XLOC_038008 (upf3a)


Basic Information

Item Value
gene id XLOC_038008
gene name upf3a
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007120.7
NCBI id CM002893.2
chromosome length 56459846
location 34902971 ~ 34915394 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00074572
AGAGTTAGCGGATTTCGGACAGCGAAGAGGGCGAAATGGAGATATGAGGTCTGAAAAGGAGCAGAGGACAGGCAGCAGGGAGAGAGGAAGCGTCGAAATCCAGTTCAGGGACTGTCAGGACAACGCCGCTGTGAACCCCAAGCACAAGGAGGAGAAAAAGGAGATCTTCAGCAAGGTTGTCATCCGCCGACTGCCACCCAGTCTATCAAAAGACCAGCTCCAGGAGCATCTGAGTCCTCTTCCATCTTTTGACTATTTTGAGTTCTTTCCTGCTGATCAGAGCTTATACCCTCATCTCTTCTCAAGAGCATACATAAACTTCAAAAACCCAGAGGATATCATAATATTCAGAGATCGCTTTGATGGCTATGTATTTATTGACAATAAAGGTCAAGAATATCCAGCTGTTGTAGAATTTGCCCCATTTCAGAAGGTTTCCAAGAAAAAGCTAAAGAAGAAAGATGCGAAAGCTGGGACCATTGAAGAAGACCCAGAATACAGGCGATTTCTGGAAAACTACTCTTGTGATGAGGAGAAATCGATGGCCAACCCAGAAACGCTTTTGGGAGAGATTGAAGCTAAAACCCGAGAGCTCATAGCCAAAAGGACGACACCCTTGCTGGAATACATCAAAAACAAGAAATTAGAGAAACAGAGAATAAGAGAAGAAAAAAGAGAAGAGAGGCGAAGAAGAGAACTGGAAAAGAAGAGGCAGAGGGAAGAGGAGAAGAGGAAACGCAGAGAAGAGGAGAGACAAAAGCGGAAGGAGGCAGAAAAGCAGAAAAAGCTCTCTGAGAAAGAGATAAAGATCAAGCTTTTGAAGAAGTGTGACCGAGACGATGACGTGGATTCAGACAGACTGAAAGATAAAGGAGACAGTGGAGAGACGGAGAAGAACAGATGGGAAAAGCCTGGAGGACACACTAAGTCAAAGGATTCAAAGGATAATAGGAGCCAAATGGAAAATGACAAGGAGCAGCGTGAGGGCCACGGCCGACGGCAGAGGGACAAAGATCACCGTGGCCGAGATGAGGAACGTAAACGACAGAGGCATCACTACGAATTTGACAAGTTCATGCGACGCAAGGAAGAGACCAAATGGGGCAAAGGCTACTGCCAGGACAGGGCCAAGAAAGACCAACACCATGGGTATTCCTACTGCCCAGAGACTGGAGACAAACTGGGCAAAGAGGACCGAGAGGACATGGGCAGCAGGAAAGAACGCATCCGCAATAAGTCTGTGTTAGTGCATCAGGAGAAAAGGACTTCCCAGTCTGAGGGGCCAGACCAGATAGGAGGGGCTCTGCCAGCAAAGGACCGACCGGCAATGCAACTGTACCAACCAGGTGCTAGAAACCGCAAACGCATGGGCTCTGGAAACAAGACATTTGACTTCCCGCCGATCTCTCCCGAACATGCAGGAGAACACTGCTACAAAACAGTCATTGGTACAGGCTCTGAAAAGAGTGCTGACgagtgaaaaaacaaaacactattgacaGGAAGATGCCTAAGCAAGGGTCACACAAGTGTAGAAAAAAACACTAAACCTCAACCTTGTTTTCTGTCATGTGTGAGTACAGTGCATTGAAATCCCCTCTTAATATTTTCTACACAACAACGTCAACTGTGTCATAAACGATCGGCTTCTGTTTGCTTGTCAAGGATTCACAACCACTCCATTGAGAAAAATACCTCATTATTTACAAAGATCGGATTTGTATGCCTTTTTGTAGTGCAAGACTCCATTGATCAAGAGAATTAATATATATCTA
>TCONS_00074573
