XLOC_004553 (smarcd2)


Basic Information

Item Value
gene id XLOC_004553
gene name smarcd2
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007123.7
NCBI id CM002896.2
chromosome length 49182954
location 10134366 ~ 10160941 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00009055
accattatgataaatgggGGCTTGACAAGCTTTAGAGGAAGAGATGACACGCTCAACCGACATCGATAGACAGTTACACAGATACTGACGAATATATCGACATGTGAACGCAATGTGCTCACGCCTGACTCAACCGGACGCTTTTCGAGTAACTCAATAACTGTTTTGATTCGTTTATTAGCAATTATTAGCGTTGAAAACCATCAAACATGTCTTCGAGATCGGGTTTCTCGGTCAACCCCAGTACCCCAATAAACCCCGGGATGAACCCCATGAACCCCGGTCACAGCAGCGCCCCGAGAATGCCAGCATTGCCTTTGAATTCACCCTACAGAGGGATGAGCAGCACCCCGAACCAGTACCACCAAAGTGAAGAGGCGTAAGATGGCTGACAAAGTCCTCCCACAGAGGATCAGGGATTTGGTCCCAGAGTCTCAGGCATACATGGACCTTCTGGCCTTTGAAAGAAAACTGGACCAGACCATTGCTCGCAAACGCATGGAGATACAGGAGGCCATCAAAAAGCCCATCACGCAAAAACGCAAGCTGAGAATCTACATTTCGAACACTTACACGCCTGGCAAGCCAGAGGGCGAGGAGGCTGAAAAAGTGGCATCCTGGGAACTTCGAGTGGAAGGCAAACTCCTGGAGGATCCTGGGAAACTGAAACGAAAGTTCTCATCCTTCTTTAAAAGCTTGGTCATTGAACTGGACAAAGAACTTT
>TCONS_00009056
accattatgataaatgggGGCTTGACAAGCTTTAGAGGAAGAGATGACACGCTCAACCGACATCGATAGACAGTTACACAGATACTGACGAATATATCGACATGTGAACGCAATGTGCTCACGCCTGACTCAACCGGACGCTTTTCGAGTAACTCAATAACTGTTTTGATTCGTTTATTAGCAATTATTAGCGTTGAAAACCATCAAACATGTCTTCGAGATCGGGTTTCTCGGTCAACCCCAGTACCCCAATAAACCCCGGGATGAACCCCATGAACCCCGGTCACAGCAGCGCCCCGAGAATGCCAGCATTGCCTTTGAATTCACCCTACAGAGGGATGAGCAGCACCCCGAACCAGTACCACCAACGGCCAAGTATGCCACTCAGCCGAGGAATGCCAATGGGGGGCATGGGGTCTATTGGTTCCCCACTGCCTGGTCCATCATATAGTGGAGCCATGCCTATGCGACCTGGAATGCCTCAATCTGCGATGGACCCGACCCGAAAGAGACTCCTTCAACAGCAGCCTGGGGGTCTTATGGGCCCAAGAAGAGGAGTGAAGAGGCGTAAGATGGCTGACAAAGTCCTCCCACAGAGGATCAGGGATTTGGTCCCAGAGTCTCAGGCATACATGGACCTTCTGGCCTTTGAAAGAAAACTGGACCAGACCATTGCTCGCAAACGCATGGAGATACAGGAGGCCATCAAAAAGCCCATCACGCAAAAACGCAAGCTGAGAATCTACATTTCGAACACTTACACGCCTGGCAAGCCAGAGGGCGAGGAGGCTGAAAAAGTGGCATCCTGGGAACTTCGAGTGGAAGGCAAACTCCTGGAGGATCCTGGGAAACTGAAACGAAAGTTCTCATCCTTCTTTAAAAGCTTGGTCATTGAACTGGACAAAGAACTTTATGGCCCAGACAATCACTTGGTGGAGTGGCACAGAATGCCCACGACTCAGGAGACGGATGGATTTCAGGTGAAGAGACCAGGAGATGTGAATGTGAAATGCACTCTGCTTCTCATGCTGGACCACCAGCCTCCACAGTACAAGCTGGACCCACGTCTGGCTCGACTGCTGGGTGTCCACACTCAGACCAGAGCCAGTATCATGCAGGCCCTGTGGCTCTACATCAAGAACAACAAGCTGCAAGATTGCCACGAGAAAGAGTACATTAACTGCAACCGATACTTTAGACAGATCTTTGGCTGCCCCAGGATGAGATTTTCGGATATCCCCATGAAGCTCGCCAGCCTCCTTCAACACCCCGACCCCATCGTCATCAATCATATCATCAGTGTGGATCCCAACGATCAGAAGAAGACTGCTTGCTTTGATATTGATGTTGAGGTTGACGACCCTCTGAAGGCTCAGATGACCGGCTTCCTGTCCTCCACAACCAGTCAGCAGGAGATTGCTACTCTGGAGATGAAGATCCATGAGACTATTGAGTCCATCAACCAGCTGAAGACCCAGAGAGACTTCATGCTCAGCTTTAGTAACAGCCCACAGGAGTTCATCCAGGACTGGCTCAAGTCTCAGAGCCGAGACCTCAAGcTAATGACAGATACTGTGGGAAATCCAGAAGAGGAGAGGAGGACTGAATTTTACCACTCACCCTGGGTCACAGAAGCTGTTGGACGATATATATTTTCAAAGGTCCAGCAGAGGAGACAGGAGTTGGAGCAGGTACTTGGAATCCGACTCACTTAAGAAGATTCAGACTCCAAATCCACAATCATCCGAGCAACTGATTCAACAAATGTTGAATCAGTTTCTGTTTCATAACCAGCGGATGCACTTCATGTGGGTTTTTGGTACTGGTCATAAACAGCTTGTCAGGTGCAGCATTTGCAGTACCATTACACACATCTGGCCAAATATATTTCAAGCGCTGTTACAATAACTGGAATGCCTCAGTTGCTATCTTCCCTTCTCTGGTCTTTATTTCTATATTGTGaaaagaaaatatgaaaataagcCATTGAGTTCATGGCCTTTATttgacatacactcatacacaataatactcttgtaatttttttacagtacaatGCAGTACTGTAGTTTGTTTGTTAAAACCCCATTGGAAATAGATAACAATCTTGATTTTGTGTTTTTAGTAGGAATTGCTGAAGTCAATTTGCCATTTTGTTTCTGATTCTTACAGCAAAGGATATTCCAACAAAATTAATTGCACACGTTTTGAGTTTATATGCTTGCAATTAAGTAGACTAGCAATGAAATGTTTTCAATATTGTGGATTTTTCCATTTGGTCTCTCAGGAAAAATATGTGCTGCACTGCGTTCAAGAGCCATGTCTTTGTGTTTCCACCCCAGCACATTTGGATATCCAGCTGTTTTAGTTCAATTTACCAGACTTTCTGTCTTCATCTAGTTAGTGgtattagtctttttttatttagtgtttgaAAGTCTGCTAAAGAGACACAGCAGTGACCACATTTGTCAAAGACGATGTTTTAGATATGCAAGCCATCAGCATAATTGATATTTTCAGGTATACCGAAGCCATAATGTTACTTAATAATAAGTAGTTCACTTCAGCGTGCACTTTTACATTCCAAAAAGCTGTTGGACGTTTTGTTTAAGtgtgttttaattcattttttgcaGTCGCTTATGTTAAGTATAGATGACAGCaaactgaattttaaaacaaGGAATATAACAGgtggttataataataaaaataataagacaggaAGACTGGTGAGGAAAAAATGTGCTGACAGTAGGATGTTGAAAATTAAATTCTAGCTTCTATTTTTAATGCATCTCTGATGGTTGAGCTGAAAGCATGTCACAGATTTCTTTCCATAAAGTTTTGTgtttttcaatagtttattttGCTAATTGCTCAATTGCTCAGACAGTATTAATGCTGATCTGAAATGCAActagtgtttttgttttacgcCTTTGTGCCTTTGATTTACTTGTTAACTGattacatttgtgtttgtgtgtgttaaatgCAATTAAGTTCTTACAACtgttctgttttatatttttgtattaatcaAATGCTTatcttttgtacttttttatgaGAAATTTGAGTATTTTCAGCAATAAAGTTGGTTTCATAAA

