XLOC_033119 (tardbp)


Basic Information

Item Value
gene id XLOC_033119
gene name tardbp
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007117.7
NCBI id CM002890.2
chromosome length 60270059
location 45937777 ~ 45949121 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00064366
TTCCTTCATGACTTAGGTGATGCCATCTTGATTCGAAAATAGTGTCGCATGAGTTGTGTGATACGGAGgattattgtgtttatattttatacagaGATAGCTTTTTGCGTTATTGTAATTTGAACAGAAAGGGACGCTTTTGAGGGTCGTTCTTGGTCAGAGTTTTGTTGAgtggttcattcattcacatttctTTTCTGGACGAGGAGCTGCTGGCGGTGCTAACAAAGGAATAACTGGACCCGAGCAGTTGTTTATTGCTCGACTGAGGAAAGATGGCCGAGATGTACATTCGAGTTGCGGAGGAGGAGAATGAGGAGCCGATGGAGATCCCGTCAGAGGATGATGGCACGGTTTTGCTTTCCACAGTGTCCGCTCAGTTTCCAGGGGCTTGTGGTCTGCGCTTCCGGAGCCCAGTGTCTCAGTGCATGAGGGGGGTTCGTCTGGTGGACGGCATTCTGCATGCACCTGAGAACGGCTGGGGAAACCTAGTCTATGTGGTTAATTACCCAAAAGAAACTGTTCTGCCAGATAATAAGAGGAAGATGGATGAGATCGATGCTTCATCTGCGACCAAGATCAAGAGAGGAGATCAGAAGACTTCAGATCTGATTGTGCTGGGTCTGCCATGGAAGACTTCAGAGCAAGACTTAAAAGACTACTTCGGTACATTTGGGGAAGTCATCATGGTGCAGGTCAAGCGGGATGTGAAGACAGGAAATTCAAAAGGGTTTGGCTTTGTGAGGTTTGGAGACTGGGAGACTCAGAGTAAGGTGATGACACAGCGGCACATGATTGATGGCCGGTGGTGCGACTGCAAACTGCCCAACTCAAAGcaAGGTATAGATGAACCAATGAGGAGCCGTAAAGTGTTTGTGGGCCGCTGCACAGAGGACATGACTGCCGATGAGCTCCGTCAGTTCTTCATGCAGTACGGAGAGGTCACAGACGTCTTTATTCCCAAACCGTTCAGAGCGTTTGCTTTTGTCACCTTTGCAGATGACCAGGTTGCCGCCGCTTTGTGTGGAGAAGATCTGATCATCAAGGGCGTCAGTGTGCATATCTCAAACGCTGAGCCCAAACACAATAACACTAGGCAGATGATGGAGCGGGCAGGGCGCTTTGGGAATGGGTTCGGAGGTCAGGGTTTTGCAGGCAGCCGAAGCAACatgggtggtggtggtgggggtaGCTCCAGCAGCTTGGGAAATTTTGGCAATTTCAATCTAAACCCGGCCATGATGGCTGCCGCCCAGGCTGCCTTGCAGAGTAGTTGGGGTATGATGGGAATGCTAGCTCAGCAGAATCAGTCGGGTACTTCAGGCACAAGCACAAGTGGCACCAGTTCCTCTCGAGACCAAGCCCAAACATATAGCTCGGCTAACAGCAATTACGGCAGCAGCTCAGCTGCTCTCGGCTGGGGCACCGGCTCTAACTCGGGCGCTGCCAGTGCTGGCTTTAACTCCAGTTTTGGCTCTAGTATGGAGTCCAAGTCATCGGGGTGGGGTATGTAAGTGCTTTGTGTTTGAAGTGTCGGTATTCCTAGCGTGTTTTGGTAAGTATTTTATTTCGAGAGACTTATCTCATCACGTGTGTTTGGGAGTGGGGATGGGTGAAAAGAGGGAGTCTGGGGacgaaacaaagaaaaaaagaatgttttGTACACTGAATGGGATTTGAGTTAGTGTTTGAAGTGAGATGTTAACAAGGGTGCTATGTTAATGTACcatctttgatgtttagtttttttctcccCAATGTTGTATTGTCTTGACTGATGCAAACAAAAGCATTTCAACTGGATTCTTATAATGCATGTTCAATCTGTGAAAATGCATGAGTTGCATCATTTAATAGTACAAATCAAGAAAAGAAACCTGCATTGGAAAGAATCTGGTTGAAACCTGAACATGTATATTATTGTAAGTTCAGCTTTATTTCAGTCCAGTTGTTTGGAAATCCTTTAAAACAAGCCTTCATCAACATCTCTTCTGCAGTTGACATCTGTGGGGTTTGCCTGGGAAGAGCGCCCTCTATGGCAGCACAGTGTGGCTGAGGTCATTATGTCACCTTCCTCCCCATGTCTAAATGCTCTCATCGCACGGCTCGATGACACGGTGGGTGtcttcttttttaatccactttttAAAACAAGAAGTGCGCAAGAAAgtgacctttttttaaaaaaaaacaacccttGAGTGCGATTGGTGATGGCGAAGAGTGAGAAGGCTGCGAGTGAGCGAAGAAAGTGTGGAGCGCACGAACGAAAAGACTTGCGAGTGCAATGAACGAGCCCAAATGTGACTGCAGTGGTGAGCGTGTGAATGAGAGCTGCTGATTCTTCCCAGCTTCCCCCTTAATTGAGCCCAAATTGATGGACATTTAGTTCATGTGTACTTAAAGagatatatttaatttgttttttggtCACCCTAGATCCCCATTTTGCTTTTTCTCCTTTAGTATACTGACAATGTGCTTATATAGTTAGTGGAAtgttgtgatgatgatgatgcataCTTTGTCTTGCTTCTATAATCCCATCTGAATGCTGTATGGTGTGTGTGCTTTATTTCCTTGTAACTTGACCTGTAAGTGTGAACTTTGATGTGGATGACATCTTCAGTGGACACTGAGGGGGAAAACATGAGTGATGGTGTAAGTGCGAACTGTATGTTGAGTGCTGTGGATGTCTGTGGAGTTTCCCTCTAGATTACGTCGCTCAGTGTTTTCAGAGGCATTTTATATGACTTGTCAAATGAAGGGAGTGCTTCAATAAAACTAATTTGAATAGA

