTTTATTTCCCATTTCCATTAGTAATTgcctttttattttctatttttatgtaGTTTGAGCGCTCTGATGTTACAGGATCTGGTGTTCAGATCAGAGCTTCCATTGGGTTTTGTAAATAAAGAATCTTTGTCTCCATCTTTGAGCTCATCTCTGTTTTATTCGAGTTCTTTATTGTTTACCGTACATCAGGTCTTGAGATTATAGATtagttgcattttaaaataaatgttaaattaaatgtaaattaagctTAGTAAtatccttatttttatttatttatttatttatatctctatttttattttaacctgttgccaaaataatttttttatattgtttttatttagtttgacttGGTGCATTAAAATATcttacaatattaaaatattacaggaTGGGTTAAAGATAAGCATAATTAAATTTAATCTCTAAATTTatcatattaaatacaatttcatATTTTTTGAGTCGGTAATGCAGGCAGTATAGGGAATATTCACTATGCCACTCGTTTTTAATGCCTTGTTACTCTTCACCCAGTCTCTATACACTCCACAGGCACATTTAACCACTGAAGAATaatacaaaaatgacaaaaacaagacCACTAGAGCAATCAAATCCTAACTATTGTAACCCTTCAGTGTGAATTCAGGAAATTCTAACTATTTCCTCGTTATTATCATGCCTATTTTTaacattggctgtttattagtctTCATAAATTAGATATATTCTGCATGAGGATATCCTACATCCATAATCCTACAAATACCTCATTTAACTACTACTACCCtgttaactattaataagcagcaagtTAATTGAGGCAAATCATGCTTGAACCATAAAtaaatttattgttaattattacaaCAATGTACAATGATACTGAAATGGTGCAGGATATTTATGTTGCTCAATCTGTGTGATGAGGCTGTGCCTTTTAGAAAGATTCATATAGATTCATATATCAAGATTAAAAGAGAATGATAAAGCTGTTGAGTTATTTTCCACTTTAGGATGTGTATAGTCTTCTGGAGAGTCATCGCTCTGGAGTTTGCAGGtatattattgctattatattattttcttcaatattgttttacattaaaatggtttattttgtCGGTAACAcgttacaataaggttgtattagttaatataaatgcatttactaacatgaacaaacaattaacaatatTACAGTGTTGATGCTTGTTAACGttactaaatgaaaataaaatcatttattattagtttatcatAACTGATGGTGCATTAATTAGTCAACAAGCATGAACTCTGATGCTcacaataatgcattagtaaatgttcaactgTGATTAATGCTGTTCATGTGTCGTtcatagttcatgttagtaaattcattaactaatacaaccttattgtaaagtgtgactgtgtgtgtgtgtgtgtgtttgttaatgtACTGATGAATGAATGCGTCTCTGTGTAAGAGTGAAGCTCcagctgattctctctcacacacgtgACTGTGGATGAGCTGCTGTAACCATGGAGACAGACCATAATCACTGACACCATTCACTCACGCCGTCTGCTATAGAGCTCATTTGACCTGCTTTTTCATGCTGTTTACTAATCTTTATCAACTTaatgatttacacacacacacacacacacacacacacactgtaaaagcgtttaacagtttccatattctGTGATTTGCAGGTGTTTTCAGATTATTTGCGGGTATAAATTGCAGTG

Function

GO:

id name namespace
GO:0000381 regulation of alternative mRNA splicing, via spliceosome 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:0071013 catalytic step 2 spliceosome cellular_component
GO:0005634 nucleus cellular_component
GO:0016607 nuclear speck cellular_component
GO:0005681 spliceosomal complex cellular_component
GO:0005730 nucleolus cellular_component
GO:0005737 cytoplasm cellular_component
GO:0071006 U2-type catalytic step 1 spliceosome cellular_component
GO:0005524 ATP binding molecular_function
GO:0016787 hydrolase activity molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0000166 nucleotide binding molecular_function
GO:0003723 RNA binding molecular_function
GO:0003724 RNA helicase activity molecular_function
GO:0003729 mRNA binding molecular_function
GO:0004386 helicase activity molecular_function

