XLOC_033093 (usp4)


Basic Information

Item Value
gene id XLOC_033093
gene name usp4
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007117.7
NCBI id CM002890.2
chromosome length 60270059
location 42345005 ~ 42369186 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00064306
AACTTATTTcagttaataaaaaatgtttattaaccGCTGTACCAGAGGGCTCGGTTTGTTTCATTTATCAGCCGCTCCCAGATTGCATGTAGCGGCTAGTCGAGCTCGGCAGTAGCTCCAGTGTGCGCGCTCCCTTTAGCGCTGCGCGTCCCCGGTATACTTCAGCAGCGCGCTCGCGGTCACTGCGGGTTCACTCGCTGCACGATGGCGGAGGGAGGCGGACCCGAGTCGGGTAACGCTTCGGACCCTGACGAGAAGCCGGTGATCACACAGACACCAGTACCGTCCACCGAGAGTCAAAAGCAGAGCATCGGGACACTGCTAAAAACGCTACTTCGAAAGGGAGACGAGTgGTATTTGATTGACAGCCGGTGGTTCAAACAGTGGAAGAAATATGTTGGCTTTGACAGCTGGGATTTGTACAATGTTGGAGAGCACAATCTCTACCCGGGACCCATTGACAACTCTGGCCTCTTTTCAGATCGCAAGTCCCAGTCGCTGAAAGAACATCTTATAGATGAGTTAGACTATGTTTTAGTGCCTACTGAGGCCTGGAATAAGCTGGTCAGTTGGTATGGCTCTCTGGGAAATCAGAAACCCATCATCAGAAAGGTTGTTGAACATGGGATGTTTGTTAAACACTGTAAGGTTGAAGTGTATTTGCTTGAGTTGAATCTGTGTGAAAATGACAACATGGACAAAGTTGTCACTCGCCATTTCAGCAAAGCAGACACTATAGATACTATTGAAAAGGAAATGAGGTCTTTATTTGACATCCCATCTGAAAAGGAAACTCGTCTTTGGAATAAATATATGAGTAACACCTATGAACAGCTTAACAAGCTTGACAGCACCGTACAGGATGCAGGGCTTTTTCAGGGCCAGGTGCTTGTTATAGAGAAGAAGAATGAGGATGGCACATGGCCCAGACAGAGCTGCCATTCAAAGTCCAGCACTTCAACTTCTCGGAATTATACAACCTCCCCAAAGCCTTCTTCAAACTCATCTGCCACCATATCTTCCACAATTACCAATGGAGATAGCAATAGCAACTCTGGTTACATGCTGAACAACAGTACTTCTGGTAACAGATTGGGAAGTTACAACTCGTACAGCTCGTCCTACAGTTACAGAGAATCTGCTGCTCAGCCGGGCCTCTGCGGCCTGAGCAACTTGGGCAACACCTGCTTTATGAACTCTGCCCTCCAGTGCCTGAGCAACACCCCCCCTCTGACGGAATATTTCTTGGAGGATCGATATGAAGCTGAGATCAACCGGGAAAATCCATTAGGGATGAGAGGAGAGATTGCGGAGGCCTATGCGGATCTGGTCAAACAGATGTGGCTTAGTCGGAGCAGTTATGTGGCTCCACGCACTTTTAAAACCCAGGTGGGTCGGTTTGCCCCGCAGTTCTCAGGGTACCAGCAACAAGACTCTCAGGAGCTGCTAGCCTTTTTGTTAGACGGCTTACATGAAGACCTTAACCGTGTCAAGAAGAAGCCTTACCTGGCCCTGAGAGATGCAGAGGGACGACCTGATGAGATTGTAGCCAAGGAAGCATGGGCGAATCACCGGTTGCGGAATGATTCCATAATCGTAGACATTTTCCATGGCTTGTTTAAATCTACCCTGGTCTGTCCCGAATGCTCCAAAGTTTCCGTTACCTTTGACCCATTCTGCTACCTCACACTGCCCCTTCCCATGAAAAAGGATCGCACTATGGAGGTGTACCTTGTCCGCACTGACCCGCAGTTCAGAGCCATGCAATTTCGTGTTGTGGTTCCCAAAATGGGTGCTGTGGCAGACCTGTGCAGCGCTTTGGCCAAGCTATCTGGAGTTCCTTCAGAAAACATGGTTGTGGCGGATGTTTACAATCACAGATTTCACAAAATCTACAAACGGGATGATGGTCTCAATCAAATTATGGAGAAAGATGACATATTTGTTTATGAGGTGTTAGAAGAAGACAGTGAGAGGATGAATCTGCCAGTGTACTTTAGAGAGAGGCATGCTAAACACAGTGGAGGCTCTTCGGGCACAATGCTCTTCGGTCAACCTCTTCTCATCACCGTCCCGCGCCTCAACCTCACCGTGGATACCCTCTACGAGCGCGTGCTGGAGAGAATTGGgcgATACGTTAAACGTTCACAAGGTACCATTACAGAGAGTAGAGCATCTGCTTCAGCCACATCTTCTAGCAGCAGCCAATCACCAGAATGCCTCGCTTCAGTGTCCAGTCACGGCACAGGCCTGAGTGGCTGCAGCAGCCCAGTTTCAGATGGAGCTTCCTGCAGCGCTGGATCCAACGGCAGCAACCATTCTGGAACCTGCAACGGCCCTAATGGAGTTTGTGATGgAGATGAGGAAGCTATGGACCACCAGGAGAGTCCAGAGCCAGAAAACAGCCATTCGGACACTGTGGACGGAGAGGAGGATTCTGAACCAGAGAATGGGCCAAATAGTAGCGGAGGAAAATCTTTTAATTCTCGGCCAAAACTCTTTTCTTTCAGCATGGTCAACTCCTACGGCACAGCCAACATCAGTTCTCTTCCATTTGATGGCAATCTACTGAAGCTAACAACTCACTCAACAGTAGCCATTGATTGGGACTCGGACACAAAAAGATTGTGCTATGATGATCAGGAAGCTGAGGCCTATGACAAACACGAGAGTATGCTTCATGCTCAAAAGAAGAAGACTACAGTAGCTTTACGGGAATGCATTGAGCTCTTTACTACAATGGAGACTTTAGGAGAGCATGATCCATGGTACTGCCCCACGTGTAAGAAACACCAGCAGGCCACTAAGAAGTTTGATCTGTGGTCTCTTCCACGCATTTTGGTTGTGCATCTGAAGCGCTTCTCCTACAACCGCTGCTGGAGAGACAAGCTCGACACTGTTGTGGACTTTCCAATTAGGGACTTAAACATGTCAGAGTTTGTGTGTGACCCCAAAGCTGACCCATACATCTACGACCTCATTGCTGTTTCCAACCATTATGGAGGAATGGGCGGAGGCCACTACACGGCTTACGGCAAGAACAAGGCGGATGGCAAATGGTATTACTTTGACGACAGCAGTGTGTCTGCTGCTACTGAGGATCAGATTGTGACTAAAGCAGCCTACGTGCTCTTTTACCAACGCAGAGATGCAGACACGCCGTCCAAATCCCCCCCGTCCGCTTCACTAGGAGGAGCTCCGGAGACTCCCGACGACCACATGGACACCAACTGAATttcttttagtctttttttttttttttgaggactgGCACTGAAACAAAAAACTACATATGAAATCATCAATGCATCGACGCACATCCCTGGCTACTTCAGTGACTATTAAAGGCTCACAAACTGGCCCTttgtttttagctttattttactttttctttgaCACATGCGTCTTTATCAAGAGCCAAAAAAacgaaaaaacagaaaaagaatattaataataaataaagagaatTTTAGTTTGAAGCGTGACATGAAAGACTTTATTCTTGGACCTCGATGCCTGCTGAATCATAGGAGCTTGATTCTTATAGTCTGAAATGAGGAGGGTGAAACGGCAATATAACCTCTCTTTGGACGACATGAATGTTAGATGAACTAGATCGGGAGAGGGGAAATGCCTAGAAATAGACTATGTATGCAACATTATGCTCATCTGAAATGTTTAAATTATGCCTCGACTACACACTTGCGTTGGACTCTTTAGCTCTCAGCATCTTGTAAACATGTGCCTCGTGTGAAAAatagactctctgtgtttaatAACTTAAGCGTGTGGTGAGAAGCACAGAGATTCTCTCGGAGAAGCTTGCGCTCTTATATTAAATATTGTCTCCATGTTTTGTTTCTCCTATCACAAGTCACGCTTTTTGTTCAATATACCACGCTGGAGGGGGTTTCACTTTAAAACTTGCAGAACTATAAGGTTCTTAGAGGGGGGAGGGTTGATTATCTAATGTTTTCACTCcccaaacactaaaaaaaaaaaagggatatTAAAGTAACAAAGAGAAAAAGGAGTGGATCAAATCACACTTCCAAAGCTTTTCGTTTCAGAATTGATGGTTTGGGCTTTATAACacttgtttttcttctgttttattcattttgctgGTTGTTTCTCCTCCCCGAATGGCTTTGTCCTGAGGAATATCACGTCTGATTGAACATGGTGCTAAATGTGACACTTAAAAAGGTATACTTACAATTAAAGAGGAACACACAAACCGGCCGTTGTTTGAACAGCTTTAAAGAGGGTTACAATTAACCGAAGATGTACATTAGCACatgtgccatgtgattggttatCAAATGACAACGCTCAAAACAAGTGCTTcatattgctaataataacaaTGCACAAAGCATAttctttttgtttgtgtgtgagtggcAAAACAGCATGCAAATGTTTGAATCTGCAAAATGGTAAATAGTTGGTTGTTCCTGGTGTTTACCTTACTATGGTATTAGCCGTCACTCACTGATAAATccacaattgttttatttttttattaacttaatgATCTTGGACTGAGCTGTTCCCCCTGCGGCTTCTTCAGCAGTAAACATCCATTTTAACGTTTTGGTTGTTTCGtaatttcatagatttttttttcttgcatagaTGTACATAATCATCATCTGGAGCACAGTAGATAGCTGCTTTGTGTTCTTCTATTTATCATGCCAAGATGTGCGACACCAGATTTTGATTAAAGCCTATTTGaactgaaaatataataaaatgtggaAGCCTGATTATAGAtcatgcttttgtttttgttttcttaagcCGATCAGgtcaattaaagggatagtttaaataaaaatgcactcaTTATTAAGGGTTCCAAA

