XLOC_000680 (smarca5)


Basic Information

Item Value
gene id XLOC_000680
gene name smarca5
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007112.7
NCBI id CM002885.2
chromosome length 59578282
location 52792439 ~ 52820954 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00001151
GTTTTGCGGGAACGGTGTCAACAGAAAAGCCGGGGACCGTGAATGACGCGTGGTGCGCTTGCTCAATTTGGGCAATATTTTGAAACTTTCCAATCAAACCAATATACTTTTTCGGCTTATCTGACATATTTTTAACGGAAAAACTCGGATCCATCGCGAAATAACGGAATTATCCAGCCTATCATGTCACAAACAGAAAGCAGCATGGAGCAGCAGCGGGAAGAAGAGCCGAGCCAACTCGACCCGGCCGGTCCGGCAGAGGATGATACTTCAGAAAATGGCCATGATGAAGCATCAGATACAGCTATGGATAGTGAAGCACAGTCGTCATCACCTCCCTCAGCAAAGGGAAAGGACCTGCTGGGTGGATATGAGGAAAAAGTGCAAACAGACCGGACCAACAGATTTGAGTACCTCTTGAAGCAGACAGAAGTGTTTGCTCATTTCATTCAACCAGCAGCCCAGAAGACCCCAACTTCACCTCTGAAGATGAAGCCTGGCCGTCCTCGTATTAAAAAAGATGAGAAGCAGAACCTGCTGTCTGCTGGAGAtaaccGCCATCGTCGGACGGAGCAGGAGGAGGATGAGGAGCTGCTAAGTGAGAACAGTAAAGCCACCAGTGTCTGCACACGTTTTGATGACTCTCCTTCCTATGTGAAAACCGGTAAACTGAGAGACTACCAGGTCCGTGGACTGAACTGGCTCATTTCCCTTTATGAAAATGGAATTAATGGAATCCTTGCTGATGAAATGGGTCTTGGTAAGACCCTCCAGACCATCTCTCTGCTGGGCTACATGAAGCACTATAGAAACATTCCTGGACCCCACATGGTTCTGGTGCCCAAATCCACCCTGTATAACTGGATGAATGAGTTCAAGCGTTGGGTTCCCTCCCTAAAAGCCGTCTGCCTCATCGGGGACAGGGAGGAAAGAACGGCTTTTATCCGCGACACACTGCTGCCTGGCGAATGGGATGTGTGCGTTACCTCTTACGAGATGCTCATTATCGAGAGAGCCGTCTTCAAAAAGTTCAACTGGAGATACCTGGTTATTGATGAGGCTCACCGTATCAAGAACGAGAAGTCCAAGCTTTCCGAGATCGTGCGAGAGTTCAAGACTACAAATCGATTGCTGCTGACTGGAACCCCACTGCAGAACAACCTTCATGAGCTGTGGGCGCTGCTCAACTTCCTGCTGCCAGATGTTTTCAACTCCTCCGAGGATTTTGATGCCTGGTTTGACACCAACAACTGTCTGGGTGACACAAAGTTGGTGGAACGTTTGCATACTGTTCTGCGTCCATTCCTGCTGAGACGTATCAAAGCGGATGTGGAGAAGTCTTTACTTCCCAAAAAGGAAATCAAGATATATGTTGGGCTCAGCAAGATGCAGAGAGAATGGTACACCAAGATTTTGATGAAGGACATTGACATTCTGAACTCTGCTGGCAAGATGGACAAAATGCGTCTGCTGAACGTGCTGATGCAGCTGAGGAAATGCTGCAATCATCCCTACCTGTTCGACGGAGCGGAGCCTGGCCCGCCATACACCACTGATCTCCACCTGGTGGTCAACAGCGGGAAGATGGTGGTGCTGGACAAGCTGCTGCCCAAGCTCAAAGAGCAAGGTTCTCGTGTGTTGATCTTCAGTCAGATGACCAGGGTGCTGGACATTCTGGAGGATTATTGTATGTGGCGTAACTATGGTTACTGTAGGCTCGATGGACAGACTCCTCACGAGGAGCGACAGATTTCCATCAATGCCTTCAACGAGCCCAACAGCTCCAAGTTTCTGTTCATGTTGAGCACCAGAGCAGGAGGACTCGGCATCAATCTGGCCACCGCAGACGTGGTCATCATCTACGACTCTGACTGGAATCCTCAAGTGGATCTTCAGGCTATGGATCGTGCTCACAGGATTGGTCAAAAGAAACAAGTGCGGGTTTTCCGTTTCATCACCGACAATACAGTTGAGGAAAGAATTGTCGAGCGTGCAGAAATGAAGCTCCGCTTGGACTCTATTGTCATTCAACAAGGCAGACTGGTTGATCCTAGCATGAACAAACTGGGCAAAGACGAGATGCTTTCCATCATTCGGCACGGTGCCACTCACGTGTTTGCCTCAAAAGAGAGCGAGATCACAGATGAGGATATTGATGGCATTTTGGAGAGGGGAGAGCGGAAGACCATGGAGATGAAGGAGAAGATGGCCAATCTTGGAGAAGGCTCTCTGAGAAACTTCACCATGGACACAGAGAACAGCGTGTATAACTTTGAGGGTGAAGATTACAGAGAAAAGAAGAAGGTCGTCACTAACTGGATTGAGCCACCCAAGAGAGAGCGTAAGGCCAACTACGCTGTAGATGCCTACTTTCGAGAAGCCCTGCGCGTCAGCGAGCCCAAAGCACCAAAgGCTCCACGTCCTCCCAAACAGCCCAATGTTCAGGACTTTCAGTTCTTTCCACCTCGGCTCTTTGAGCTGCTGGAGAAGGAGATCCTCTATTACAGGAAGACTATTGGCTATAAGGTGCCAAGAAACCCTGATCTGCCCAACTCTGCTGAAATGCAGAAAGAGGAGCAGGCCAAGATTGACGAAGCTGAACCACTTAAtgaggaagagctggaggagaagGAGAACCTCCTCTCACAGGGCTTTACTATCTGGACCAAGCGTGACTTTAACCAGTTCATTAAGGCCAACGAGAAGTGGGGACGAGATGACATTGAGAACATCGCTCGTGAGGTTGAGGGCAAAACCCCAGAGGAGGTCATGGAATATTCTGctGTGTTCTGGGAGCGCTGCAATGAGTTGCAGGACATCGAGAAGATCATGGCTCAGATCGAGAGAGGAGAGGCCAGAATCCAGAGGAGGATCAGTATCAAGAAAGCACTCGACTCGAAAATTGGCCGCTATAAGGCGCCGTTCCATCAGCTCAGGATCTCGTACGGCACAAACAAAGGGAAAAACTACACAGAGGAGGAGGATCGCTTTCTCATCTGCATGCTGCACAAACTGGGCTTCGACAAGGAGAGCGTTTACGATGAGCTGCGCCAGTGCATACGCAACTCGCCACAGTTCCGCTTCGACTGGTTCCTCAAGTCTCGCACAGCCATGGAGCTTCAGAGGAGATGCAACACACTGATCACACTCATCGAACGTGAAAACATGGAGTTGGAAGAGCGAGAGAAAGCCGAGAAGAAGAAGAGAGGACCGCGCACATCTTCGGCTCAGAAACGCAAGCAGGACGGGACCCCTGATGGACGTGGCCGCAAGAAAAAGCTGAAATTGTGAGCAGGCAGGCATTTCACACACCTCACTCGGCGAGGAGCTTCAGTACAGCAATACTGCATTGATTGTTACGGGTCCCACTCATGTACTGTATGGATTTGCAGCACTGATCCTCGCCTCTCAAGTAGCTTGGCCTTCTTAACAAGGTGTAGAGTTGTAAATTAGGTCTCTTTTAGTTATATAATGTAACTACGGCTGTGCTGTCGGATGTGTTTTGTATTTATGGCtacttcaaatttttttttgtaccacATTCCATTTGCTTGTATCAGTTTAATTTGCAGTCTTTACCCCCTCATTATTAGTGTCTTCAGTATTGTATTGTCTCTGTATCCGCCATTGGAAAGTGACTAATAAATGTGGTTTTTATAAATGCTGCTCTGTATGTTTCctacaaataaatgtaatgtcTTTTGCCTTGTA

