XLOC_001858 (sptlc1)


Basic Information

Item Value
gene id XLOC_001858
gene name sptlc1
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 5234327 ~ 5265160 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00003682
GGAAGTCGCGCAGAGCGATCATGTGACTCAGTCAAAATGGCGTCGGGGCAACAGTGGGTGTTGGTGGAGATGGTGCAAGCTTTTTACGAGgCCCCAGCATATCACTTAATTTTAGAAGGTTTTCTCATTTTATGGATTATCCGACTGCTGTTTTCCAAAACGTATAAACTTCAGGAGAGATCAGACCTCACAGAAAAGGAGAAAGAGGAGTTAATTGAAGAGTGGCAACCCGAACCGCTGGTCTCCCCCGTATCTAAAGACCACCCTTCCCTCAATTATGATGTGGTCACAGGGCCTCCAAGCCACAAAATCATTGTAAATGGCAAAGAGTGCATTAACTTTGCCTCGTTTAACTTCTTGGGTCTGCTTGACAATGAGCGCGTGAAGTTGAAGGCATTGGCGTCACTCAAAAAATATGGCGTGGGAACTTGTGGACCAAGAGGATTCTATGGGACCTTCGATGTTCATCTGGAGTTAGAGGAGCGATTAGCGAAGTTCATGAGGACGGAGGAGGCCATTATCTACTCGTACGGCTTCGCCACCATCGCCAGTGCCATTCCAGCTTACTCCAAACGAGGAGACATCATCTTTGTTGATGAAGCAGCCTGTTTCTCTATTCAGAAAGGCCTTCAGGCGTCACGCAGCTTCATTAAATACTTCAAACACAATGATATGGAGGATCTTGAACGCCTTCTGAAGGAGCAAGAGATTGAAGATCAGAAGAATCCGCGTAAGGCAAGAGTGATCCGGCGATTCATTTTAGTCGAGGGTCTCTACATCAACACTGCAGATATCTGCCCACTGCCTGAACTGGTAAAATTGAAGTACAAATATAAAGTGCGAATCTTTCTGGAGGAGAGCATGTCTTTTGGAGTGCTTGGCGAACACGGAAGAGGAGTCACAGAGCATTTTGGGGTCAACATCGACGATATTGACCTCATAAGTGCAAACATGGAGAATGCGTTGGCATCCATCGGAGGTTTCTGCTGTGGAAGATCATTCGTTATTGATCATCAGcGTTTGTCAGGTCAGGGTTACTGTTTCTCAGCATCTCTTCCCCCCATGCTGGCTGCTGCTGCTATCGAAGCCCTGAACATCATGGAGGAAGATCCAGGAATTTTCAGGGTTCTGCGGGAGAAGTGCAGAAATGTTCACAAAGCACTACAAGGGACCGCAGGGCTGAAAGTAGTGGGTGAGTCTTTTGCTCCGGCTCTTCATCTACAGCTGGAAAACAGCACAGGATCCCGAGTGAATGACCTGAAGCTGCTCCGAGCCATTGTCGATTACAGTTTGGACAGACAGGTCGCACTAACGTTGGCTCGCTACCTGGACAAAGAAGAGCGCTTTCTTCCACCGCCAAGCATTCGAGTAGTTGTGACCGTCGAACAAACGCAGGAGGAAATCGAGAAGGCAGCACAGTGTATTCGAGAAGCAGCTTTACATGTTCTGAAATGAAGACCAGTCGCTTCAACATCCATCACACACGCACACCGTAAAGCTTTAAAAGTGTCATCACTGACCGGAGGAAGGAAAGCGAGAGCCTGGCAGGTTCTGTGACCTTTGACCTCAGAGAAATACACTCggattgtttgtatatttatgtttggtGTACAGAAAATGTGGATTATTTTAGTAGTCTTCATTTCACATTGAAATAAATGCAATTGACTCCCGACACTCTCATGTGCAGCATCAAACCCGTTTATGTTCTGTTCAAAGCCTTGAAAAACCTTGAAATCTTTACTAATCAATGGTAATTATAGCTTTTATATACACAAGTATCTTTTTATGTACACTAGTATTTACATTCTTTTGTAACCTTTGACCAAAGAGATGCTTCTTTACCACATTTCAGAATATTTATGCCttgaatgtgattttttttttctaatttctttCTGTCAGGATCcataaattaattattgttataattattgttgTAATTTTGGACTTTTTGGTAATGAATGCTATGTGAATGTACTCCGCATTTGTCATTTTCTTGCACTCATTCAGCGGAGATCTTAAATATGGTCTGGTTTTGAATCTGTAATTGTCAAAATGTATGTAAATTCAAAGAATAAAACACATTTCAgtctttatataaataaa
