XLOC_002848 (vps11)


Basic Information

Item Value
gene id XLOC_002848
gene name vps11
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007121.7
NCBI id CM002894.2
chromosome length 45420867
location 29751029 ~ 29768556 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00005277
ACATGACCGTAATGCGAGTCACATGATTTTGCTAAACAAGAACTGCTCAGAAAATGGCAGCGTTTTTACAGTGGAGACGATTTGTGTTTTTCGATAAAGAAACTGTGAAGGATCCGAGCGAAAATGGGAAAAACTTCCAGCTACCGATGGGCATATCGGCCTGTGATTCAGGCCGAGGACACATTGTGCTCGGAGATATGGATGGTCAGATCTGGTTTTTGACCCGCTCTCTCCAGCTATCAAGCTTCCAGGCATATAAGCTGCGGGTGACGCACCTGTACCAGCTCAAACAACACAACATCCTGGTGTCAGTGGGGCAGGATGAACCTGGCATCAATCCTCTGGTGAAGGTGTGGAATCTTGATAAGAGGGACAGTGGCAGTCCTCTGTGTACCCGAATATTCCCTGCCATTCCTGGAAACAAACCCACTGAAGTGTCTTGTCTCAGCGTACATGAAAACCTTAATTTCATGGCTATAGGTTTTACAGATGGCAGTGTTGTGCTGACGAAGGGTGACATCACCAGAGATCGACACAGCAAAACGCTCAGCCTCCATGAGGGCAACTGTCCAATCACAGGCCTGGCTTTCAGACAGGCTGGGAAAATCACACACCTGTTTGTTGCCACCTTAGAGAAAGTGCAGTGTTACACGTTGTCAGTGAAAGAGTATCCTCGTGTAGAATTGGACACACACGGCTGTGCTCTCCGCTGTTCTGCGCTCACTGACCCGTCACAGGACTCGCAGTTTATAGTGGCTGGAGATGATTGTGTGTATCTGTACCAGCCTGATGAGAGAGGACCCTGCTTCGCTTTTGATGGGCATAAGCTTTTGACACACTGGCACAGAGGATACCTGCTGCTGCTCACACACAGTAACAAGTCGCCCAGCAAATCTGATTATGGCAGCAGACAGACGTCCCCTACAGAAAAGCACATCCTGACCATTTACGATTTAGACAACAAGTTCATCGCTTACAGTGCGGTGTTTGATGATGTCATTGACGTTCTGGCTGAATGGGGGTCTTTCTACGTCCTAACAAGTGACAGGACGGTGTATATGCTGCAGGAGAAAGACACACAGACCAAGCTGGAGATGCTGTTTAAGAAGAATCTGTTTGTGATGGCCATTAACTTGGCCAAAAGTCAACACCTGGACAATGATGGTCTGTCTGAGATATTCAGGCAATATGGAGACCATCTCTACGTCAAAGGAGATCATGATGGAGCTATTCAACAATATATCCGCACCATTGGGAAGCTCGAACCATCCTATGTTATCCGCAAGTTTTTGGATGCACAGAGAATACACAACCTAACCGCATACCTGCAGGCCCTTCACAGGCAGTCACTGGCCAACGCTGATCACACTACACTACTGCTCAACTGCTACACCAAACTGAAGGACAGCTCCAAGCTGGAGGAGTTCATAAAGAGCAATGAGAGCGAGGTGCATTTTGATGTTGAAATTGCCATCAAAGTGTTACGCCAGGCTGGTTATCACAGTCACGCCGTGTTTCTGGCAGAGAGACACATGCACCATGAATGGTATCTGAAGATCCAGCTAGAGGATTTGAAGAATTATCAAGAGGCTTTGCGCTACATCGGTAGGTTGCCATTTGATCAGGCTGAAAGTAACATGAAGCGTTATGGTAAAACTCTTATGCACCATGTTCCCGAGAGCTCCACCATCCTCTTAAAGCGCCTCTGCACCGACTATCACCCCAGCAAAGACTCCACCGACCGGGACAGTCTGGACAGGCCTGTGGAAAAcaagGCCAATCCAGAGGAGTTCATCCCAGTGTTTGCCAATAACCCGCGAGAGCTGCGATTGTTTCTGGAGCACATGATCGAGGTGGACCCGTTCTCTCCTGAAGGAGTTTATGACACTCTGCTAGAGCTCAGACTGCAGGACTGGGCACATGAGCAGGACCCAGGGAAGAAAAAAGTCCTGCAGGAGGCAGCACTCTCCCTTCTGAGGAGCGACAACACTGTGTTTGACAAGGCCCTCGTGCTCTGCCAGATGCACAACTTTAAAGAAGGAGTGCTGTATTTGTATGAAAAGGGCAAACTGTATCAGCAGATCATGCATTACCACATGCAGAATGAGGAGTATGGGAAAGTGGTGGAGGCCTGTAAGCGCTATGGGGACAGCGAAGTGTGCTTGTGGGAGCAGGCACTGGGCTATTTCGCACGCAAAGAAGAAAACTGCAAGTCCTACATTAGTGAAGTCTTGAAGCACATCGACGACAATAACCTGATGCCTCCGCTTCTGGTGGTGCAGACTTTGGCCCATAATTCCACAGCATCTTTATCAGTCATCAAAGACTACCTGATTAATAAACTGGAGAGGGAGACCCAGCAGATTGAGGAAGACGAAAGGAAGATTCGCCAGTATAGAGAAGAGACGGCTCATTTACGGTCTGAGATACAAGAACTTAAAACTTGTGCAAAGATCTTTCAGAAGACCAAGTGCAGCATGTGCAACAGCCCGCTCGAGCTGCCGTCTGTGCACTTCCTGTGTGGCCACTCTTTCCATCAACACTGCTTAGAGAGCTTCGCTGAGAGTGAGGCAGAGTGTCCCACCTGCACCCCTGAGAACAGGAAGGTCATGGACATGTTGCGTGCGCAGGATCAGAAACGAGATCTGCATGACCATTTTCACAGACAGTTGAGATGCTCTAACGACGGCTTCTCAGTCATCGCTGACTACTTTGGCCGTGGAGTGTTCAACAAACTCACTCTGATAACGGATCCTCCCGGAGGAAAGGGTGGAGCTGGGAATCTGGAGGCTGAATTCAACAGAGATCTGCTCATTAACACCAAGAGAAACGTTTGAAGGGCTGGGCTGGACTGGAGTTCACTTTAAAAGAAGAGCAGATCTAGGGTCGGACACGTGACCTTGCGCTACTTTAACGGTCTTATAACAAAATCCAAATTTACCTTTGCAGTTCCTCTTCTTGGTGTTGatttatttataggctgtatAGTGGAAAGAGAGATGAAAGCTCTTGCAAAATCTCTCCATCTGTGTCGTCTGCAAGATCAAATCAGCAGAAAGAGGAAAGTATCAAAACCGCTGTGGGTGATGATGAGAAACGCAAGAACTTGCACTTCAGGACTGTGTGACATTTTCAAGCTTTTGCTGGTGCACTCTAGAGATGGACTTGCACATTATTTTGCATCCTTTAATGATTcatgtataatgtataattagTGTAACAACCACTTATTACTGTAGCTAAAGCAACTAATCTAAATTAATCAGGCAAAAGCTTGTAAAAGTgttgttaataaatgtatgaaaTTA

