XLOC_010966 (smarcc1a)


Basic Information

Item Value
gene id XLOC_010966
gene name smarcc1a
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007127.7
NCBI id CM002900.2
chromosome length 55266484
location 42423530 ~ 42461263 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00021437
ttttccacGGACTAGCCTCTATCGCTAATAAAGAAACAATGGCGACAGCGGCGACTGCAGCGGGCGGAACGGGCTCCGGAGGACCATCTGCCGGCCAAACGGGCGCCGGTTCCTCGATCGGACGTAAAAAAGACGGAGGGCCATCTTCCAAGTATTGGGAGAGCTCGGAAACGGTGTCCCAGTTGGAGACAGTTCGCTTGTGGATCGGGAAACATTATAAGAAGCATGTCCAGACTGACTCTCCTACAAGCAAAACATTGGCTGCACTGGTGGTGCAATTGCTGCAGTTTCAAGAGGATGCATTTGGACGTAGAGTCAGCAATCCTGCCCTCACCAAACTACCTGCAAAGAGCTTTCTGGACTTCAAACCTGGAGGAGCCCTTTGCCACATTTTGGGATCTGCATACAAATTCAAAAGCGAGCAGGGCTGGAGGAGGTTTGATCTTCAGAACCCATCCAGAATGGATAGAAATGTGGAGATGTTCATGACTATTGAAAAGACTCTTGTTCAGAACAACTCTTTGACCAGACCTATTGTGTACATTGTGTCTGACGTTGAGCAGAAGCAAGCCAACAAGCTTAAAGACATCATTAAGAGAcatcagGGAACCATCACTGAAGACAAGTCAAAGGCCACTCATATTATTTATCCCTCCCCAACCCAGATGGAGGAAGAGGAATGGCTGCGTCCTGTTATGCGCAAAGACAAGCAAGTGCTTGTTCACTGGGGATATTACCCTGACAGTTACGATATATGGGTGTCAACAAGTGATGTGGATGCAGATGTTGAGGATCCTCCAAGTTCTGAGAAGCCATGGCGGGTGCATGCTAAATGGGTCATTGACACCGATGCTTTCAACGAGTGGATGAATGAGGAAGATTATGAAGTAGATGAGAACAAGAAGCCTGTGAGTTTCCGCCAGCGGATCTTCCCAGGGGAAGATGTGTCTTCCCGTACACCCGATCGTAAGGAACGCAAGTCCCTGGTTGCTGGCAAGAAGAGGAGACGCTCTCCATCTCCACCTAGCACCCCTGTGGAGTCGCGCAAGAAGGGCAAGAAAGGGAATCCTGGAAGTCAGTGGAGGCGGCGTGGACAACCAATTGATGACGAACAGGATGAAGATTCAACAAAGGACCTTGAAGATCCCTCTCCTGTGCCGGGAATGGAGGAAGTTACATTGCCAAAAAATGTCAATCAGAAAAAGGACAGCGAGAACACACCAGTGAAGGGTGGAATTCACAATGATTTAGATGACCAGGAAGATGACTCTGTGACATCTGGTGGCAAGGAGGATGATGAACAGAGCAAAGCAGAGGTCAATCGTCTGATCGACTCTGAGGACAACGTGACTGAGCAAACCCATCACATCATCATCCCCAGCTATGCTGCCTGGTTTGACTATAACAGTATACATGAAATTGAGAGACGTGCCCTGCCAGAGTTCTTCAATGGCAAAAACAAATCGAAGACTCCGGAGATTTATCTTGCCTATCGTAACTTCATGATTGACACTTACCGGCTGAATCCTCAGGAGTACCTGACCTCAACCTCCTGCAGGAGGAACCTCACTGGAGATGTCTGTGCGGTCATGAGAGTGCATGCCTTCTTGGAGCAGTGGGGACTGGTGAACTACCAGGTGGACGCGGAGAGCAGACCTCTCCCTATGGGCCCTCCACCAACCTCACATTTCAATGTTCTGGCTGATACTCCCTCTGGCCTGGTGCCGCTGCACCACCGTCCCCCACAGGTTCCCCCTGCTCAGCAGATGCTGAACTTCCCAGAAAAGGGCAAAGACAAGCCAACCGACCTGCAGAACTTTGGCCTCCGTACAGATATTTACTCCAAGAAGAATCTCAAGGGTAAAGGAGCTGCAGGTGGCAGAGACTGGACAGAACAAGAAACATTGCTTCTGTTAGAGGCTTTGGAAATGTACAAGGATGACTGGAATAAAGTTTCTGAGCATGTGGGCAGTCGTACACAAGATGAGTGCATCTTGCACTTCCTGCGGTTGCCCATAGAGGATCAGTACCTGGAGAGCTCTGACGCTTCGCTAGGCCCTCTTGCCTACCAGCCGATCCCATTCAGTCAATCAGGGAATCCAGTTATGAGCACGGTTGCGTTCCTCGCCTCTGTTGTGGATCCGCGTGTGGCCGCGGCTGCTGCCAAAGCTGCTCTGGATGAGTTCTCCCGTGTGCGTGAGGAGGTTCCTGCAGAGCTAGTGGAGGCTCATGTGAAGAAGGTGCAGGAAGCCGCACGCAGCACAGGGAAAGTGGACCCTGCATTTGGCCTGGAGAGCAGTGGCATTGCTGGCACAGCTCCTGAAGAACCCGAGAAGACGGAACCTACAGAGACTGAGAAAATGGACACAGACTCCGACTCCCAGCAGCCTGATAAGGCGGAGTCAAAGGATGAAGCAGAGAAACCCAGCGAGTCTGCAGAAAAGCCAGCCGAGACAGAGAAGGAAAAAATTGAGACTACAGAGAAATCTGAGCCACAGGAAGAGGAAGAAAGTGAGGCAGGAGAGACCAAGACAGCAGagaaagaaaaagaggaggCCATGGAGACCACAGAGGAAGGgaaggaggatgaggaggagcaggaggaagGAAAGAAAAAGCTGGAGTTGGATATTGGAGAGGGCAACATCGCCACCGCTGCAGCCGCCGCTCTGGCCTCTGCCGCCACCAAGGCAAAGCACCTGGCTGCAGTGGAAGAGAGGAAGATCAAATCTCTTGTTGCTCTGCTAGTGGAGACTCAGATGAAGAAGCTGGAGCTCAAACTCAGACACTTTGAAGAGCTGGAGACCATTATGGACCGTGAAAAGGAAGctCTGGAGCTCCAGAGGCAGCAGCTTTTGACCGAGCGACAGGCGTTCCACATGGAGCAGCTGAAGTATGCTGAGATGAAGGCCCGTCAGCAGATGGAGCAGCAGGCAGCGGTGCAGCAAAACGCTGGAGGACATCATGGTCCTCCTCCACATGGACCACCTCCAGGCATGCACCCTGGACATCCAGGACATCCTGGACACCCCGGCCCTGGATTTCCACCAATGCACCACCCCATGGGTCCACATCACACCCCTCAGACAGGACCAATGGTTGGACCAGGTCAGCCTATGCCAGGCCGAATGATGTCTGGACCTCCCCCACAGGGTGGAATAGCACCAATGATGGGACCTCGACACCCTGGGCCACCAAACGGCATGTACCCAGGTCCTCCTCCTCCAACCGCACAGCCTGATGGGATGCCTCCCGGCCCAGTGGGACCCCCTCCATCTGTGCCCGCTACTCGTGCTGCTGAAAACTAAACTATTGCCCCCCTCCCCACCATCCCCACACACGCGTTCACATCCACTCgcagatacacacgcacactgaAATCCAGATTAATCCGGGATCCCCGCAGACCTGCTGTCGTCGCCTTCTGTAGATTTGCCTTGCTGATGGGTGGGTCATCTCTAAAGCCTCTCTCTCATTCTCATTCTTTCTGTCCGACTGAGCTGAGCATTCTCCGTAAACATTCACACGCTCAGGGCACAAAGTCAAGAGTCAGTCCTCCGTCTCTTGTCTAGTAATAGCACTGGCCTCTCTTCCTTCTCTGTCCCCAGTGTTTGTTTGAAAAGCGTGTCGCAGGCTCCAGCGTCCTCCCTGTAATGTGACCGATGGAATCATATATGTATATTGTGTGCTAATCCGCGTAAAAGCTAAACGCTCCCAGATTGAACCCGCACTGTAGCTGCGAGACGTTTTCTGCGCTGACCTGGAGTCCTGCGGCATCCGCTATCGTACGTGTTCATGGTGCGGTATCCATTTCAGCCGGTGGCTTCATTGAGCTTCCTCTAACTATTTACATCCTCATCTAGCTGATAATCTACCTCACCGGTGCAATCCTATTCAATCAGTGCACGGTGTGTGAAGCAGACTCGCTTTAAAGTGGAGATCGCAACTCACACACGCCCCTACAACTGCTGTGTTCTGTTATTTAGAGATGTACCCACACATGCATTAACCCTTGTTTGCTTCAGATGCTGTGCAGATGTTGGAACACGTACACAAACACGCCTCTGTGTAGTTCTGCTGACGGAGGTCTATATGGTATCACGCTGAAGTGATGGAGGAACCTTGCTTGTTTTAGGTGTAGCTGGCCTTCCCCTTAGGTGCTGACAGAGTAGCTGCCCCGCCTCGCTCTACCTCTCTCACTTTACTACCTCTCTTCTCTCCTTCTCTCTTCCCGTTTTTGgctgttctctctctctgtttccttTTTGTGTGTGCGCCCATGTGACTGCTGCATTACTGCTGTGTGGAGGCTtttgtcctcctcctcctcaggtGAACCAAGCCCTCGCTTCAACACGGCCCGCCCTGCTACActactacaaacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacatatatatatatttcctcttCCAAAACTTTCCAGGCTGTACATCACAGGAAAATTGGGTTAAACCCTGATCCCCTGACCCCCCCCATATATAacttttattgctttttattttatggtaatgtatttttaagaaaataaagttTGTGTAGACTCA