>TCONS_00003683
ATCATGTGACTCAGTCAAAATGGCGTCGGGGCAACAGTGGGTGTTGGTGGAGATGGTGCAAGCTTTTTACGAGgCCCCAGCATATCACTTAATTTTAGAAGGTTTTCTCATTTTATGGATTATCCGACTGCTGTTTTCCAAAACGTATAAACTTCAGGAGAGATCAGACCTCACAGAAAAGGAGAAAGAGGAGTTAATTGAAGAGTGGCAACCCGAACCGCTGGTCTCCCCCGTATCTAAAGACCACCCTTCCCTCAATTATGATGTGGTCACAGGGCCTCCAAGCCACAAAATCATTGTAAATGGCAAAGAGTGCATTAACTTTGCCTCGTTTAACTTCTTGGGTCTGCTTGACAATGAGCGCGTGAAGTTGAAGGCATTGGCGTCACTCAAAAAATATGGCGTGGGAACTTGTGGACCAAGAGGATTCTATGGGACCTTCGATGTTCATCTGGAGTTAGAGGAGCGATTAGCGAAGTTCATGAGGACGGAGGAGGCCATTATCTACTCGTACGGCTTCGCCACCATCGCCAGTGCCATTCCAGCTTACTCCAAACGAGGAGACATCATCTTTGTTGATGAAGCAGCCTGTTTCTCTATTCAGAAAGGCCTTCAGGCGTCACGCAGCTTCATTAAATACTTCAAACACAATGATATGGAGGATCTTGAACGCCTTCTGAAGGAGCAAGAGATTGAAGATCAGAAGAATCCGCGTAAGGCAAGAGTGATCCGGCGATTCATTTTAGTCGAGGGTCTCTACATCAACACTGCAGATATCTGCCCACTGCCTGAACTGGTAAAATTGAAGTACAAATATAAAGTGCGAATCTTTCTGGAGGAGAGCATGTCTTTTGGAGTGCTTGGCGAACACGGAAGAGGAGTCACAGAGCATTTTGGGGTCAACATCGACGATATTGACCTCATAAGTGCAAACATGGAGAATGCGTTGGCATCCATCGGAGGTTTCTGCTGTGGAAGATCATTCGTTATTGATCATCAGcGTTTGTCAGGTCAGGGTTACTGTTTCTCAGCATCTCTTCCCCCCATGCTGGCTGCTGCTGCTATCGAAGCCCTGAACATCATGGAGGAAGATCCAGGAATTTTCAGGGTTCTGCGGGAGAAGTGCAGAAATGTTCACAAAGCACTACAAGGGACCGCAGGGCTGAAAGTAGTGGGTGAGTCTTTTGCTCCGGCTCTTCATCTACAGCTGGAAAACAGCACAGGATCCCGAGTGAATGACCTGAAGCTGCTCCGAGCCATTGTCGATTACAGTTTGGACAGACAGGTCGCACTAACGTTGGCTCGCTACCTGGACAAAGAAGAGCGCTTTCTTCCACCGCCAAGCATTCGAGTAGTTGTGACCGTCGAACAAACGCAGGAGGAAATCGAGAAGGCAGCACAGTGTATTCGAGAAGCAGCTTTACATGTTCTGAAATGAAGACCAGTCGCTTCAACATCCATCACACACGCACACCGTAAAGCTTTAAAAGTGTCATCACTGACCGGAGGAAGGAAAGCGAGAGCCTGGCAGGTTCTGTGACCTTTGACCTCAGAGAAATACACTCggattgtttgtatatttatgtttggtGTACAGAAAATGTGGATTATTTTAGTAGTCTTCATTTCACATTGAAATAAATGCAATTGACTCCCGACACTCTCATGTGCAGCATCAAACCCGTTTATGTTCTGTTCAAAGCCTTGAAAAACCTTGAAATCTTTACTAATCAATGGTAATTATAGCTTTTATATACACAAGTATCTTTTTATGTACACTAGTATTTACATTCTTTTGTAACCTTTGACCAAAGAGATGCTTCTTTACCACATTTCAGAATATTTATGCCttgaatgtgattttttttttctaatttctttCTGTCAGGATCcataaattaattattgttataattattgttgTAATTTTGGACTTTTTGGTAATGAATGCTATGTGAATGTACTCCGCATTTGTCATTTTCTTGCACTCATTCAGCGGAGATCTTAAATATGGTCTGGTTTTGAATCTGTAATTGTCAAAATGTATGTAAATTCAAAGAATAAAACACATTTCAgtctttat

