XLOC_018154 (cpsf3)


Basic Information

Item Value
gene id XLOC_018154
gene name cpsf3
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007131.7
NCBI id CM002904.2
chromosome length 55201332
location 29619820 ~ 29633507 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00035794
GTCCTGTGTCTACAGCGTGTGGTTTTCAGTTCACTTGATCGTTGTTTGGTATTATTGGAGGTATCGCTAAATATGCAAGAAGTATTACTTATTTAAGATTAAAACCATCACAAACATGGCTACCAAACGTAAAGCCGATGTACCAGTGCCTGCGGAAGAGAGTGATCAGCTCCTCATCAGACCGCTAGGAGCTGGGCAGGAGGTTGGCAGGTCCTGTATCATCCTGGAGTTCAAAGGCCGCAAAATCATGCTGGACTGTGGCATCCACCCTGGACTGGAGGGCATGGATGCATTGCCTTACATTGATTTAATAGACCCAGCTGAGATTGACCTGCTGCTCATCAGCCATTTTCACTTGGATCATTGTGGAGCTTTACCATGGTTTTTACAGAAGACAAGTTTCAAAGGGAGGACATTCATGACCCATGCCACCAAAGCCATCTACCGCTGGTTACTTTCAGACTATGTCAAAGTCAGCAATATTTCAGCTGACGACATGCTGTACACCGAGACTGATCTAGAAGAAAGCATGGACAAGATAGAAACCATCAACTTCCATGAAGTGAAAGAGGTGGCCGGCATCAAGTTTTGGTGTTATCATGCAGGGCATGTTTTGGGAGCAGCCATGTTCATGATTGAGATTGCAGGAGTGAAGCTGCTGTACACCGGTGATTTCTCACGCCAAGAAGACCGACATCTCATGGCTGCTGAGATTCCCAGCGTCAAACCAGACATTCTCATTACTGAGTCCACATATGGTACACACATCCATGAGAAGCGAGAGGAGAGAGAGGCTCGTTTCTGTAACACAGTCCATGACATAGTGAACCGTGAGGGCCGCTGTCTCATCCCCGTGTTTGCTTTGGGCCGAGCCCAGGAGCTGCTTCTCATTCTAGATGAATACTGGCAGAATCATCCTGAGCTCCATGACATTCCTATTTACTATGCTTCGTCTCTGGCTAAGAAGTGCATGGCTGTGTATCAGACCTATGTGAATGCAATGAATGACAAGATCCGCAAGGCCATCAATATTAATAACCCTTTTGTCTTTAAGCATATCAGCAATCTCAAGAGCATGGACCATTTCGATGACATCGGCCCAAGTGTAGTGATGGCATCTCCAGGTATGATGCAGAGTGGCCTCTCCAGAGAGCTGTTTGAGAGCTGGTGCACAGACAAGAGGAACGGCGTCATCATAGCGGGTTACTGTGTGGAAGGAACACTCGCAAAGCATATCATGTCTGAGCCTGAGGAGATCACCACCATGTCTGGACAGAAGCTTCCGCTGAAGATGTCAGTGGATTACATCTCATTCTCTGCTCATACAGACTACCAGCAGACCAGCGAGTTCATCCGAGCTCTGAAACCTCCTCATGTGatTTTGGTTCATGGAGAGCAGAATGAAATGGCTCGGTTGAAGGCTGCGCTGATCCGAGAGTATGAGGACAATGATGAGGTTCACATTGAGGTGCACAATCCTCGAAACACAGAGGCTGTCACACTCAACTTCAGAGGAGAGAAACTGGCCAAGGTGATGGGCTCTCTTGCGGATAAGAAGTGTTCACAGGGTCAGAGAGTCTCCGGGATCCTGGTGAAAAAGAACTTCAGTTACCACATCCTCTCTCCTTCTGACCTCTCTAATTACACTGATCTTGCCATGAGCACGGTGAAACAGACTCAAGCCATTCCCTTCACTGGCCCTTTTCCCTTGCTGTTGAGTCAGTTACGTCACCTGACAGGTGATGTAGAGGAGATTGAGATGTCAGAGAAGAGCACAGTGAAAGTCTTTAACAGCATCACAGTGATTCATGAGAACAACTTGGTGGTTTTGGAGTGGTTTGCCAATCCTCTGAATGACATGTACGCCGATGCCGTCACCACAGTGGTTCTGGAAGTGCAGTCAAACCCCAAAGCTCAGAAAGCTCTTCAGCCCCAAGAAAAGAAAGTGGATGTAAATGTTTTTCAGAATAGACTACTGAAAATGTTCCAAGACATGTTTGGAGAGGAGTGTGTCGACTTTAAAGACAAGAACTGTCTCGCCGTGAATGTAGATGAGAAGACGGCCTTCATTGACCTGGAAACAAGAACGGTGGAGTATGAAGAGCCCAATCCTGAAGATGATTCTCTCAGAGAAATGCTGGAGCTCGCCGTACAGAGGCTGTATGAAGCCATAAACCCAGTGTTGTGAGATGACATCTGCCCTCTCTCAGGCTATTCACTTCCCACAAAAACTGTTGATATCAGAGTCCTTTAACTTAAACTATTAAGCCAGACTGAAGAAGACACCAGATACTGAACTGGACAAAGCACTTCAAATGAAAgtgtaataaaaaaaggaaaacagttTACGGTGTATGTTGATGCTTGTCTTTTTCCAGGTCTGTCAATTATACAATAGCCTAAACTGTGATTGTTTGGTATGTTGTTTTTTCTAAGTTGTTTTGTTTAAGTTGTAATTGGTTTAAAATCAGTgcatttgctttaataaatgaGGTCTTTGAAGTACGAATGTGCTCTATGCTTTTGATAATATCGTAACTGTTTTAATATCAAATAATACAGTTGGAATAATAATT
>TCONS_00035795
GGACCATTTCGATGACATCGGCCCAAGTGTAGTGATGGCATCTCCAGGTATGATGCAGAGTGGCCTCTCCAGAGAGCTGTTTGAGAGCTGGTGCACAGACAAGAGGAACGGCGTCATCATAGCGGGTTACTGTGTGGAAGGAACACTCGCAAAGGTGAATCAGCTCAATCTTCCACAAAACCTGTCCCCAGAGTTCAGCATTATCTTTTTGAGCATGACTGACCTGTTCTGACCTCACCCTGTTTTCCGTGCAGCATATCATGTCTGAGCCTGAGGAGATCACCACCATGTCTGGACAGAAGCTTCCGCTGAAGATGTCAGTGGATTACATCTCATTCTCTGCTCATACAGACTACCAGCAGACCAGCGAGTTCATCCGAGCTCTGAAACCTCCTCATGTGatTTTGGTTCATGGAGAGCAGAATGAAATGGCTCGGTTGAAGGCTGCGCTGATCCGAGAGTATGAGGACAATGATGAGGTTCACATTGAGGTGCACAATCCTCGAAACACAGAGGCTGTCACACTCAACTTCAGAGGAGAGAAACTGGCCAAGGTGATGGGCTCTCTTGCGGATAAGAAGTGTTCACAGGGTCAGAGAGTCTCCGGGATCCTGGTGAAAAAGAACTTCAGTTACCACATCCTCTCTCCTTCTGACCTCTCTAATTACACTGATCTTGCCATGAGCA
>TCONS_00035796
GAGCAGAATGAAATGGCTCGGTTGAAGGCTGCGCTGATCCGAGAGTATGAGGACAATGATGAGGTTCACATTGAGGTGCACAATCCTCGAAACACAGAGGCTGTCACACTCAACTTCAGAGGAGAGAAACTGGCCAAGGTGATGGGCTCTCTTGCGGATAAGAAGTGTTCACAGGGTCAGAGAGTCTCCGGGATCCTGGTGAAAAAGAACTTCAGTTACCACATCCTCTCTCCTTCTGACCTCTCTAGTAAGCTGATGATTATGATTGTTTCGTTGTTCATATATGTGTGCAGGGCCTAAAACTAACATTCGCTGTAATTACAAAGTGCTTGTAATTCTAATAACCACACAACACCATTTCTGTATTCTCGGACATTGTATTTGAATTTGTAGGAAGTTACCAGTCAACTGGCCAGTAACATTGTTTCATACACTCACAAATGGTGTGTGTTTGCTTCTgtgctgttgtttttaaatattgcagATTACACTGATCTTGCC