Function

symbol description
smarcc1a Predicted to enable histone binding activity. Acts upstream of or within definitive hemopoiesis and heart morphogenesis. Located in cytoplasm and nucleus. Is expressed in head and tail bud. Orthologous to human SMARCC1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1).

GO:

id name namespace
GO:0043044 ATP-dependent chromatin remodeling biological_process
GO:0060216 definitive hemopoiesis biological_process
GO:0045893 positive regulation of transcription, DNA-templated biological_process
GO:0003007 heart morphogenesis biological_process
GO:0071564 npBAF complex cellular_component
GO:0071565 nBAF complex cellular_component
GO:0016514 SWI/SNF complex cellular_component
GO:0005634 nucleus cellular_component
GO:0005737 cytoplasm cellular_component
GO:0042393 histone binding molecular_function
GO:0003677 DNA binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-080514-3 Predicted to enable histone binding activity. Acts upstream of or within definitive hemopoiesis and heart morphogenesis. Located in cytoplasm and nucleus. Is expressed in head and tail bud. Orthologous to human SMARCC1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1).

Ensembl:

ensembl_id ENSDARG00000017397

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00021437 True 4601 mRNA 0.51 28 42423530 42461263

Neighbor

gene id symbol gene type direction distance location
XLOC_010965 cspg5a coding downstream 32890 42319438 ~ 42390640 (-)
XLOC_010964 ppox coding downstream 116933 42289076 ~ 42306597 (-)
XLOC_010963 zgc:162160 coding downstream 185410 42193163 ~ 42238120 (-)
XLOC_010962 fbl coding downstream 237437 42177659 ~ 42186093 (-)
XLOC_010961 alkbh8 coding downstream 247913 42156064 ~ 42175617 (-)
XLOC_010967 tbx20 coding upstream 47748 42509011 ~ 42523744 (-)
XLOC_010968 slc4a7 coding upstream 231984 42693247 ~ 42770064 (-)
XLOC_010969 txnipb coding upstream 407791 42869054 ~ 42872572 (-)
XLOC_010970 CR854827.1 coding upstream 412477 42873740 ~ 42874709 (-)
XLOC_010971 hjv coding upstream 422536 42883799 ~ 42894628 (-)
XLOC_010626 CR392024.2 misc downstream 21528355 20895112 ~ 20895175 (-)
XLOC_010954 BX649388.1 non-coding downstream 458221 41955855 ~ 41965309 (-)
XLOC_010953 BX649388.3 non-coding downstream 474414 41948075 ~ 41949116 (-)
XLOC_010951 CR318611.1 non-coding downstream 540970 41882445 ~ 41882560 (-)
XLOC_010944 NA non-coding downstream 685532 41684868 ~ 41737998 (-)
XLOC_010942 BX005012.3 non-coding downstream 880667 41542079 ~ 41542863 (-)
XLOC_010975 NA non-coding upstream 511822 42973085 ~ 42974540 (-)
XLOC_010976 NA non-coding upstream 513284 42974547 ~ 42993892 (-)
XLOC_010981 NA non-coding upstream 657850 43119113 ~ 43124227 (-)
XLOC_010987 NA non-coding upstream 897662 43358925 ~ 43368871 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000027_03524553_03546701 SMARCC1, SMARCC1A coding CI01000027 null 3523607 ~ 3546701 (+)