RNA id: TCONS_00028899


Basic Information

Item Value
RNA id TCONS_00028899
length 4356
RNA type mRNA
GC content 0.50
exon number 37
gene id XLOC_014621
representative False

Chromosome Information

Item Value
chromosome id NC_007130.7
NCBI id CM002903.2
chromosome length 48449771
location 11897631 ~ 11977783 (-)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

ATGTACGCGGTGTACCGTCAGGCTCACCCGCCCACCGCAGTGGAGTTTGCCGTTTACTGCAACTTCATCTCCAGCCAAGAGAAAAACTTGGTGGTGGCAGGAACATCTCAGCTGTACGTCTACAGGATCATTTATGATGTGGAGAGCACTTCCAAGTCTGAAAAGTCATCAGATGGCAAGAGTCGTAAAGAGAAACTGGAGCAGGTGgcatctttctctctctttggAAATGTGATGTCAATGGCCAGCGTTCAGCTGGTGGGCACCAACAGAGACGCCTTGCTTCTCAGCTTCAAAGATGCCAAGCTGTCAGTAGTGGAGTATGACCCTGGCACGCATGATCTCAAGACTCTGTCGCTGCATTATTTTGAGGAACCGGAGTTGAGAGATGGGTTTGTTCAGAATGTGCACATTCCTATGGTTCGAGTGGATCCAGAGAATCGATGTGCTGTCATGCTGGTGTACGGCACTTGCCTGGTGGTTCTGCCTTTCAGGAAGGACACGCTTGCTGACGAACAGGAGGGGATTGTGGGAGAGGGGCAGAAATCTAGTTTCCTACCCAGCTACATCATCGATGTTCGTGAACTGGATGAGAAACTCCTAAACATCATCGATATGAAGTTTCTCCATGGCTACTATGAGCCCACACTGCTTATTCTGTTCGAGCCCAATCAAACATGGCCAGGGCGTGTGGCGGTGCGTCAGGACACTTGCAGTATTGTGGCGATCTCTCTAAACATCATGCAGAAGGTTCATCCAGTCATCTGGTCTCTGAGTAACCTGCCCTTTGACTGCAATCAGGTCATGGCTGTCCCCAAACCCATCGGTGGAGTTGTGGTGTTTGCTGTGAATTCGTTGCTGTATCTTAATCAGAGTGTTCCTCCGTTTGGAGTGTCTCTCAACAGTCTGACTAACGGAACCACAGCTTTCCCTTTGAGACCTCAGGAGGAAGTAAAGATCACCCTGGATTGTTCTCAAGCCTCCTTCATCACCTCTGACAAGATGGTCATCTCACTAAAAGGAGGAGAAATTTATGTGTTGACGCTCATCACTGATGGCATGAGAAGTGTTCGTGCGTTTCACTTTGATAAGGCTGCTGCCAGTGTCCTGACTACCTGTATGATGACTATGGAGCCAGGCTATCTGTTTTTGGGCTCTCGCCTGGGAAACTCACTGCTGCTCAGGTACACTGAGAAACTCCAGGAAACACCCATGGAGGAGGGCAAAGAGAATGAGGAGAAGGAGAAACAGGAAGAGCCTCCAAATAAGAAAAAACGTGTGGATTCCAACTGGGCAGGGTGTCCAGGAAAGGGCAATCTACCTGATGAGCTGGATGAAATTGAGGTGTATGGGAGTGAAGCTCAGTCAGGCACTCAGCTGGCCACATACTCATTTGAGGTTTGTGACAGCATACTAAACATTGGACCCTGTGCCAGTGCCTCCATGGGAGAACCAGCTTTTCTGTCTGAAGAGTTTCAAACCAACCCTGAGCCAGATCTGGAGGTGGTGGTGTGTTCAGGATATGGCAAGAATGGAGCACTGTCTGTATTACAGAAAAGCATCAGACCACAGGTGGTGACGACGTTCGAACTTCCTGGATGCCATGACATGTGGACAGTCATATACTGTGAGGAGAAACCCGAAAAGCCTTCAGCTGAGGGTGATGGAGAGAGTCCTGAGGAGGAGAAGCGCGAGCCCACAATAGAGGATGACAAGAAGAAACACGGCTTCCTCATCCTCAGCAGAGAAGACTCCACCATGatTCTCCAGACGGGTCAAGAGATCATGGAACTGGACACCAGTGGATTCGCCACACAGGGTCCTACAGTTTACGCGGGCAACATCGGAGACAATAAATACATCATCCAGGTGTCCCCCATGGGCATCAGACTGCTCGAGGGAGTTAATCAGCTCCACTTTATCCCTGTGGACCTGGGCTCTCCCATAGTGCACTGCTCTGTGGCCGATCCTTACGTGGTCATCATGACGGCAGAGGGAGTGGTCACTATGTTTGTCTTGAAGAATGACTCGTATATGGGAAAGAGTCACCGCCTGGCACTTCAGAAACCACAGATACACACGCAATCACGTGTTATTACGTTATGTGCATATCGCGATGTCAGTGGTATGTTCACAACTGAGAACAAGGTCAGCTTCCTGGCAAAAGAGGAAATTGCTATCAGAACCAACTCAGAGACAGAAACCATCATCCAGGACATCAGTAATACAGTGGATGATGAAGAGGAGATGCTGTACGGGGAGTCAAACCCCCTGACGAGCCCCAACAAAGAAGAGTCCAGCCGTGGCTCTGCAGCAGCAAGCTCCGCTCACACAGGAAAAGAGAGCGGCTCCGGCAGACAGGAGCCCTCACACTGGTGCCTGCTGGTTAGAGAGAATGGAGTCATGGAGATCTACCAGCTTCCAGACTGGCGTTTGGTTTTCCTGGTGAAAAATTTCCCAGTCGGTCAGCGTGTTTTGGTTGACAGCTCTGCCAGCCAGTCAGCTACTCAAGGGGAGcttaaaaaagaggaagtgacgAGGCAAGGTGACATTCCATTGGTCAAAGAGGTTGCTCTTGTGTCATTAGGCTACAACCACAGCCGTCCCTACCTTCTGGCTCATGTTGAACAAGAGCTTCTCATCTATGAGGCCTTTCCGTACGACCAGCAGCAAGCTCAAAGCAACCTGAAAGTGCGCTTCAAGAAGATGCCTCATAACATTAACTACAGAGAGAAGAAGGTCAAAGTGAGGAAGGACAAGAAGCCTGAGGGTCAGGGAGAGGACACTCTCGGCGTCAAAGGTCGTGTGGCCAGATTCAGATACTTCCAGGACATCTCTGGATACTCAGGGGTGTTTATCTGTGGTCCCTCTCCACACTGGATGTTGGTGACCTCTCGCGGGGCGATGCGCCTCCACCCCATGACAATAGATGGAGCCATTGAGTCTTTCTCTCCCTTTCACAATATCAACTGCCCCAAAGGATTTCTCTACTTCAACAAACAGGGTGAGCTGAGGATCAGTGTGTTGCCAACATACCTCTCTTATGATGCTCCCTGGCCTGTGCGCAAGATCCCTCTTAGGTGCACCGTCCACTATGTATCATACCATGTGGAATCCAAGGTGTATGCAGTGTGCACCAGTGTTAAAGAGCCGTGCACGCGCATCCCCAGAATGACTGGAGAAGAGAAGGAATTTGAGACCATTGAAAGAGACGAGCGATATATTCACCCTCAACAGGACAAGTTCTCAATTCAGCTCATCTCTCCAGTGAGCTGGGAGGCGATTCCAAACACACGCGTTGACCTTGAGGAGTGGGAGCATGTGACGTGCATGAAGACGGTGGCTCTGAAGAGTCAGGAGACAGTGTCAGGACTAAAGGGATACGTGGCTCTTGGGACGTGTCTCATGCAGGGAGAAGAGGTCACCTGTAGAGGCAGAATCCTGATTCTGGATGTGATAGAGGTGGTCCCAGAGCCCGGACAGCCCCTCACCAAGAACAAGTTTAAAGTGCTGTATGAAAAGGAGCAGAAAGGTCCCGTCACTGCTCTTTGTCACTGCAGTGGATTCCTGGTGTCTGCTATTGGACAGAAGatcTTCCTGTGGAGTCTGAAGGATAATGATCTGACGGGAATGGCATTCATTGACACACAGCTCTACATTCATCAGATGTACAGCATCAAGAACTTCATCCTCGCAGCAGATGTGATGAAGAGCATCTCTCTGCTGCGCTACCAGCCGGAGAGCAAGACGCTTTCACTCGTCAGCAGGGATGCAAAGCCCCTTGAGGTTTACAGCATAGAGTTTATGGTAGACAATAACCAGCTTGGTTTTTTGGTTTCAGACAGAGACAAAAACCTTATGGTCTACATGTACCTGCCTGAAGCCAAAGAGAGTTTTGGAGGCATGCGTTTGTTGCGGAGAGCAGATTTTAACGTGGGATCGCATGTGAACGCCTTCTGGAGGATGCCATGCCGCGGGACACTGGACACAGCCAACAAGAAGGCCCTCACCTGGGACAACAAACACATCACCTGGTTTGCTACGCTGGATGGTGGTGTCGGTCTGCTTTTACCAATGCAGGAGAAGACGTACCGCAGACTGCTGATGTTGCAGAACGCTCTCACCACCATGCTGCCACATCATGCCGGGCTCAATCCAAAGGCTTTCAGGATGCTGCACTGTGACCGGCGAACGCTCCAGAATGCTGTCAAGAACATCCTGGATGGAGAGCTGCTCAATAAATACCTGTATCTCAGTACCATGGAGAGAAGTGAACTGGCCAAGAAGATCGGCACGACCCCTGACATTATCTTGGATGATCTTCTGGAGATTGAAAGAGTCACTGCTCACTTCTGA

