XLOC_006771 (sptlc3)


Basic Information

Item Value
gene id XLOC_006771
gene name sptlc3
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007124.7
NCBI id CM002897.2
chromosome length 52186027
location 34804243 ~ 34862484 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00013032
GCGCACAGTCGCGTCGCGTCGCTCCTCTGATCTCCGTGAACACTTCCTGGTCCAAAGTTGTATGTAGCTACACAAATCAAAGTCATTTGAGCATGAAGCCGGATGGTGGACTCACATCAGGGAATTACACTTCATCGGACTCGCACACATTTATCTAAACTGAGGGACAGAGAAGTTCAATATCGCTATAATTCATCCCTGATGCTTCGCAAACATGATACGAACTGAGGAACTTCATTCATGCAACGGGACGCTGAAGTCTCGTTCTGGCCAGAAGCAAACGGAAAACTACACCTTGAAAAATGGATATCACAAAAATGAAAAGGTGCAGAAAAATGGAAACGGTTTTCATCAGCCTCGAGTTAGGGGTGAAGATTCATTCGAGGAGGCCCCCATGTATGTGGCGGTCCTAACATACATGGGTTATGGGATTGTAATACTTTTTGGATATTTCAGGGACTTCTTAAGAGCTGTTGGGTTAGAGAAGTGCCATCAGGCCCAGGAGAGAGAAGAGCAGAAGGACTTTGTTCCCCTTTACCAAGATTTTGAAAACTTCTACAAACGAAATCTGTACATGAGAGTCAGGGACAACTGGAATCGGCCCATATGCAGTCTTCCCGGTCCGGTTTTTGACCTCATGGAAAGGGTCTCGGATGATTACAACTGGACTTTCCGATTAACTGGGAGAACCATTGAGAACGTCATAAACATGGGCTCCTACAACTATCTGGGTTTCGCTGAAAACAACGTTGACTTCCTTAAAACTGTGGCAGAGAAGACCAGACAATACGGGGTGGGTGTCTGCAGCACAAGACAGGAACTAGGTAACTTCAGCATTCATGAGGAACTGGAGCATCTCGTGGCTGACTTCTTGGGTGTGGAGTCTGCCATGGCGTTTGGAATGGGTTTCGCAACCAATTCCATGAACATTCCAGCTCTAGTCGGAAAGGGCTGTCTGATCCTGAGCGATGAGCTAAATCACACGTCCCTCATTCTGGGAGCCAGGTTGTCAGGAGCAACCATTCGAGTCTTCAAACACAACAACATGCAGAGTCTAGAAAAGCTGCTGAAGGAAGCGATTTGCTCCGGGCAGCCTCGTACCCATCGCTCCTGGAAGAAGATTCTTATAATGGTGGAGGGCATTTACAGtatGGAAGGCTCTCTCGTCAGGTTGCCAGAGATCATAGCGCTAAAGAAGAAGTACAAGGCTTATCTATACCTCGATGAGGCCCACAGCATTGGAGCCGTGGGGCCTACCGGTCGGGGAGTTACAGAACATTTTGGGGTGGACCCTAAAGAAATAGACGTTCTGATGGGCACCTTCACCAAGAGTTTCGGGGCTACCGGCGGGTACATTGCTGGCAAAAAGGAATTGGTGGATTATCTGCGGTGTCACTCTCACAGTGCGGTTTACGCTACAGCCATGTCGCCACCTGTCGTGGAGCAGATCATCAGGGCAATCAAATGCATCATGGGAGTCGATGGAACCACAGAAGGCCAACGAAGAGTTCGACAGCTGGCTGAGAACACGCACTACTTCAGATCTCGGCTGAAAGAGATGGGCTTCATCATTTACGGCAACAAAGACTCTCCGGTGATACCGCTCCTGCTATATCAACCAGGGAAAGTCGGAGCGTTCTCACGGGCCATGTTGAAGAGGAAGATCGGTGTGGTTGTTGTTGGTTTTCCAGCTACTACTATTACAGAAGCCAGAGCTCGATTCTGTGTGTCTGCTGCTCACACCAGAGACATGCTCAACAAGGTACTTCAGAGCCTTGATGAACTTGGAGACTACATCAGGGTGAAATTCTCCCGTCACAGACGCCCTTATCGTCCAGAGCTGTACAATGTAACAAACTTTGGGCTGGACAGTTGATCGTTCACCCAGTGAGTGTGATGCCTTGTCCACATTGAGGGACCACCAAGGGCACCTTAGTGTGAATGccttggtttttatttttttaaataaatcataaaataaaatgtcttgcCATTCCATGCAGGACCGTTCAGCTTttccaaaaacagaaaaaagtttgCAGTGTTTCTAACAGCTTTTAAAGTTTGTCCTACCACGAGGCTTGGacatttatatgtgtatatattgtacaattctatttaattgtttattttaactgCTGTTTCAGAGTTTTGTGCAGTTTGATAAATAATTTTCATCTCAGGGGATTGTGGGACAAAGGGAGGGTCGCGACGGCTGTGTTTATAGAACGCAAATCAAAAGCTGCTCTAAATATATCAAACAATTAACTCCCTTAACACTGACCTACATCAAAACTCGAGCTGCGGATAAGAAAGCCCTTGAAGTGAccctgttttgttgtttttgttgtttttatcctGCTGCTGAGATGGACTGATGAAAGACCTTCATTCTGTGCTGGATGATGTGTTTGTGTGATCCACAAGTGCATTGATTGAAAGATTGAACAAGGCTGGGTGTTACACACCCGGCGCAGCTCATTCACAGTCATTAAACATTCATACATTGC
>TCONS_00013033