Function

symbol description
usp4 Predicted to enable thiol-dependent deubiquitinase. Acts upstream of or within convergent extension; negative regulation of toll-like receptor signaling pathway; and protein deubiquitination. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Orthologous to human USP4 (ubiquitin specific peptidase 4).

GO:

id name namespace
GO:0016579 protein deubiquitination biological_process
GO:0006511 ubiquitin-dependent protein catabolic process biological_process
GO:0060026 convergent extension biological_process
GO:0034122 negative regulation of toll-like receptor signaling pathway biological_process
GO:0005634 nucleus cellular_component
GO:0004843 thiol-dependent ubiquitin-specific protease activity molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-041008-187 Predicted to enable thiol-dependent deubiquitinase. Acts upstream of or within convergent extension; negative regulation of toll-like receptor signaling pathway; and protein deubiquitination. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Orthologous to human USP4 (ubiquitin specific peptidase 4).

Ensembl:

ensembl_id ENSDARG00000014770

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00064306 True 4871 mRNA 0.45 22 42345005 42369186

Neighbor

gene id symbol gene type direction distance location
XLOC_033092 fancd2 coding downstream 8010 42291308 ~ 42336995 (-)
XLOC_033091 tex264a coding downstream 54746 42145626 ~ 42290259 (-)
XLOC_033090 grm2a coding downstream 232814 42051480 ~ 42112191 (-)
XLOC_033089 parp3 coding downstream 295655 42038358 ~ 42049350 (-)
XLOC_033088 gpr61l coding downstream 308320 42031836 ~ 42036685 (-)
XLOC_033094 emc3 coding upstream 813 42369999 ~ 42377307 (-)
XLOC_033095 sec61a1l coding upstream 8725 42377911 ~ 42388608 (-)
XLOC_033096 ip6k2a coding upstream 39896 42409082 ~ 42418225 (-)
XLOC_033097 edem1 coding upstream 563571 42932757 ~ 42949184 (-)
XLOC_033098 arl8ba coding upstream 582774 42951960 ~ 42971184 (-)
XLOC_033085 NA non-coding downstream 892117 41451670 ~ 41452888 (-)
XLOC_033077 NA non-coding downstream 1376664 40963686 ~ 40968341 (-)
XLOC_033076 CR293534.1 non-coding downstream 1398530 40946357 ~ 40946475 (-)
XLOC_033074 NA non-coding downstream 1480927 40856139 ~ 40864078 (-)
XLOC_033070 CR450814.1 non-coding downstream 1525239 40795898 ~ 40819766 (-)
XLOC_033102 NA non-coding upstream 688276 43057462 ~ 43072882 (-)
XLOC_033106 BX927362.1 non-coding upstream 977743 43346929 ~ 43349086 (-)
XLOC_033111 NA non-coding upstream 1610525 43979711 ~ 44002542 (-)
XLOC_033118 NA non-coding upstream 3554756 45923942 ~ 45929175 (-)
XLOC_033121 BX005101.1 non-coding upstream 3798831 46168017 ~ 46251940 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000340_10648767_10660257 USP4 coding CI01000340 null 10648548 ~ 10660257 (-)
rainbow trout (Oncorhynchus mykiss) G1471723 LOC100380707 unknown NC_048581.1 CM023235.2 60972478 ~ 60999063 (+)