Function

symbol description
sptlc1 Predicted to enable serine C-palmitoyltransferase activity. Predicted to be involved in ceramide biosynthetic process and sphingosine biosynthetic process. Predicted to act upstream of or within biosynthetic process. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum. Human ortholog(s) of this gene implicated in hereditary sensory and autonomic neuropathy type 1A. Orthologous to human SPTLC1 (serine palmitoyltransferase long chain base subunit 1).

GO:

id name namespace
GO:0046512 sphingosine biosynthetic process biological_process
GO:0046513 ceramide biosynthetic process biological_process
GO:0009058 biosynthetic process biological_process
GO:0005783 endoplasmic reticulum cellular_component
GO:0016020 membrane cellular_component
GO:0016021 integral component of membrane cellular_component
GO:0004758 serine C-palmitoyltransferase activity molecular_function
GO:0030170 pyridoxal phosphate binding molecular_function
GO:0003824 catalytic activity molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-050522-61 Predicted to enable serine C-palmitoyltransferase activity. Predicted to be involved in ceramide biosynthetic process and sphingosine biosynthetic process. Predicted to act upstream of or within biosynthetic process. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum. Human ortholog(s) of this gene implicated in hereditary sensory and autonomic neuropathy type 1A. Orthologous to human SPTLC1 (serine palmitoyltransferase long chain base subunit 1).

Ensembl:

ensembl_id ENSDARG00000042995

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00003682 False 2109 mRNA 0.43 15 5234327 5265160
TCONS_00003683 True 2083 mRNA 0.43 15 5234344 5265151

Neighbor

gene id symbol gene type direction distance location
XLOC_001857 NA coding upstream 77 5232327 ~ 5234250 (+)
XLOC_001856 cdc42se2 coding upstream 12790 5159475 ~ 5221537 (+)
XLOC_001855 si:ch211-249h16.8 coding upstream 77528 5149359 ~ 5156799 (+)
XLOC_001854 zgc:113274 coding upstream 86745 5135842 ~ 5147582 (+)
XLOC_001853 carm1l coding upstream 143935 5060191 ~ 5090392 (+)
XLOC_001859 ror2 coding downstream 2894 5268054 ~ 5407509 (+)
XLOC_001860 si:dkey-60d5.3 coding downstream 144348 5409508 ~ 5410985 (+)
XLOC_001861 nfil3 coding downstream 149064 5414224 ~ 5419256 (+)
XLOC_001862 auh coding downstream 157415 5422575 ~ 5475690 (+)
XLOC_001863 NA coding downstream 262030 5527190 ~ 5543141 (+)
XLOC_001851 NA non-coding upstream 238278 4987766 ~ 4996049 (+)
XLOC_001850 CU074419.1 non-coding upstream 246844 4986050 ~ 4987483 (+)
XLOC_001848 NA non-coding upstream 271027 4961815 ~ 4963300 (+)
XLOC_001845 NA non-coding upstream 424076 4809883 ~ 4810251 (+)
XLOC_001864 NA non-coding downstream 322800 5587960 ~ 5588230 (+)
XLOC_001867 NA non-coding downstream 523247 5788407 ~ 5793526 (+)
XLOC_001868 NA non-coding downstream 615540 5880700 ~ 5881233 (+)
XLOC_001871 NA non-coding downstream 851134 6116294 ~ 6116936 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000304_02066780_02080386 SPTLC1 coding CI01000304 null 2066551 ~ 2080386 (-)