XLOC_009359 (hmgb1b)


Basic Information

Item Value
gene id XLOC_009359
gene name hmgb1b
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007126.7
NCBI id CM002899.2
chromosome length 48040578
location 31513065 ~ 31516583 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00018391
GGATTCGTGACTGTAGACTGTGTCTCTCGTGAACGGGGAGCTCAACACGCACTTGGAAGAGCGCGCATCGGTGTTATTGTACTTCAAAGCCCCATTATCTAGGCATCCACAGAAGCTGCAGATAGAGAAGAGGATAAAGATGGGTAAAGATCCAAGGAAGCCCAGAGGAAAGATGTCCTCTTATGCCTACTTTGTGCAAACCTGTCGTGAGGAGCACAAAAAGAAGCACCCTGAAGCCAGTGTGAACTTCTCTGAATTCTCCAAGAAGTGTTCAGAGCGATGGAAGACAATGTCTGCCAAAGAGAAGGGCAAGTTTGAGGATATGGCCAAGCAAGATAAGGTTCGCTATGAGAGGGAAATGAAGAACTACATCCCACCAAAGGGTGAGAAGAAGAAGAGGTTTAAGGATCCCAACGCACCCAAGAGACCACCgTCAGCGTTCTTCATTTTCTGTGGTGATTACCGCCCTAAGATAAAGGGTGAAAACCCTGGTCTGTCCATCGGCGACATTGCCAAAAAGCTTGGAGAAATGTGGAACAGCTCATCAGCTGAAGTGAAGCAGCCCTATGAAAAGAAAGCCGCAAAGCTCAAGGAGAAGTACGACAAGGATATTGCCCTGTACCGCACAAAGGGAATTGCAGGCTTTTCAAAGAAAGAAGGTGGGGAGGATGATGAGGAGGATGAAGACGACGATGAGGAGGAGGACGACGaagaggaggaggatgatgaGTAGATTAGCTACTGATGTGGCCTAGGTTCTTGTTCATGCCATAACCCCAATTGTACATGATTCACATCTTCAAACGTAATACAGCAGATACAAGAATGGTTAGGCTGTGTATATGCGACGTTTTTAAGATGTACAGTGTTATTCTCCTTTTGTAAAGTTAACACTATGTGTCTCgagtcttattatttttttatctttgtttttgttaGTGGTAGTTCTTGCCAGGAACAGTTTAAGGTTGAATAATATAAACTGTACTGTTTCTCTGAAGGTGCACAGCACAATTATCTGGTTTATGTAGATCTGTAGTGCACTAtcatattagtttttacaaatatttttcgtATTTGCAGTCATAAGGTCCTTTAACTGTACTTTGAATACCACTCTAATTACAAGAATGCAGTTTTGTTTGACATTTAAGAATGTGTCTgaattaaacatttctttttttaag
>TCONS_00018392
CTCGTGAACGGGGAGCTCAACACGCACTTGGAAGAGCGCGCATCGGTGTTATTGTACTTCAAAGCCCCATTATCTAGGCATCCACAGAAGCTGCAGATAGAGAAGaatattttgtTTTCCAGAGGATAAAGATGGGTAAAGATCCAAGGAAGCCCAGAGGAAAGATGTCCTCTTATGCCTACTTTGTGCAAACCTGTCGTGAGGAGCACAAAAAGAAGCACCCTGAAGCCAGTGTGAACTTCTCTGAATTCTCCAAGAAGTGTTCAGAGCGATGGAAGACAATGTCTGCCAAAGAGAAGGGCAAGTTTGAGGATATGGCCAAGCAAGATAAGGTTCGCTATGAGAGGGAAATGAAGAACTACATCCCACCAAAGGGTGAGAAGAAGAAGAGGTTTAAGGATCCCAACGCACCCAAGAGACCACCgTCAGCGTTCTTCATTTTCTGTGGTGATTACCGCCCTAAGATAAAGGGTGAAAACCCTGGTCTGTCCATCGGCGACATTGCCAAAAAGCTTGGAGAAATGTGGAACAGCTCATCAGCTGAAGTGAAGCAGCCCTATGAAAAGAAAGCCGCAAAGCTCAAGGAGAAGTACGACAAGGATATTGCCCTGTACCGCACAAAGGGAATTGCAGGCTTTTCAAAGAAAGAAGGTGGGGAGGATGATGAGGAGGATGAAGACGACGATGAGGAGGAGGACGACGaagaggaggaggatgatgaGTAGATTAGCTACTGATGTGGCCTAGGTTCTTGTTCATGCCATAACCCCAATTGTACATGATTCACATCTTCAAACGTAATACAGCAGATACAAGAATGGTTAGGCTGTGTATATGCGAC
>TCONS_00018393
GTGTCTCTCGTGAACGGGGAGCTCAACACGCACTTGGAAGAGCGCGCATCGGTGTTATTGTACTTCAAAGCCCCATTATCTAGGCATCCACAGAAGCTGCAGATAGAGAAGAGGATAAAGATGGGTAAAGATCCAAGGAAGCCCAGAGGAAAGATGTCCTCTTATGCCTACTTTGTGCAAACCTGTCGTGAGGAGCACAAAAAGAAGCACCCTGAAGCCAGTGTGAACTTCTCTGAATTCTCCAAGAAGTGTTCAGAGCGATGGAAGACAATGTCTGCCAAAGAGAAGGGCAAGTTTGAGGATATGGCCAAGCAAGATAAGGTTCGCTATGAGAGGGAAATGAAGAACTACATCCCACCAAAGGGTGAGAAGAAGAAGAGGTTTAAGGATCCCAACGCACCCAAGAGACCACCgTCAGCGTTCTTCATTTTCTGTGGTGATTACCGCCCTAAGATAAAGGGTGAAAACCCTGGTCTGTCCATCGGCGACATTGCCAAAAAGCTTGGAGAAATGTGGAACAGCTCATCAGCTGAAGTGAAGCAGCCCTATGAAAAGAAAGCCGCAAAGCTCAAGGAGAAGTACGACAAGGTAAAGCAGCCTTTTCCTACATTTACTTGCTAGCTTGTAGATGCACTTGCCTCATTTGTTAATGCTTTTATCTTCTGTAGGATATTGCCCTGTACCGCACAAAGGGAATTGCAGGCTTTTCAAAGAAAGAAGGTGGGGAGGATGATGAGGAGGATGAAGACGACGATGAGGAGGAGGACG
>TCONS_00018394
gtacattgtttctatattacataaatgtgtcTGCTACACTGGATGATGAAAAAACTGAGTTTCACCCATGTTTCTATTATGTTCacaaaaaatacttaaatcattAAAGTAGACACTTTGCTCactatgtatattatatatttttgtatatgtcACTGTTTTGAAAACTACATACACTACATAGCATTTTATAGAGCTAAAGAacctaaaatattaaattaaatttattaaattactcgaAATATTAACTAAGACACTTTACTTGCACATGACATGATGCTCATTTATCATATGTTAATATACcaattaattaaataagaaaCCGTATTATAAGTCATTATAGCATGTCACTTTCACttattttagaatattttgtTTTCCAGAGGATAAAGATGGGTAAAGATCCAAGGAAGCCCAGAGGAAAGATGTCCTCTTATGCCTACTTTGTGCAAACCTGTCGTGAGGAGCACAAAAAGAAGCACCCTGAAGCCAGTGTGAACTTCTCTGAATTCTCCAAGAAGTGTTCAGAGCGATGGAAGACAATGTCTGCCAAAGAGAAGGGCAAGTTTGAGGATATGGCCAAGCAAGATAAGGTTCGCTATGAG
>TCONS_00018395
GGTGTTATTGTACTTCAAAGCCCCATTATCTAGGCATCCACAGAAGCTGCAGATAGAGAAGAGGATAAAGATGGGTAAAGATCCAAGGAAGCCCAGAGGAAAGATGTCCTCTTATGCCTACTTTGTGCAAACCTGTCGTGAGGAGCACAAAAAGAAGCACCCTGAAGCCAGTGTGAACTTCTCTGAATTCTCCAAGAAGTGTTCAGAGCGATGGAAGGTACTGGATGAATATTATGCTGTTATAAAAATAGTACATTTGTTGATTTTTCTAAGGAatatttggggggaaaa