ATGAGGTCTGAAAAGGAGCAGAGGACAGGCAGCAGGGAGAGAGGAAGCGTCGAAATCCAGTTCAGGGACTGTCAGGACAACGCCGCTGTGAACCCCAAGCACAAGGAGGAGAAAAAGGAGATCTTCAGCAAGGTTGTCATCCGCCGACTGCCACCCAGTCTATCAAAAGACCAGCTCCAGGAGCATCTGAGTCCTCTTCCATCTTTTGACTATTTTGAGTTCTTTCCTGCTGATCAGAGCTTATACCCTCATCTCTTCTCAAGAGCATACATAAACTTCAAAAACCCAGAGGATATCATAATATTCAGAGATCGCTTTGATGGCTATGTATTTATTGACAATAAAGGTCAAGAATATCCAGCTGTTGTAGAATTTGCCCCATTTCAGAAGGTTTCCAAGAAAAAGCTAAAGAAGAAAGATGCGAAAGCTGGGACCATTGAAGAAGACCCAGAATACAGGCGATTTCTGGAAAACTACTCTTGTGATGAGGAGAAATCGATGGCCAACCCAGAAACGCTTTTGGGAGAGATTGAAGCTAAAACCCGAGAGCTCATAGCCAAAAGGACGACACCCTTGCTGGAATACATCAAAAACAAGAAATTAGAGAAACAGAGAATAAGAGAAGAAAAAAGAGAAGAGAGGCGAAGAAGAGAACTGGAAAAGAAGAGGCAGAGGGAAGAGGAGAAGAGGAAACGCAGAGAAGAGGAGAGACAAAAGCGGAAGGAGGCAGAAAAGCAGAAAAAGCTCTCTGAGAAAGAGATAAAGATCAAGCTTTTGAAGAAGTGTGACCGAGACGATGACGTGGATTCAGACAGACTGAAAGATAAAGGAGACAGTGGAGAGACGGAGAAGAACAGATGGGAAAAGCCTGGAGGACACACTAAGTCAAAGGATTCAAAGGATAATAGGAGCCAAATGGAAAATGACAAGGAGCAGCGTGAGGGCCACGGCCGACGGCAGAGGGACAAAGATCACCGTGGCCGAGATGAGGAACGTAAACGACAGAGGCATCACTACGAATTTGACAAGTTCATGCGACGCAAGGAAGAGACCAAATGGGGCAAAGGCTACTGCCAGGACAGGGCCAAGAAAGACCAACACCATGGGTATTCCTACTGCCCAGAGACTGGAGACAAACTGGGCAAAGAGGACCGAGAGGACATGGGCAGCAGGAAAGAACGCATCCGCAATAAGGACCGACCGGCAATGCAACTGTACCAACCAGGTGCTAGAAACCGCAAACGCATGGGCTCTGGAAACAAGACATTTGACTTCCCGCCGATCTCTCCCGAACATGCAGGAGAACACTGCTACAAAACAGTCATTGGTACAGGCTCTGAAAAGAGTGCTGACgagtga
>TCONS_00074574
AGCGGATTTCGGACAGCGAAGAGGGCGAAATGGAGATATGAGGTCTGAAAAGGAGCAGAGGACAGGCAGCAGGGAGAGAGGAAGCGTCGAAATCCAGTTCAGGGACTGTCAGGACAACGCCGCTGTGAACCCCAAGCACAAGGAGGAGAAAAAGGAGATCTTCAGCAAGGTTGTCATCCGCCGACTGCCACCCAGTCTATCAAAAGACCAGCTCCAGGAGCATCTGAGTCCTCTTCCATCTTTTGACTATTTTGAGTTCTTTCCTGCTGATCAGAGCTTATACCCTCATCTCTTCTCAAGAGCATACATAAACTTCAAAAACCCAGAGGATATCATAATATTCAGAGATCGCTTTGATGGCTATGTATTTATTGACAATAAAGGTCAAGAATATCCAGCTGTTGTAGAATTTGCCCCATTTCAGAAGGTTTCCAAGAAAAAGCTAAAGAAGAAAGATGCGAAAGCTGGGACCATTGAAGAAGGCATCTTAAAAAAGAtttcttaatatttataattttgaagTATTCAAGAATTGACGTCATTGTGTAAattacagttgatgtcagaattaacaacccccttcaaatttttttcttctttttgaaatattttccaaattatgtttaacagagcaagggagttttctcagtatgtctgataatattttttcttctggaaaaagtttttttttatttagtctagaataaaagcagtttgaatttttttaaacaccattttagggacaaaattattagcccttttaagctattttttttcttgaaaatctacagaacaaagcattgttatacaataacttgcctaattaccctaactcacCTAGTtaccccaattaacctagttaaacctttaaatgtccctttaaactgtatagaagtgtcttgaaaaatatctagtaaaatattatttactgtcatcatggcaaagataaaataaatccattattagaaatgagttattaaaactattatgtttagaaatgtgttaaagaaatctgctctccattaaatagaaattggggaaaaaaataaacaagcggtctaataattcaggggggctaataattctgacttcaactgtatatactgcaatatattaattaatttgttaaacaCTGTTTTCAGACCCAGAATACAGGCGATTTCTGGAAAACTACTCTTGTGATGAGGAGAAATCGATGGCCAACCCAGAAACGCTTTTGGGAGAGATTGAAGCTAAAACCCGAGAGCTCATAGCCAAAAGGACGACACCCTTGCTGGAATACATCAAAAACAAGAAATTAGAGAAACAG