Function

symbol description
tardbp Enables double-stranded DNA binding activity; identical protein binding activity; and mRNA 3'-UTR binding activity. Involved in several processes, including negative regulation by host of viral transcription; nuclear inner membrane organization; and regulation of mRNA stability. Located in nucleoplasm. Implicated in Parkinson's disease; amyotrophic lateral sclerosis; amyotrophic lateral sclerosis type 10; and motor neuron disease. Biomarker of Lewy body dementia; neurodegenerative disease (multiple); and progressive supranuclear palsy.

GO:

id name namespace
GO:0007519 skeletal muscle tissue development biological_process
GO:0007528 neuromuscular junction development biological_process
GO:0048514 blood vessel morphogenesis biological_process
GO:0007626 locomotory behavior biological_process
GO:0048675 axon extension biological_process
GO:0007409 axonogenesis biological_process
GO:0005654 nucleoplasm cellular_component
GO:0003676 nucleic acid binding molecular_function
GO:0003723 RNA binding molecular_function

KEGG:

id description
ko03015 mRNA surveillance pathway
ko05014 Amyotrophic lateral sclerosis
ko05022 Pathways of neurodegeneration - multiple diseases
ko03019 Messenger RNA biogenesis

ZFIN:

id description
ZDB-GENE-030131-3777 Predicted to enable RNA binding activity. Acts upstream of or within several processes, including axon extension; neuromuscular junction development; and skeletal muscle tissue development. Predicted to be located in nucleus. Predicted to be active in nucleoplasm. Is expressed in several structures, including brain; eye; gill; heart; and liver. Used to study amyotrophic lateral sclerosis. Human ortholog(s) of this gene implicated in Parkinson's disease; amyotrophic lateral sclerosis; amyotrophic lateral sclerosis type 10; and motor neuron disease. Orthologous to human TARDBP (TAR DNA binding protein).

Ensembl:

ensembl_id ENSDARG00000040031

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00064366 True 2798 mRNA 0.46 6 45937777 45949121

Neighbor

gene id symbol gene type direction distance location
XLOC_033118 NA coding downstream 8602 45923942 ~ 45929175 (-)
XLOC_033117 epha2a coding downstream 32031 45874595 ~ 45905746 (-)
XLOC_033116 rbm19 coding downstream 68613 45843193 ~ 45869164 (-)
XLOC_033115 cntn3b coding downstream 1225835 44584775 ~ 44711942 (-)
XLOC_033114 pdzrn3b coding downstream 1535419 44243070 ~ 44402358 (-)
XLOC_033120 ca16b coding upstream 2772 45951893 ~ 46162585 (-)
XLOC_033121 BX005101.1 coding upstream 218896 46168017 ~ 46251940 (-)
XLOC_033122 BX005101.2 coding upstream 278996 46228117 ~ 46228232 (-)
XLOC_033123 CU041346.1 coding upstream 345240 46294361 ~ 46310011 (-)
XLOC_033124 camk1a coding upstream 404789 46353910 ~ 46403475 (-)
XLOC_033111 NA non-coding downstream 1935235 43979711 ~ 44002542 (-)
XLOC_033106 BX927362.1 non-coding downstream 2588691 43346929 ~ 43349086 (-)
XLOC_033102 NA non-coding downstream 2864895 43057462 ~ 43072882 (-)
XLOC_033085 NA non-coding downstream 4484889 41451670 ~ 41452888 (-)
XLOC_033135 CABZ01055240.1 non-coding upstream 1207181 47156302 ~ 47156416 (-)
XLOC_033138 AL929512.1 non-coding upstream 1653478 47602599 ~ 47602715 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000340_12571142_12574655 TARDBPL, TARDBP coding CI01000340 null 12571021 ~ 12574678 (-)