Function

symbol description
vps11 Predicted to enable protein-macromolecule adaptor activity. Acts upstream of or within several processes, including animal organ development; melanocyte apoptotic process; and melanocyte differentiation. Predicted to be located in cytoplasmic vesicle and vacuole. Predicted to be part of HOPS complex. Predicted to be active in endosome. Is expressed in brain; heart; immature eye; and retina. Human ortholog(s) of this gene implicated in hypomyelinating leukodystrophy 12. Orthologous to human VPS11 (VPS11 core subunit of CORVET and HOPS complexes).

GO:

id name namespace
GO:0006886 intracellular protein transport biological_process
GO:0006904 vesicle docking involved in exocytosis biological_process
GO:0006914 autophagy biological_process
GO:0035542 regulation of SNARE complex assembly biological_process
GO:0048794 swim bladder development biological_process
GO:0003406 retinal pigment epithelium development biological_process
GO:0003407 neural retina development biological_process
GO:1902362 melanocyte apoptotic process biological_process
GO:0016192 vesicle-mediated transport biological_process
GO:0007032 endosome organization biological_process
GO:0007033 vacuole organization biological_process
GO:0015031 protein transport biological_process
GO:0010507 negative regulation of autophagy biological_process
GO:0001889 liver development biological_process
GO:0030318 melanocyte differentiation biological_process
GO:0060036 notochord cell vacuolation biological_process
GO:0005764 lysosome cellular_component
GO:0005765 lysosomal membrane cellular_component
GO:0005768 endosome cellular_component
GO:0005769 early endosome cellular_component
GO:0005776 autophagosome cellular_component
GO:0030136 clathrin-coated vesicle cellular_component
GO:0031902 late endosome membrane cellular_component
GO:0033263 CORVET complex cellular_component
GO:0031410 cytoplasmic vesicle cellular_component
GO:0030897 HOPS complex cellular_component
GO:0016020 membrane cellular_component
GO:0030674 protein-macromolecule adaptor activity molecular_function
GO:0046872 metal ion binding molecular_function

KEGG:

id description
ko04138 Autophagy - yeast
ko05132 Salmonella infection
ko04131 Membrane trafficking

ZFIN:

id description
ZDB-GENE-050731-5 Predicted to enable protein-macromolecule adaptor activity. Acts upstream of or within several processes, including animal organ development; melanocyte apoptotic process; and melanocyte differentiation. Predicted to be located in cytoplasmic vesicle and vacuole. Predicted to be part of HOPS complex. Predicted to be active in endosome. Is expressed in brain; heart; immature eye; and retina. Human ortholog(s) of this gene implicated in hypomyelinating leukodystrophy 12. Orthologous to human VPS11 (VPS11 core subunit of CORVET and HOPS complexes).

Ensembl:

ensembl_id ENSDARG00000036338

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00005277 True 3308 mRNA 0.47 16 29751029 29768556

Neighbor

gene id symbol gene type direction distance location
XLOC_002847 ift46 coding downstream 6108 29735900 ~ 29744921 (-)
XLOC_002846 si:ch73-261i21.2 coding downstream 17835 29731060 ~ 29733194 (-)
XLOC_002845 CU861448.1 coding downstream 42847 29708068 ~ 29708182 (-)
XLOC_002843 NA coding downstream 259942 29266270 ~ 29491087 (-)
XLOC_002844 tmem126a coding downstream 478272 29269998 ~ 29272757 (-)
XLOC_002849 si:ch73-261i21.5 coding upstream 25261 29793817 ~ 29809105 (-)
XLOC_002850 hist2h2l coding upstream 47088 29815644 ~ 29816467 (-)
XLOC_002851 zpr1 coding upstream 51616 29820172 ~ 29831944 (-)
XLOC_002852 bsx coding upstream 121979 29890535 ~ 29892486 (-)
XLOC_002853 lim2.1 coding upstream 127719 29896275 ~ 29903165 (-)
XLOC_002841 BX005332.1 non-coding downstream 613025 29128202 ~ 29138004 (-)
XLOC_002838 BX537347.1 non-coding downstream 827396 28923517 ~ 28923633 (-)
XLOC_002837 BX537347.2 non-coding downstream 828778 28922135 ~ 28922251 (-)
XLOC_002854 CT737197.1 non-coding upstream 762587 30531143 ~ 30531257 (-)
XLOC_002858 NA non-coding upstream 1494296 31262852 ~ 31295006 (-)
XLOC_002862 NA non-coding upstream 2309255 32077811 ~ 32084624 (-)
XLOC_002863 NA non-coding upstream 2447857 32216413 ~ 32250846 (-)
XLOC_002867 NA non-coding upstream 2816129 32584685 ~ 32591462 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000304_14296254_14303852 VPS11 coding CI01000304 null 14295795 ~ 14303882 (-)
bowfin (Amia calva) AMCG00004360 vps11 coding CM030121.1 CM030121.1 44606289 ~ 44617399 (-)