Function

symbol description
smarcd2 Predicted to enable transcription coregulator activity. Acts upstream of or within hematopoietic progenitor cell differentiation and neutrophil differentiation. Predicted to be part of SWI/SNF complex. Predicted to be active in nucleus. Orthologous to human SMARCD2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2).

GO:

id name namespace
GO:0002244 hematopoietic progenitor cell differentiation biological_process
GO:0006337 nucleosome disassembly biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0043044 ATP-dependent chromatin remodeling biological_process
GO:0030223 neutrophil differentiation biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0016514 SWI/SNF complex cellular_component
GO:0005634 nucleus cellular_component
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-080215-1 Predicted to enable transcription coregulator activity. Acts upstream of or within hematopoietic progenitor cell differentiation and neutrophil differentiation. Predicted to be part of SWI/SNF complex. Predicted to be active in nucleus. Orthologous to human SMARCD2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2).

Ensembl:

ensembl_id ENSDARG00000088877

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00009055 False 724 nonsense_mediated_decay 0.48 5 10134366 10145811
TCONS_00009056 True 3116 mRNA 0.43 13 10134366 10160941

Neighbor

gene id symbol gene type direction distance location
XLOC_004552 si:dkeyp-118b1.2 coding upstream 8589 10115964 ~ 10125777 (+)
XLOC_004551 slc4a1b coding upstream 33862 10053852 ~ 10100504 (+)
XLOC_004550 NA coding upstream 183877 9941133 ~ 9950489 (+)
XLOC_004549 ndufa4 coding upstream 250040 9880493 ~ 9884326 (+)
XLOC_004548 fam117ab coding upstream 258290 9849476 ~ 9876076 (+)
XLOC_004554 psmc5 coding downstream 2644 10163585 ~ 10175487 (+)
XLOC_004555 si:ch73-103l1.2 coding downstream 18511 10179452 ~ 10193551 (+)
XLOC_004556 CU459020.1 coding downstream 49991 10210932 ~ 10211048 (+)
XLOC_004557 snu13b coding downstream 282844 10443785 ~ 10447178 (+)
XLOC_004558 crym coding downstream 287285 10448226 ~ 10462503 (+)
XLOC_004546 NA non-coding upstream 321880 9797037 ~ 9812486 (+)
XLOC_004542 NA non-coding upstream 684635 9443721 ~ 9449731 (+)
XLOC_004536 NA non-coding upstream 1163334 8968317 ~ 8971032 (+)
XLOC_004533 NA non-coding upstream 1577207 8556636 ~ 8557159 (+)
XLOC_004565 CR450852.1 non-coding downstream 1482610 11643551 ~ 11643671 (+)
XLOC_004568 NA non-coding downstream 2254315 12415256 ~ 12415835 (+)
XLOC_004569 BX548041.1 non-coding downstream 2452394 12613335 ~ 12613451 (+)
XLOC_004579 BX649204.1 non-coding downstream 3296296 13457237 ~ 13457356 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000047_00434216_00448665 SMARCD3.S, SMARCD2, SMARCD2.L coding CI01000047 null 433964 ~ 448721 (+)