XLOC_019061 (hmgb3b)


Basic Information

Item Value
gene id XLOC_019061
gene name hmgb3b
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007132.7
NCBI id CM002905.2
chromosome length 45934066
location 34119759 ~ 34129776 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00037797
GTTTTAAATGCCTTCCGGGACTGACCAATCAGGTAGGTCTCGTAGTGAGCTAGCGCGAGGCTGTGTGGTCTTCCATAGAGGAAGCGTGAGGCCGTGTGATTGAGGAGAACAGACGACAGGACAAACATAAGAAGGTGTGGGAATATTTTAGTGGCTTTGTAATAATGGCTAAGGGTGATCCAGGGAAACCCAAGGGCAAGATGTCTGCCTATGCCTACTTTGTCAAGACATGTCGTGAAGAGCACAACAAGAAGAACCCTGGTGTTACGGTTAACTTCTCAGAATTTTCCAAGAAGTGCTCTGAGAGATGGAAAACCATGTCTCCGAAAGAGAAGACTAAATTTGAAGACCTGGCCAAACAGGACAAGGCTCGTTATGATCAGGAAATGATGCACTACAATCCAGGAAAGAAAGGTCGGAAGCAGAAGAAAGACCCTAATGCTCCAAGGCGGCCACCGTCTGGATTTTTCCTGTTCTGTGCAAAGCAGAGGCCAATTATCAAGGCTCAGAACCCCAGCCTTGGCATTGGAGATGTAGCCAAGAAACTGGGAGGGATGTGGAACAACCTGTCTGATTCTGAGAAGCAGCCCTTCCTATCAAATGCTGACAAACTGAAGGACAAGTATCAGAAGGATATGGCCTTTTACAGAAAAAAGGGAAGTGGAGGCTCATCGTCTGCCAAATCTGAACCAAAGGATGACGACGAGGACGATGATGAGGAAGAAGAggatgacgacgatgatgatgaggatgatgactAAATGACTGGTTTCTCCTAATTGGGCAGTAAGGTGTTTGATCACTTAAGTCTGGGTCTAAAAGGTCTTTGTGTCAAGGCTGCTATACACTGATAATCAGTAAAAGAGCCCAATGCTTGCAAGCTCTGTCTTCAGACAACCTCTCTCAATGGTGAGTTTGCTGGTGGACCTGTTACAGCTTGCTATTAAACTGTTGGTAAGAGCATAATGTTTCCACACTGTCGAACAAAAAGTATTAGCAGtacaaactttttaaaagtatttaagtgGTGTCTATATATGGCTGTTAaacttaacaacaacaaaaaatctttCTGTAACTTTCTGTGTTGTTGGAAGGATGTTCATTAtatgcaaaattattattatttcttgagTGATTAAGTTGAGTGAATTTTATGTTTGCAAAGTCTAGGAACTTTATCAGCTTAAACCAGAGGCAAGTGATCAAATGTTTAGGGGACATGAGCTATTATTTGCTCCTTCAGTTGTTTGATGTTGTGTATCAATGATACTGTGATTTGAAATAAACATggcatttttagatgttaaatgtttttttattattttttttatgcatttctcatGCATAAAGTAGCATTTAAATATTTGGAGTATTTGTCAGTTAATAAAAGGATACATGTAGCTATTA
>TCONS_00037798
ATTGAGGAGAACAGACGACAGGACAAACATAAGAAGGTGTGGGAATATTTTAGTGGCTTTGTAATAATGGCTAAGGGTGATCCAGGGAAACCCAAGGGCAAGATGTCTGCCTATGCCTACTTTGTCAAGACATGTCGTGAAGAGCACAACAAGAAGAACCCTGGTGTTACGGTTAACTTCTCAGAATTTTCCAAGAAGTGCTCTGAGAGATGGAAAACCATGTCTCCGAAAGAGAAGACTAAATTTGAAGACCTGGCCAAACAGGACAAGGCTCGTTATGATCAGGAAATGATGCACTACAATCCAGGAAAGAAAGGTCGGAAGCAGAAGAAAGACCCTAATGCTCCAAGGCGGCCACCGTCTGGATTTTTCCTGTTCTGTGCAAAGCAGAGGCCAATTATCAAGGCTCAGAACCCCAGCCTTGGCATTGGAGATGTAGCCAAGAAACTGGGAGGGATGTGGAACAACCTGTCTGATTCTGAGAAGCAGCCCTTCCTATCAAATGCTGACAAACTGAAGGACAAGTATCAGAAGGTGGTGAATGCATTAATAAAAGTCTCTCTGAAAAATCTCATGTGCTCCCATTAGTCTTCACATAACATATTAAAATCTGAATATTACTGCTTTCacagtattttattaaattacatttatttatttttttaaatgtggctaTTCATAGCATAAGACTTTGGTTAATTTTACGTTGTTTTGGTTTCTCAGGATATGGCCTTTTACAGAAAAAAGGGAAGTGGAGGCTCATCGTCTGCCAAATCTGAACCAAAGGATGACGA
>TCONS_00037799
ATGGCTAAGGGTGATCCAGGGAAACCCAAGGGCAAGATGTCTGCCTATGCCTACTTTGTCAAGACATGTCGTGAAGAGCACAACAAGAAGAACCCTGGTGTTACGGTTAACTTCTCAGAATTTTCCAAGAAGTGCTCTGAGAGATGGAAAACCATGTCTCCGAAAGAGAAGACTAAATTTGAAGACCTGGCCAAACAGGACAAGGCTCGTTATGATCAGGAAATGATGCACTACAATCCAGGAAAGAAAGGTCGGAAGCAGAAGAAAGACCCTAATGCTCCAAGGCGGCCACCGTCTGGATTTTTCCTGTTCTGTGCAAAGCAGAGGCCAATTATCAAGGCTCAGAACCCCAGCCTTGGCATTGGAGATGTAGCCAAGAAACTGGGAGGGATGTGGAACAACCTGTCTGATTCTGAGAAGCAGCCCTTCCTATCAAATGCTGACAAACTGAAGGACAAGTATCAGAAGGATATGGCCTTTTACAGAAAAAAGGGAAGTGGAGGCTCATCGTCTGCCAAATCTGAACCAAAGGATGACGACGAGGACGATGATGAGGAAGAAGAggatgacgacgatgatgatgaggatgatgactAAATGACTG