Function

GO:

id name namespace
GO:0006378 mRNA polyadenylation biological_process
GO:0031290 retinal ganglion cell axon guidance biological_process
GO:0060216 definitive hemopoiesis biological_process
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex cellular_component
GO:0005634 nucleus cellular_component
GO:0016740 transferase activity molecular_function
GO:0016757 transferase activity, transferring glycosyl groups molecular_function
GO:0003950 NAD+ ADP-ribosyltransferase activity molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003723 RNA binding molecular_function

KEGG:

id description
ko03015 mRNA surveillance pathway
ko03021 Transcription machinery
ko03019 Messenger RNA biogenesis

ZFIN:

id description
ZDB-GENE-040709-2 Predicted to enable nucleic acid binding activity. Acts upstream of or within definitive hemopoiesis; mRNA polyadenylation; and retinal ganglion cell axon guidance. Predicted to be located in nucleoplasm. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. Predicted to be active in nucleus. Is expressed in brain; gut; head; and pectoral fin. Human ortholog(s) of this gene implicated in myopia. Orthologous to human CPSF1 (cleavage and polyadenylation specific factor 1).

Ensembl:

ensembl_id ENSDART00000163478

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00030168 lncRNA downstream 670294 11219761 ~ 11227568 (-) True XLOC_014612
TCONS_00028870 lncRNA downstream 1021032 10875733 ~ 10876830 (-) False XLOC_014603
TCONS_00028865 lncRNA downstream 1033063 10859194 ~ 10864799 (-) False XLOC_014603
TCONS_00028866 lncRNA downstream 1037413 10859122 ~ 10860449 (-) False XLOC_014603
TCONS_00028835 lncRNA downstream 1578900 10313927 ~ 10318962 (-) True XLOC_014586
TCONS_00028909 lncRNA upstream 184795 12134791 ~ 12138739 (-) False XLOC_014624
TCONS_00028922 lncRNA upstream 448548 12398544 ~ 12404316 (-) False XLOC_014631
TCONS_00030169 lncRNA upstream 670930 12620926 ~ 12623962 (-) True XLOC_014632
TCONS_00030170 lncRNA upstream 1017023 12967019 ~ 13008216 (-) False XLOC_014635
TCONS_00030171 lncRNA upstream 1017023 12967019 ~ 13009415 (-) True XLOC_014635
TCONS_00028896 mRNA downstream 50904 11632834 ~ 11846958 (-) True XLOC_014619
TCONS_00028895 mRNA downstream 351346 11508960 ~ 11546516 (-) True XLOC_014618
TCONS_00028894 mRNA downstream 466584 11429263 ~ 11431278 (-) True XLOC_014617
TCONS_00028892 mRNA downstream 472270 11331823 ~ 11425592 (-) False XLOC_014616
TCONS_00028902 mRNA upstream 2313 11952309 ~ 11977783 (-) False XLOC_014621
TCONS_00028903 mRNA upstream 5339 11955335 ~ 11966015 (-) True XLOC_014621
TCONS_00028904 mRNA upstream 80836 12030832 ~ 12078583 (-) True XLOC_014622
TCONS_00028906 mRNA upstream 171948 12121944 ~ 12145765 (-) False XLOC_014624
TCONS_00028908 mRNA upstream 182479 12132475 ~ 12145390 (-) False XLOC_014624
TCONS_00028897 other downstream 172231 11725496 ~ 11725631 (-) True XLOC_014620
TCONS_00028885 other downstream 704499 11193249 ~ 11193363 (-) True XLOC_014611
TCONS_00028867 other downstream 1037396 10859217 ~ 10860466 (-) False XLOC_014603
TCONS_00028860 other downstream 1167384 10692166 ~ 10730478 (-) False XLOC_014599
TCONS_00028905 other upstream 96458 12046454 ~ 12046570 (-) True XLOC_014623
TCONS_00028907 other upstream 181049 12131045 ~ 12131180 (-) True XLOC_014625
TCONS_00028910 other upstream 184851 12134847 ~ 12145765 (-) True XLOC_014624
TCONS_00028911 other upstream 186740 12136736 ~ 12136871 (-) True XLOC_014626
TCONS_00028921 other upstream 436301 12386297 ~ 12392758 (-) True XLOC_014630

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000320_00207493_00228007.mRNA True 4569 mRNA 0.50 36 CI01000320 207311 ~ 228092 (-)
bowfin (Amia calva) AMCG00021766 True 4338 mRNA 0.51 37 CM030130.1 29025563 ~ 29041941 (+)