TAATTGTCATTAAATACAATTACCTGCGTCACAGAGTCGCCTCTTCACGAGCACGCGCAGAACTTCACAACAAACGATGTCTTTCATTTAAGAATATAACTTAGCTTAGCTTTCTTGTCGATAAATTTCAACTCCATCGCGTGAACTCTTACTTTGGCGGAAACAGggtcttcacaaaaaaaaaaacaggatctcTTTCATTATCAACGAAGGTGTCAGAAGGCAGCGCACAGTCGCGTCGCGTCGCTCCTCTGATCTCCGTGAACACTTCCTGGTCCAAAGTTGTATGTAGCTACACAAATCAAAGTCATTTGAGCATGAAGCCGGATGGTGGACTCACATCAGGGAATTACACTTCATCGGACTCGCACACATTTATCTAAACTGAGGGACAGAGAAGTTCAATATCGCTATAATTCATCCCTGATGCTTCGCAAACATGATACGAACTGAGGAACTTCATTCATGCAACGGGACGCTGAAGTCTCGTTCTGGCCAGAAGCAAACGGAAAACTACACCTTGAAAAATGGATATCACAAAAATGAAAAGGTGCAGAAAAATGGAAACGGTTTTCATCAGCCTCGAGTTAGGGGTGAAGATTCATTCGAGGAGGCCCCCATGTATGTGGCGGTCCTAACATACATGGGTTATGGGATTGTAATACTTTTTGGATATTTCAGGGACTTCTTAAGAGCTGTTGGGTTAGAGAAGTGCCATCAGGCCCAGGAGAGAGAAGAGCAGAAGGACTTTGTTCCCCTTTACCAAGATTTTGAAAACTTCTACAAACGAAATCTGTACATGAGAGTCAGGGACAACTGGAATCGGCCCATATGCAGTCTTCCCGGTCCGGTTTTTGACCTCATGGAAAGGGTCTCGGATGATTACAACTGGACTTTCCGATTAACTGGGAGAACCATTGAGAACGTCATAAACATGGGCTCCTACAACTATCTGGGTTTCGCTGAAAACAACGTTGACTTCCTTAAAACTGTGGCAGAGAAGACCAGACAATACGGGGTGGGTGTCTGCAGCACAAGACAGGAACTAGGTAACTTCAGCATTCATGAGGAACTGGAGCATCTCGTGGCTGACTTCTTGGGTGTGGAGTCTGCCATGGCGTTTGGAATGGGTTTCGCAACCAATTCCATGAACATTCCAGCTCTAGTCGGAAAGGGCTGTCTGATCCTGAGCGATGAGCTAAATCACACGTCCCTCATTCTGGGAGCCAGGTTGTCAGGAGCAACCATTCGAGTCTTCAAACACAACAACATGCAGAGTCTAGAAAAGCTGCTGAAGGAAGCGATTTGCTCCGGGCAGCCTCGTACCCATCGCTCCTGGAAGAAGATTCTTATAATGGTGGAGGGCATTTACAGtatGGAAGGCTCTCTCGTCAGGTTGCCAGAGATCATAGCGCTAAAGAAGAAGTACAAGGCTTATCTATACCTCGATGAGGCCCACAGCATTGGAGCCGTGGGGCCTACCGGTCGGGGAGTTACAGAACATTTTGGGGTGGACCCTAAAGAAATAGACGTTCTGATGGGCACCTTCACCAAGAGTTTCGGGGCTACCGGCGGGTACATTGCTGGCAAAAAGGAATTGGTGGATTATCTGCGGTGTCACTCTCACAGTGCGGTTTACGCTACAGCCATGTCGCCACCTGTCGTGGAGCAGATCATCAGGGCAATCAAATGCATCATGGGAGTCGATGGAACCACAGAAGGCCAACGAAGAGTTCGACAGCTGGCTGAGAACACGCACTACTTCAGATCTCGGCTGAAAGAGATGGGCTTCATCATTTACGGCAACAAAGACTCTCCGGTGATACCGCTCCTGCTATATCAACCAGGGAAAGTCGGAGCGTTCTCACGGGCCATGTTGAAGAGGAAGATCGGTGTGGTTGTTGTTGGTTTTCCAGCTACTACTATTACAGAAGCCAGAGCTCGATTCTGTGTGTCTGCTGCTCACACCAGAGACATGCTCAACAAGGTACTTCAGAGCCTTGATGAACTTGGAGACTACATCAGGGTGAAATTCTCCCGTCACAGACGCCCTTATCGTCCAGAGCTGTACAATGTAACAAACTTTGGGCTGGACAGTTGA
>TCONS_00013034
AGAGTCGCCTCTTCACGAGCACGCGCAGAACTTCACAACAAACGATGTCTTTCATTTAAGAATATAACTTAGCTTAGCTTTCTTGTCGATAAATTTCAACTCCATCGCGTGAACTCTTACTTTGGCGGAAACAGggtcttcacaaaaaaaaaaacaggatctcTTTCATTATCAACGAAGGTGTCAGAAGGCAGCGCACAGTCGCGTCGCGTCGCTCCTCTGATCTCCGTGAACACTTCCTGGTCCAAAGTTGTATGTAGCTACACAAATCAAAGTCATTTGAGCATGAAGCCGGATGGTGGACTCACATCAGGGAATTACACTTCATCGGACTCGCACACATTTATCTAAACTGAGGGACAGAGAAGTTCAATATCGCTATAATTCATCCCTGATGCTTCGCAAACATGATACGAACTGAGGAACTTCATTCATGCAACGGGACGCTGAAGTCTCGTTCTGGCCAGAAGCAAACGGAAAACTACACCTTGAAAAATGGATATCACAAAAATGAAAAGGTGCAGAAAAATGGAAACGGTTTTCATCAGCCTCGAGTTAGGGGTGAAGATTCATTCGAGGAGGCCCCCATGTATGTGGCGGTCCTAACATACATGGGTTATGGGATTGTAATACTTTTTGGATATTTCAGGGACTTCTTAAGAGCTGTTGGGTTAGAGAAGTGCCATCAGGCCCAGGAGAGAGAAGAGCAGAAGGACTTTGTTCCCCTTTACCAAGATTTTGAAAACTTCTACAAACGAAATCTGTACATGAGAGTCAGGGACAACTGGAATCGGCCCATATGCAGTCTTCCCGGTCCGGTTTTTGACCTCATGGAAAGGGTCTCGGATGATTACAACTGGACTTTCCGATTAACTGGGAGAACCATTGAGAACGTCATAAACATGGGCTCCTACAACTATCTGGGTTTCGCTGAAAACAACGTTGACTTCCTTAAAACTGTGGCAGAGAAGACCAGACAATACGGGGTGGGTGTCTGCAGCACAAGACAGGAACTAGGTA