Function

symbol description
cpsf3 Predicted to enable 5'-3' exonuclease activity; RNA binding activity; and endoribonuclease activity. Predicted to be involved in mRNA 3'-end processing by stem-loop binding activity and cleavage and mRNA polyadenylation. Predicted to act upstream of or within mRNA processing. Predicted to be located in nucleus. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. Orthologous to human CPSF3 (cleavage and polyadenylation specific factor 3).

GO:

id name namespace
GO:0006378 mRNA polyadenylation biological_process
GO:0006398 mRNA 3'-end processing by stem-loop binding and cleavage biological_process
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex cellular_component
GO:0008409 5'-3' exonuclease activity molecular_function
GO:0004521 endoribonuclease activity 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-030131-3275 Predicted to enable 5'-3' exonuclease activity; RNA binding activity; and endoribonuclease activity. Predicted to be involved in mRNA 3'-end processing by stem-loop binding activity and cleavage and mRNA polyadenylation. Predicted to act upstream of or within mRNA processing. Predicted to be located in nucleus. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. Orthologous to human CPSF3 (cleavage and polyadenylation specific factor 3).

Ensembl:

ensembl_id ENSDARG00000027649

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00035794 False 2576 mRNA 0.45 18 29619820 29633507
TCONS_00035795 False 687 lncRNA 0.49 4 29623551 29626488
TCONS_00035796 True 501 lncRNA 0.43 2 29623558 29625984

Neighbor

gene id symbol gene type direction distance location
XLOC_018153 taf1b coding downstream 86810 29513470 ~ 29533010 (-)
XLOC_018152 klf11a coding downstream 113957 29502065 ~ 29505863 (-)
XLOC_018150 rrm2 coding downstream 120394 29492469 ~ 29499426 (-)
XLOC_018151 BX248136.1 coding downstream 124385 29495300 ~ 29495435 (-)
XLOC_018149 actc1a coding downstream 136306 29476852 ~ 29483514 (-)
XLOC_018155 si:ch211-195d17.2 coding upstream 43367 29676874 ~ 29683783 (-)
XLOC_018156 NA coding upstream 54128 29687635 ~ 29691465 (-)
XLOC_018157 id2b coding upstream 151420 29784927 ~ 29787210 (-)
XLOC_018158 NA coding upstream 156435 29789942 ~ 29834538 (-)
XLOC_018159 rnf144ab coding upstream 202769 29836276 ~ 29864530 (-)
XLOC_017928 CU539064.1 misc downstream 19566119 10053405 ~ 10053701 (-)
XLOC_018147 NA non-coding downstream 190358 29426938 ~ 29429462 (-)
XLOC_018140 NA non-coding downstream 755938 28860442 ~ 28863882 (-)
XLOC_018136 BX569801.1 non-coding downstream 1007498 28611272 ~ 28612322 (-)
XLOC_018130 NA non-coding downstream 1386228 28233277 ~ 28233592 (-)
XLOC_018160 NA non-coding upstream 293678 29927185 ~ 29933758 (-)
XLOC_018162 NA non-coding upstream 458752 30092259 ~ 30099019 (-)
XLOC_018163 NA non-coding upstream 489983 30123490 ~ 30258573 (-)

Expression


Co-expression Network