CI01000340_10648767_10660257 (USP4)


Basic Information

Item Value
gene id CI01000340_10648767_10660257
gene name USP4
gene type coding
species grasscarp (Ctenopharyngodon idella)
category of species economic fish

Chromosome Information

Item Value
chromosome id CI01000340
NCBI id null
chromosome length 19571558
location 10648548 ~ 10660257 (-)
genome version v1_2015/06_NatureGenetics_grasscarp_Genome

Sequence

>CI01000340_10648767_10660257.mRNA
CGCGCTCGCGATTACTGCGGGTTCACTCGCTGCACGATGGCGGAGGGAGGCGGACCCGAGTCGGGTACCGCTTCGGACCCTGACGAGAAGCCGGGGATCACACAGACACCAGTACCGTCCACCGAGAGTCAAAAGCAGAGTATCGGGACACTGCTGAAAACGCCACTTCGAAAGGGAGACGAGTGGTATTTGATTGACAGCCGGTGGTTCAAACAATGGAAGAAATATGTGGGCTTTGACAGTTGGGATTTGTACAATGTTGGAGAGCACAATCTGTACCCGGGACCCATTGACAACTCTGGACTCTTTTCAGATCACGAGTCCCAGACGCTGAAAGAGCATCTCATAGATGAGTTAGACTATGTTTTAGTGCCTACAGAGGCCTGGAATAAGCTGGTCAGCTGGTATGGCTGTCTGGAGGATACTATTGAGAAGGAGATGCGGTCTTTATTTGACATCCCATCTGAAAAGGAAACTCGTCTTTGGAATAAATACATGAGTAACACTTATGAACAACTTAACAAGCTTGACAGCACTGTACAGGACGCAGGGCTTTTTCAGGGGCAGGTGCTTGTTATAGAGAAGAAGAATGAGGATGGCACATGGCCCAGACAGTCCTGCCATTCCAAGTCCAGTACTTCCACCTCTCGGAATTATACAACCTCCCCAAAACTCTCTTCAAACTCATCTGCTACCATATCCTCTACAATAACGAATGGGGATAGCAATAGCAACTCTGGCTACATGCTGAACAACAGTACTTCTGGTAACAGATTGGGAAGTTATAACTCCTACAGCTCCTCCTACAGTTACAGAGAATCTGCTGCTCAACCGGGCCTCTGCGGTCTGAGCAACCTGGGCAACACCTGCTTTATGAACTCTGCCCTCCAGTGCCTGAGCAACACTCCCCCTCTGACGGAATATTTCCTGGAGGACCGGTATGAAGCAGAGATCAACCGAGAAAATCCATTAGGGATGCGAGGGGAGATTGCAGAGGCCTATGCAGATCTGGTCAAACAGACGTGGCTTAGTCGGAGCAGTTATGTGGCTCCACGCACTTTTAAAACCCAGGTGGGTCGGTTTGCCCCGCAGTTCTCAGGGTACCAGCAACAAGACTCTCAGGAGCTGCTGGCCTTTCTGCTGGACGGTCTACATGAGGACCTTAACCGTGTTAAGAAGAAGCCTTACCTGGCCCTGAGAGATGCTGAGGGGCGGCCTGATGAGATTGTAGCTAAGGAAGCATGGGCGAATCACCGATTGCGGAATGATTCCATTATCGTGGACATCTTCCATGGCTTGTTCAAATCTACACTGGTCTGCCCAGAATGCTCCAAAGTTTCTGTTACCTTCGACCCCTTCTGCTACCTCACACTGCCCCTGCCCATGAAAAAGGATCGCACTATGGAGGTGTTCCTGGTCCGCACTGACCCGCAGTTCAGACCCATGCAATACCGTGTAGTGGTTCCCAAAATGGGTGTAGTAGCAGACCTGTGCAGCGCTTTGGCCAAGCTATCTGGACTTCCTACAGAGAATGTGTTAGAGGAAGATAGTGAGAGGATGAACCTGCCAGTGTACTTCAGAGAGAGGCATGCTAAGCACAGCGGAGGCTCTTCAGGCACAATGCTCTTTGGTCAGCCTCTCCTCATAACCGTCCCACGCCACAACCTCACCGTGGATACCCTCTATGAGCGCGTGTTGGAGAGGATCGGGCGTTACGTTAAACGTTCACAGGGTACCATTACAGACAGCAGAGCATCTGCCTCAGCAACATCATCTAGCAGCAGCCAATCACCAGAATACCTCGCTTCAGTGTCCAGTCACAGCACAGGACTGAGTGGTTGCAGCAGCCCAGTTTCAGATGGAGCTTCCTGCAGCGCTGGATCCAACGGCAGCAACCACTCCTGCAATGGCCCCAATGGAGTTTGTGATGGCGATGAGGAAGCCATGGACCACCAGGAGAGTCCAGAACCAGAAAATAGCCACTCGGATGCTGTGGATGGAGAGGAGGATTCTGAACCAGAGAATGGGCCCAATAGCAGCGGTGGAAAATCTTTTACTTCTCGGCCCAAACTCTTTTCTTTCAGCATGGTCAATTCCTACGGCACAGCCAACATCAGTTCTCTCCCGTTTGATGGCAATCTCCTAAAGCTCACAACTCACTCGACAGTAGCCATTGATTGGGACTCAGACACGAAGAAACTGTGCTACGATGACCAGGAAGCTGAGGCCTATGACAAACATGAGAGCATGCTACATGCTCAGAAGAAGAAGACTACAGTAGCTTTACGAGAATGCATCGAGCTCTTTACTACAATGGAGACCCTAGGAGAACATGACCCCTGGTACTGCCCCACGTGTAAGAAACACCAGCAGGCCACAAAGAAGTTTGACCTGTGGTCTCTCCCACGCATTCTGGTTGTTCATCTGAAGCGTTTCTCTTACAACCGCTGCTGGAGAGACAAGCTTGACACGGTCGTGGATTTTCCAATTAGGGACTTGAATATGTCCGAGTTTGTTTGCGACCCCAAAGCTGACCCATATGTCTATGACCTCATTGCTGTTTCCAACCATTATGGAGGAATGGGTGGAGGCCACTACACGGCATACGGCAAGAACAAGATGGACGGAAAATGGTATTACTTTGATGACAGCAGTGTGTCTGCTGCTACTGAGGATCAGATTGTGACTAAAGCAGCCTACGTGCTCTTTTACCAACGTAGAGACGCGGACACACCGTCCAAATCCACCCCCTCTGCATCACTAGGTGGAGCTTCAGAGACCCTGGACGACCACATGGACACCAACTGAATTTCTTTTAGTCTTTCAAGGACTGGCACTGAAACAAAAACTACATAAAGATGAAATCATCAATGCATCAACGCACATCCCTGGCTACTTCAGTGACTATTAAAGGCTCACAAACAGGCCCTCTGTTTTTAGCTTTATTTTACTTTTTTTTTTCTTTCTTTTTTTTTTCTTTCACACATGCGTCTTTATCAAGAGCCAAAAAAGAATATTAATAATAAA

