XLOC_012170 (scfd1)


Basic Information

Item Value
gene id XLOC_012170
gene name scfd1
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007128.7
NCBI id CM002901.2
chromosome length 53461100
location 28771028 ~ 28797395 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00023988
GCCACGTCACCCTCGCAGTCGTCACTGCATAAACAGTAAAGATGGCGGCGTCCATCCGGGAAAAACAGACAGCTGCTCTCAAACGAATGCTCAACTTTAATGCCCCACCCCTTAAAAACACAACAGCTGAGCCAGTATGGAAGGTTCTTATTTACGATCGCTTTGGCCAAGACATTATATCTCCGCTTCTGTCTGTGAAAGAGCTACGAGACATGGGCATCACTCTGCACCTCTTGTTGCACTCAGATCGCGACCCCATTCCAGACGTTCCTGCCATTTACTTTATAATGCCCACAGAGGAGAACATCGACAGGATATGTCAAGACCTCCGAAACCAACTATATGAGTCCTACTATTTGAACTTCATCTCCGCAATTTCCAGAAGCAAATTGGAGGATATAGCAAGTGCTGCGCTTGCGGCTAATGCAGTAAACCAGGTGACCAAAGTATTTGATCAGTATTTGAACTTCATCACACTTGAGGATGATATGTTCATTCTCTGTAATCAAAACAAAGAGCACATCTCCTACCATGCAATCAATAAGCCAGATATCATGGACACAGACATGGAGGGTATAATGGACACAATAGTGGATAGTCTCTTCTGCTTCTTTGTTACTCTTGGTGCTGTCCCAATAATTCGATGTCCAAGAGGGAATGCTGCCGAAATGGTAGCAGTGAAACTTGACAAGAAACTGAGAGAGAATTTGAGAGACGCTCGTAACAGCCTGTTCACCGGAGACACCATGGGCACTGGCCAGTTCAGTTTCCAGAGGCCGTTGTTTGTTCTTGCGGATCGTAACCTGGATCTTGCGACTCCTCTCCACCACACATGGACGTATCAGGCTCTAATTCATGATGTGCTGGACTTCCACCTGAACCGAGTGAGTGTGGACGAGTCTCATGGGTCAGAGGCCAGTCCAGCCGGAGCACGacccaaaaagaaaaacaagaagagCTATGATCTCACTGCTGCTGACAAGTTTTGGCAAAAACACAAAGGAAGCCCATTCCCAGAGGTTGCAGAAGCTGTGCAGGAGGAACTGGACACATATCGAGCCCAAGAGGATGAGGTTAAACGGCTCAAGAGCATCATGGGCTTAGAAGGGGAGGACGACGGAGCCATTAGTATGTTGTCAGATAACACTGCCAAACTTACCTCAGCCGTCAGTTCTCTTCCTGAGCTCCTGGAAAAGAAGAGACTGATTGACCTCCACACCAACGTTGCCACAGCAGTTCTGGACCACATCAAGAGCCGTAAGCTTGACGTGTACTTCGAGTACGAGGAGAAGCTCATGAGCAAATCCACACTCGATAAATCCCTGCTGGACATTATCAGTGACCCTGATGCTGGAACGGCAGAGGATAAGATGAGGCTGTTTCTGATCTACTACATCACTTCCCAGCAGCCCCCATTGGAGGCTGATCTAGAACAGTACAAGAAAGCCATGGTTGATGCAGGCTGCGACCTATCCCCACTTAACTACATTAAACAGTGGAAAGCTTTCACCAAGATGGCTGCGACGCCAGCCAATTACGGGAGCAGTGGAGTGAAACCTATGGGACTGTTCTCAAGGGTGATGAACACCGGCTCCCAGTTTGTGATGGAGGGAGTGAAAAATCTGGTCTTGAAACAGCATAACCTACCGGTTACTCGCATCTTGGACAACTTGATGGAAATGAAGTCAAACCCAGAGACTGATGACTACAGATACTTTGATCCCAAGATGCTTCGTGGAAGCGAGAGCTCCATTCCGAGGAACAAGAACCCCTTTCAGGAGGCTATCGTCTTTGTTGTTGGAGGAGGCAATTACATAGAGTATCAAAATCTTGTTGACTACACAAAGACCAGGCAAGGAAAGCGGATTCTTTATGGCTGTAGTGAGCTGTTCAATGCTGCCCAGTTCATTAAACAGCTCTCTCAGCTTGGTCAGAAATAGGTGGAGTGATGAAGTCCTGTTATCCACCATTCTCAAATCTGGAATCGAGATCTCTTCAGTTGTACTCCATTAAAACCCCTCTAACTACAGAATCATGCATATTTCATTACTGGAGACTGTCTTTCTTAtactatttaattaaattctaaatgttcccaaaaataaagtttaacagtCTTAAGCA