Function

symbol description
upf3a Predicted to enable telomeric DNA binding activity. Predicted to be involved in positive regulation of translation. Predicted to act upstream of or within mRNA transport and nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Part of protein-containing complex. Orthologous to human UPF3A (UPF3A regulator of nonsense mediated mRNA decay).

GO:

id name namespace
GO:0045727 positive regulation of translation biological_process
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay biological_process
GO:0051028 mRNA transport biological_process
GO:0005634 nucleus cellular_component
GO:0005730 nucleolus cellular_component
GO:0005737 cytoplasm cellular_component
GO:0005515 protein binding molecular_function
GO:0042162 telomeric DNA binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003723 RNA binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-060721-2 Predicted to enable telomeric DNA binding activity. Predicted to be involved in positive regulation of translation. Predicted to act upstream of or within mRNA transport and nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Part of protein-containing complex. Orthologous to human UPF3A (UPF3A regulator of nonsense mediated mRNA decay).

Ensembl:

ensembl_id ENSDARG00000069297

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00074572 False 1775 mRNA 0.46 11 34902971 34915394
TCONS_00074573 False 1359 mRNA 0.47 10 34903266 34915351
TCONS_00074574 True 1309 lncRNA 0.36 5 34908935 34915388

Neighbor

gene id symbol gene type direction distance location
XLOC_038007 p2ry8 coding downstream 17069 34884933 ~ 34885902 (-)
XLOC_038006 asmtl coding downstream 20455 34872733 ~ 34882516 (-)
XLOC_038005 slc25a6 coding downstream 31071 34866576 ~ 34871900 (-)
XLOC_038004 BX601644.3 coding downstream 51167 34848860 ~ 34851804 (-)
XLOC_038003 BX601644.2 coding downstream 60557 34836068 ~ 34842414 (-)
XLOC_038009 cdc16 coding upstream 4607 34920001 ~ 34937256 (-)
XLOC_038010 dcun1d2a coding upstream 22922 34938316 ~ 34945582 (-)
XLOC_038011 METTL21C coding upstream 55024 34970418 ~ 34974416 (-)
XLOC_038012 si:ch211-160b11.4 coding upstream 63473 34978867 ~ 34986827 (-)
XLOC_038013 appb coding upstream 111021 35026415 ~ 35161005 (-)
XLOC_038001 NA non-coding downstream 90088 34592026 ~ 34812883 (-)
XLOC_038002 BX601644.5 non-coding downstream 149812 34753044 ~ 34753159 (-)
XLOC_038000 NA non-coding downstream 315164 34546666 ~ 34587807 (-)
XLOC_037996 NA non-coding downstream 547421 34350517 ~ 34355550 (-)
XLOC_038016 NA non-coding upstream 765574 35680968 ~ 35832754 (-)
XLOC_038017 CR759895.1 non-coding upstream 786261 35701655 ~ 35701772 (-)
XLOC_038019 NA non-coding upstream 1075270 35990664 ~ 35995392 (-)
XLOC_038020 BX005438.1 non-coding upstream 1203566 36118960 ~ 36120526 (-)
XLOC_038021 NA non-coding upstream 1484517 36399911 ~ 36413250 (-)

Expression


Co-expression Network