Function

symbol description
smarca5 Predicted to enable ATPase, acting on DNA and DNA binding activity. Acts upstream of or within cardiac ventricle development and retina development in camera-type eye. Predicted to be active in nucleus. Orthologous to human SMARCA5 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5).

GO:

id name namespace
GO:0006338 chromatin remodeling biological_process
GO:0043044 ATP-dependent chromatin remodeling biological_process
GO:0003231 cardiac ventricle development biological_process
GO:0016584 nucleosome positioning biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0060041 retina development in camera-type eye biological_process
GO:0005634 nucleus cellular_component
GO:0016589 NURF complex cellular_component
GO:0031491 nucleosome binding molecular_function
GO:0005524 ATP binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides molecular_function
GO:0016887 ATPase activity molecular_function
GO:0008094 DNA-dependent ATPase activity molecular_function

KEGG:

id description
ko03021 Transcription machinery
ko03036 Chromosome and associated proteins

ZFIN:

id description
ZDB-GENE-021125-1 Predicted to enable ATPase, acting on DNA and DNA binding activity. Acts upstream of or within cardiac ventricle development and retina development in camera-type eye. Predicted to be active in nucleus. Orthologous to human SMARCA5 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5).

Ensembl:

ensembl_id ENSDARG00000052348

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00001151 True 3711 mRNA 0.49 24 52792439 52820954

Neighbor

gene id symbol gene type direction distance location
XLOC_000679 wu:fc75a09 coding upstream 28992 52754085 ~ 52763447 (+)
XLOC_000678 CABZ01021532.1 coding upstream 56314 52735484 ~ 52736125 (+)
XLOC_000677 osbp coding upstream 93376 52662203 ~ 52699063 (+)
XLOC_000676 slc44a1a coding upstream 140276 52632856 ~ 52652163 (+)
XLOC_000675 abca1a coding upstream 164032 52560549 ~ 52628407 (+)
XLOC_000682 inpp4b coding downstream 108231 52929185 ~ 53225121 (+)
XLOC_000683 BX957281.1 coding downstream 400904 53221858 ~ 53271128 (+)
XLOC_000684 NA coding downstream 445446 53266400 ~ 53278288 (+)
XLOC_000685 rnf150a coding downstream 458907 53279861 ~ 53299024 (+)
XLOC_000686 NA coding downstream 499205 53320159 ~ 53320674 (+)
XLOC_000673 BX323839.1 non-coding upstream 281683 52495043 ~ 52510756 (+)
XLOC_000667 NA non-coding upstream 424241 52363402 ~ 52368198 (+)
XLOC_000668 NA non-coding upstream 424862 52365030 ~ 52367577 (+)
XLOC_000666 LO017718.1 non-coding upstream 429332 52353162 ~ 52363107 (+)
XLOC_000665 NA non-coding upstream 445540 52345955 ~ 52346899 (+)
XLOC_000687 NA non-coding downstream 499977 53320931 ~ 53321338 (+)
XLOC_000689 AL935166.1 non-coding downstream 543556 53364510 ~ 53368034 (+)
XLOC_000691 NA non-coding downstream 669145 53490099 ~ 53491305 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000302_00298902_00311424 SMARCA5 coding CI01000302 null 298182 ~ 312118 (+)
bowfin (Amia calva) AMCG00021059 LOC106567799,LOC105028962,LOC106603320,LOC103034185 coding CM030130.1 CM030130.1 1673885 ~ 1692615 (-)