Function

symbol description
scfd1 Predicted to enable syntaxin binding activity. Acts upstream of or within several processes, including fin regeneration; glycoprotein transport; and skeletal system development. Predicted to be active in Golgi membrane and cytosol. Is expressed in digestive system; head; myotome; notochord; and pharyngeal arch. Orthologous to human SCFD1 (sec1 family domain containing 1).

GO:

id name namespace
GO:0006886 intracellular protein transport biological_process
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport biological_process
GO:0034436 glycoprotein transport biological_process
GO:0006904 vesicle docking involved in exocytosis biological_process
GO:0051216 cartilage development biological_process
GO:0016192 vesicle-mediated transport biological_process
GO:0031101 fin regeneration biological_process
GO:0048702 embryonic neurocranium morphogenesis biological_process
GO:0005829 cytosol cellular_component
GO:0000139 Golgi membrane cellular_component
GO:0019905 syntaxin binding molecular_function

KEGG:

id description
ko04131 Membrane trafficking

ZFIN:

id description
ZDB-GENE-030116-3 Predicted to enable syntaxin binding activity. Acts upstream of or within several processes, including fin regeneration; glycoprotein transport; and skeletal system development. Predicted to be active in Golgi membrane and cytosol. Is expressed in digestive system; head; myotome; notochord; and pharyngeal arch. Orthologous to human SCFD1 (sec1 family domain containing 1).

Ensembl:

ensembl_id ENSDARG00000000779

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00023988 True 2124 mRNA 0.46 25 28771028 28797395

Neighbor

gene id symbol gene type direction distance location
XLOC_012169 opn6b coding downstream 228 28760586 ~ 28770800 (-)
XLOC_012168 coch coding downstream 21388 28743661 ~ 28749640 (-)
XLOC_012167 ap4s1 coding downstream 63058 28703971 ~ 28707970 (-)
XLOC_012166 BX465838.2 coding downstream 118516 28643458 ~ 28652512 (-)
XLOC_012165 BX465838.1 coding downstream 146852 28624048 ~ 28624176 (-)
XLOC_012171 g2e3 coding upstream 1330 28798725 ~ 28811747 (-)
XLOC_012172 NA coding upstream 124177 28921572 ~ 29022679 (-)
XLOC_012173 foxg1a coding upstream 319632 29117027 ~ 29119362 (-)
XLOC_012174 sptbn5 coding upstream 326795 29124190 ~ 29194219 (-)
XLOC_012175 ehd4 coding upstream 398567 29195962 ~ 29213710 (-)
XLOC_012163 BX465838.4 non-coding downstream 240446 28530467 ~ 28530582 (-)
XLOC_012158 NA non-coding downstream 1367277 27402643 ~ 27403751 (-)
XLOC_012152 AL928908.3 non-coding downstream 1785269 26982035 ~ 26985759 (-)
XLOC_012176 NA non-coding upstream 418671 29216066 ~ 29224911 (-)
XLOC_012179 AL845481.1 non-coding upstream 475568 29272963 ~ 29273081 (-)
XLOC_012182 AL928842.1 non-coding upstream 839810 29637205 ~ 29637321 (-)
XLOC_012183 CT027582.2 non-coding upstream 924690 29722085 ~ 29723213 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000189_01818502_01830933 SCFD1 coding CI01000189 null 1818397 ~ 1830933 (-)