Function

symbol description
sptlc3 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 part of serine C-palmitoyltransferase complex. Is expressed in EVL; gut; periderm; and pronephric duct. Orthologous to human SPTLC3 (serine palmitoyltransferase long chain base subunit 3).

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:0017059 serine C-palmitoyltransferase complex cellular_component
GO:0016020 membrane cellular_component
GO:0016021 integral component of membrane cellular_component
GO:0005737 cytoplasm 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-041210-281 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 part of serine C-palmitoyltransferase complex. Is expressed in EVL; gut; periderm; and pronephric duct. Orthologous to human SPTLC3 (serine palmitoyltransferase long chain base subunit 3).

Ensembl:

ensembl_id ENSDARG00000030743

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00013032 False 2510 mRNA 0.46 12 34804243 34858500
TCONS_00013033 False 2101 mRNA 0.48 13 34804877 34862484
TCONS_00013034 True 1020 mRNA 0.45 5 34854921 34862452

Neighbor

gene id symbol gene type direction distance location
XLOC_006770 ism1 coding downstream 10756 34765141 ~ 34793487 (-)
XLOC_006767 kif16bb coding downstream 120873 34627550 ~ 34683370 (-)
XLOC_006769 BX649403.2 coding downstream 159962 34644150 ~ 34644281 (-)
XLOC_006768 BX649403.1 coding downstream 165497 34638629 ~ 34638746 (-)
XLOC_006766 flrt3 coding downstream 981693 33811842 ~ 33822550 (-)
XLOC_006772 btbd3b coding upstream 179408 35041892 ~ 35051897 (-)
XLOC_006773 CR932983.2 coding upstream 320510 35182994 ~ 35194759 (-)
XLOC_006774 NA coding upstream 342813 35205297 ~ 35289437 (-)
XLOC_006775 CU138575.1 coding upstream 508085 35370569 ~ 35370684 (-)
XLOC_006776 slx4ip coding upstream 529125 35391609 ~ 35472531 (-)
XLOC_006471 BX537274.2 misc downstream 24539338 10264741 ~ 10264905 (-)
XLOC_006338 rn7sk misc downstream 33978018 825904 ~ 826225 (-)
XLOC_006757 NA non-coding downstream 1340599 33452438 ~ 33463644 (-)
XLOC_006758 NA non-coding downstream 1344925 33457523 ~ 33459318 (-)
XLOC_006752 NA non-coding downstream 1503073 33261131 ~ 33301170 (-)
XLOC_006779 BX663524.1 non-coding upstream 729758 35592242 ~ 35592377 (-)
XLOC_006784 NA non-coding upstream 1062558 35925042 ~ 35925484 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000012_06334114_06368535 SPTLC3 coding CI01000012 null 6333349 ~ 6369091 (+)