Function

symbol description
hmgb1b 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 several structures, including axis; digestive system; intermediate cell mass of mesoderm; nervous system; and pleuroperitoneal region. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis. Orthologous to human HMGB1 (high mobility group box 1).

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:0010469 regulation of signaling receptor activity biological_process
GO:0070374 positive regulation of ERK1 and ERK2 cascade biological_process
GO:0032732 positive regulation of interleukin-1 production biological_process
GO:0010508 positive regulation of autophagy biological_process
GO:0032755 positive regulation of interleukin-6 production biological_process
GO:0032760 positive regulation of tumor necrosis factor production biological_process
GO:0032502 developmental process biological_process
GO:0045944 positive regulation of transcription by RNA polymerase II biological_process
GO:0002218 activation of innate immune response biological_process
GO:0060326 cell chemotaxis biological_process
GO:1901224 positive regulation of NIK/NF-kappaB signaling 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-030131-8480 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 several structures, including axis; digestive system; intermediate cell mass of mesoderm; nervous system; and pleuroperitoneal region. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis. Orthologous to human HMGB1 (high mobility group box 1).

Ensembl:

ensembl_id ENSDARG00000030479

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00018391 False 1187 mRNA 0.42 5 31513065 31516583
TCONS_00018392 False 841 mRNA 0.47 5 31513403 31516558
TCONS_00018393 False 768 mRNA 0.47 4 31513545 31516564
TCONS_00018394 False 605 mRNA 0.33 2 31514062 31514818
TCONS_00018395 True 291 lncRNA 0.41 2 31514206 31516514

Neighbor

gene id symbol gene type direction distance location
XLOC_009358 si:dkey-1m11.5 coding downstream 4844 31500785 ~ 31508221 (-)
XLOC_009357 si:dkey-1m11.6 coding downstream 14942 31485877 ~ 31498123 (-)
XLOC_009356 or111-11 coding downstream 93260 31417886 ~ 31419805 (-)
XLOC_009355 or111-10 coding downstream 99067 31412595 ~ 31413998 (-)
XLOC_009354 or111-9 coding downstream 104052 31407840 ~ 31409013 (-)
XLOC_009360 AL929092.1 coding upstream 31151 31547734 ~ 31547852 (-)
XLOC_009361 hsph1 coding upstream 47554 31564137 ~ 31588162 (-)
XLOC_009362 CR388091.1 coding upstream 546709 32063292 ~ 32063409 (-)
XLOC_009363 c4 coding upstream 835303 32351886 ~ 32383529 (-)
XLOC_009364 NA coding upstream 896731 32413314 ~ 32433673 (-)
XLOC_009348 AL845428.2 non-coding downstream 150924 31361787 ~ 31362141 (-)
XLOC_009344 AL928851.1 non-coding downstream 197517 31315209 ~ 31315548 (-)
XLOC_009342 AL928851.2 non-coding downstream 213387 31299563 ~ 31299678 (-)
XLOC_009333 AL928870.1 non-coding downstream 500353 31005981 ~ 31012712 (-)
XLOC_009331 NA non-coding downstream 588976 30923150 ~ 30924089 (-)
XLOC_009366 CR855389.2 non-coding upstream 1116707 32633290 ~ 32635777 (-)
XLOC_009367 NA non-coding upstream 1297153 32813736 ~ 32817995 (-)

Expression


Co-expression Network