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:0005634 nucleus cellular_component

KEGG:

id description
K11835 USP4_11, UBP12; ubiquitin carboxyl-terminal hydrolase 4/11

RNA

RNA id representative length rna type GC content exon number start site end site
CI01000340_10648767_10660257.mRNA True 3027 mRNA 0.49 20 10648548 10660257

Neighbor

gene id symbol gene type direction distance location
CI01000340_10626938_10643520 FANCD2 coding downstream 4335 10626821 ~ 10644213 (-)
CI01000340_10557213_10612562 NA coding downstream 35986 10557213 ~ 10612562 (-)
CI01000340_10504461_10536413 GRM2A, GRM2 coding downstream 110855 10504353 ~ 10537693 (-)
CI01000340_10497000_10501726 PARP3 coding downstream 145971 10496636 ~ 10502577 (-)
CI01000340_10485958_10487241 NA coding downstream 161218 10485925 ~ 10487330 (-)
CI01000340_10664417_10665925 EMC3, POB, EMC3.L coding upstream 3847 10664104 ~ 10665925 (-)
CI01000340_10667602_10671566 SC61A, SEC61A1.S, S61A1, SEC61A1L, SEC61A1 coding upstream 7275 10667532 ~ 10671566 (-)
CI01000340_10690474_10697545 IP6K2, IP6K2A coding upstream 29675 10689932 ~ 10699591 (-)
CI01000340_10924696_10934000 EDEM1 coding upstream 264127 10924384 ~ 10934000 (-)
CI01000340_10935675_10941448 ARL8B, ARL8BA, ARL8A coding upstream 275075 10935332 ~ 10941681 (-)
CI01000340_10468562_10470670 CAV3 non-coding downstream 176710 10468063 ~ 10472083 (-)
G492047 NA non-coding downstream 294599 10350057 ~ 10353949 (-)
G492050 NA non-coding downstream 308617 10329861 ~ 10339931 (-)
G492037 NA non-coding downstream 412271 10235847 ~ 10236277 (-)
G491908 NA non-coding downstream 425726 10137245 ~ 10222822 (-)
G492343 NA non-coding upstream 19061 10679318 ~ 10679596 (-)
G492364 NA non-coding upstream 92471 10752728 ~ 10752946 (-)
G492371 NA non-coding upstream 121126 10781383 ~ 10784905 (-)
G492381 NA non-coding upstream 127710 10787967 ~ 10788183 (-)
G492356 NA non-coding upstream 133002 10793259 ~ 10797269 (-)
CI01000340_10357202_10357606 NA other downstream 286144 10356758 ~ 10359856 (-)
CI01000340_10025958_10028902 SRSF3 other downstream 620565 10025656 ~ 10029589 (-)
G491712 NA other downstream 1848971 8799201 ~ 8799577 (-)
G489511 NA other downstream 4321176 6320457 ~ 6327372 (-)
CI01000340_06095704_06194498 MAST2 other downstream 4427906 6095704 ~ 6194501 (-)
G493109 NA other upstream 1013489 11673746 ~ 11677994 (-)
G493266 NA other upstream 1406920 12067177 ~ 12116900 (-)
CI01000340_12577571_12625562 PTPRG, PTPRGA, CA16B other upstream 1951959 12577435 ~ 12625758 (-)
CI01000340_14318434_14336130 NA other upstream 3553091 14318365 ~ 14336258 (-)
CI01000340_14547725_14551493 NA other upstream 3886742 14546999 ~ 14552983 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
zebrafish (Danio rerio) XLOC_033093 usp4 coding NC_007117.7 CM002890.2 42345005 ~ 42369186 (-)
rainbow trout (Oncorhynchus mykiss) G1471723 LOC100380707 unknown NC_048581.1 CM023235.2 60972478 ~ 60999063 (+)