Function

symbol description
hmgb3b Predicted to enable DNA binding activity, bending. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in chromosome and nucleus. Is expressed in central nervous system; intermediate cell mass of mesoderm; ovary; and pectoral fin bud. Human ortholog(s) of this gene implicated in syndromic microphthalmia 13. Orthologous to human HMGB3 (high mobility group box 3).

GO:

id name namespace
GO:0006310 DNA recombination biological_process
GO:0045089 positive regulation of innate immune response biological_process
GO:0006338 chromatin remodeling biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0005634 nucleus cellular_component
GO:0005737 cytoplasm cellular_component
GO:0008134 transcription factor binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003682 chromatin binding molecular_function
GO:0008301 DNA binding, bending molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-050417-290 Predicted to enable DNA binding activity, bending. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in chromosome and nucleus. Is expressed in central nervous system; intermediate cell mass of mesoderm; ovary; and pectoral fin bud. Human ortholog(s) of this gene implicated in syndromic microphthalmia 13. Orthologous to human HMGB3 (high mobility group box 3).

Ensembl:

ensembl_id ENSDARG00000006408

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00037797 False 1410 mRNA 0.41 5 34119759 34129776
TCONS_00037798 False 794 mRNA 0.41 4 34119857 34129069
TCONS_00037799 True 604 mRNA 0.47 4 34122801 34129134

Neighbor

gene id symbol gene type direction distance location
XLOC_019060 mtmr1b coding upstream 1229 34088110 ~ 34118530 (+)
XLOC_019059 NA coding upstream 33534 34078735 ~ 34086225 (+)
XLOC_019058 map4k6 coding upstream 44652 34033580 ~ 34075107 (+)
XLOC_019057 BX005313.1 coding upstream 354514 33756110 ~ 33765245 (+)
XLOC_019056 BX005313.2 coding upstream 472827 33637083 ~ 33646932 (+)
XLOC_019062 trpc5b coding downstream 2971 34132747 ~ 34211658 (+)
XLOC_019063 chm coding downstream 556988 34686764 ~ 34793909 (+)
XLOC_019064 wdr55 coding downstream 684668 34814444 ~ 34843004 (+)
XLOC_019065 cdc23 coding downstream 719630 34849406 ~ 34880924 (+)
XLOC_019066 NA coding downstream 799808 34929584 ~ 34943930 (+)
XLOC_019054 NA non-coding upstream 653952 33464424 ~ 33465807 (+)
XLOC_019051 NA non-coding upstream 672149 33249220 ~ 33447610 (+)
XLOC_019073 BX247879.1 non-coding downstream 1392926 35522702 ~ 35522834 (+)
XLOC_019074 NA non-coding downstream 1767822 35897598 ~ 35899398 (+)
XLOC_019075 NA non-coding downstream 1771141 35900917 ~ 35905585 (+)
XLOC_019076 NA non-coding downstream 1774609 35904385 ~ 35906582 (+)

Expression


Co-expression Network