KEGG:

id description
ko03040 Spliceosome
ko03013 Nucleocytoplasmic transport
ko03015 mRNA surveillance pathway
ko03019 Messenger RNA biogenesis
ko03041 Spliceosome
ko03009 Ribosome biogenesis
ko03012 Translation factors

ZFIN:

id description
ZDB-GENE-040426-915 Predicted to enable RNA helicase activity and mRNA binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to act upstream of or within RNA 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 catalytic step 2 spliceosome. Predicted to be active in nucleolus. Human ortholog(s) of this gene implicated in intellectual disability. Orthologous to human EIF4A3 (eukaryotic translation initiation factor 4A3).

Ensembl:

ensembl_id ENSDART00000157615

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00008883 lncRNA downstream 19970 44852582 ~ 44858601 (-) True XLOC_004401
TCONS_00008498 lncRNA downstream 76830 44798661 ~ 44801741 (-) True XLOC_004400
TCONS_00008325 lncRNA downstream 122088 44750935 ~ 44756483 (-) True XLOC_004399
TCONS_00008882 lncRNA downstream 156240 44716828 ~ 44722331 (-) True XLOC_004398
TCONS_00008322 lncRNA downstream 256331 44618611 ~ 44622240 (-) True XLOC_004396
TCONS_00008501 lncRNA upstream 3174 44901303 ~ 44904326 (-) True XLOC_004404
TCONS_00008347 lncRNA upstream 245368 45143497 ~ 45148912 (-) False XLOC_004408
TCONS_00008348 lncRNA upstream 249057 45147186 ~ 45148912 (-) True XLOC_004408
TCONS_00008356 lncRNA upstream 308338 45206467 ~ 45207039 (-) True XLOC_004412
TCONS_00008360 lncRNA upstream 460983 45359112 ~ 45359656 (-) False XLOC_004414
TCONS_00008327 mRNA downstream 2566 44858979 ~ 44876005 (-) False XLOC_004402
TCONS_00008328 mRNA downstream 4791 44860950 ~ 44873780 (-) True XLOC_004402
TCONS_00008326 mRNA downstream 76603 44798056 ~ 44801968 (-) False XLOC_004400
TCONS_00008324 mRNA downstream 231256 44637516 ~ 44647315 (-) True XLOC_004397
TCONS_00008323 mRNA downstream 231285 44637516 ~ 44647286 (-) False XLOC_004397
TCONS_00008330 mRNA upstream 585 44898714 ~ 44906703 (-) False XLOC_004404
TCONS_00008331 mRNA upstream 12486 44910615 ~ 44931962 (-) True XLOC_004405
TCONS_00008332 mRNA upstream 39076 44937205 ~ 44945636 (-) True XLOC_004406
TCONS_00008333 mRNA upstream 55469 44953598 ~ 44979281 (-) False XLOC_004407
TCONS_00008335 mRNA upstream 55802 44953931 ~ 44999858 (-) False XLOC_004407
TCONS_00008317 other downstream 264837 44606851 ~ 44613734 (-) False XLOC_004396
TCONS_00008303 other downstream 539351 44337157 ~ 44339220 (-) True XLOC_004385
TCONS_00008295 other downstream 755113 44123327 ~ 44123458 (-) True XLOC_004381
TCONS_00008250 other downstream 3503445 41375011 ~ 41375126 (-) True XLOC_004339
TCONS_00008244 other downstream 3794208 41078191 ~ 41084363 (-) True XLOC_004334
TCONS_00008372 other upstream 533404 45431533 ~ 45435014 (-) False XLOC_004416

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000306_00474870_00478789.mRNA True 1339 mRNA 0.51 10 CI01000306 474764 ~ 478915 (-)
bowfin (Amia calva) AMCG00001437 True 1949 mRNA 0.47 12 CM030143.1 3766101 ~ 3771735 (+)