XLOC_011851 (gdf3)


Basic Information

Item Value
gene id XLOC_011851
gene name gdf3
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007128.7
NCBI id CM002901.2
chromosome length 53461100
location 4239437 ~ 4252248 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00023429
TGTTTTTATAATCTAATAATGTTCTTGGTCCTCCTCAGAGCCTGTCTTCTGACCCTCAGTCTCTGTTCTCCTGCAGAAGATGATGGTCTTGTGCAAGAAAAGCTGTTTTTGAGCTCTATGGGACTCTGGAGTCGACCCAAACCATCGCATCATGCCGCAGTGCCATCACAGATGTGGAAAATCTTTAAACAGGCCAGCAAACAGACCGTTAATGACCCATGTGTGGTGTCTGAATATGGGGTACGAGGAAACATCGTGAGGTTTATGCAGGATCAAGGTAGTCTGATATCAGCGCCGGCCGTCCACAGCTTTAACTGTGTGCGAAAGCATCTGTTTTTCAACATGTCTGTGCTGGAGGAGGTTGAGCAACTCTCGTTGGCGCAGCTGGAAATGAAGTTCAAACAGGATCTGCTTCTCCTGGGCCCGCATGTGTTCAGCGTCGACCTGTACAGAGTGTTAAAAACCACACTGAAGGGAGTAACGCATGAATCCAGCCGAAAACTCCTCCAATCTCAAACGCTCAGTCCTGGAGCTCACGCTTCAGTGCTGGTCAACCTGACCAATCTGGCCCAATcctggaggaaaccggagaaaaaCTTTGGCATGCAGTTAGAATTGCAGGTCATGCATTTAAACAACATGCTTCATGATCACGCGTATGTTCAAATCCCAGATATACATGCCACTCTAGTAGTAGTTTCATTAAACCCACTTCAGTGCAGGTCCAGAAGGAAGAGAAGTGCTTCATATTACCTCCCCGTTACTCCCAGTAACGTCTGCAAACCCAGAAGGCTCTATATTGATTTCAAAGATGTAGGCTGGCAGGATTGGATCATTGCACCTCAGGGATATTTAGCTAATTATTGTCATGGAGAGTGTCCTTTTCCTCTGAGCGAGAGTTTGAATGGGACTAACCATGCTATCCTGCAGACGCTGGTCCATTCGTTTGATCCTAAAGGAACACCTCAGCCCTGTTGCGTTCCCATCAAACTGTCCCCCATCTCCATGCTCTACTATGACAATAATGATAATGTGGTGCTCAGACATTATGAAGACATGGTGGTGGATGAGTGTGGATGCAGATGAACATGACttaatttttaaatgcacaatttgtttattacaatttttctttttttaggtgtGGATTAATGCAAAATTAGGCTTCTTTTTAGATGCAGAGAATGTGCATGTAGATGCTGTTAAAGTAACTTTTTATAATtcattgtaatgtaataataaaaacttttactAT
>TCONS_00023430
tcttattattcttatttatccatttatttattgattcatttatttattttatttattcgttcattcattcatttatttatttatttaatgattcatttgtttgCCCCACtcgttttattcattaaaatcaGTAGAGATAAAAAAATCATCTTGCAATAAATCAGATCAGTGTGTTTTCTTGTCAATTTGATGCCTTTATAAACAGAAATCAGTAAAACTGAGACTTGCAGTGTTTTGTCTGTAGCggtatataaatattttgtcataattaaataaaaaaaaaaaacagatcaccctcataaaataaaataaaaaagcaaataaaaaagtcatttttagcaTTTTCCCCtactcattttaattattaaatcattGCAGATCCCAAAATCTTCATGCAATAAATCAGAGCTGTGTCTGCCAGGCAACCTGATGCCTATAAACATCAAAGAGCTGATTTGCATGTGAATGACACCACCCCCTGCTGCTGATCAATCAACTCCTttatctccaccaatcagcttgcAGATGTGGATTTCTGGCCATGTGAAGCTGATCAGCTGGCATTTATAAGCCTAAGATGATGGTCTTGTGCAAGAAAAGCTGTTTTTGAGCTCTATGGGACTCTGGAGTCGACCCAAACCATCGCATCATGCCGCAGTGCCATCACAGATGTGGAAAATCTTTAAACAGGCCAGCAAACAGACCGTTAATGACCCATGTGTGGTGTCTGAATATGGGGTACGAGGAAACATCGTGAGGTTTATGCAGGATCAAGGTAGTCTGATATCAGCGCCGGCCGTCCACAGCTTTAACTGTGTGCGAAAGCATCTGTTTTTCAACATGTCTGTGCTGGAGGAGGTTGAGCAACTCTCGTTGGCGCAGCTGGAAATGAAGTTCAAACAGGATCTGCTTCTCCTGGGCCCGCATGTGTTCAGCGTCGACCTGTACAGAGTGTTAAAAACCACACTGAAGGGAGTAACGCATGAATCCAGCCGAAAACTCCTCCAATCTCAAACGCTCAGTCCTGGAGCTCACGCTTCAGTGCTGGTCAACCTGACCAATCTGGCCCAATcctggaggaaaccggagaaaaaCTTTGGCATGCAGTTAGAATTGCAGGTCATGCATTTAAACAACATGCTTCATGATCACGCGTATGTTCAAATCCCAGATATACATGCCACTCTAGTAGTAGTTTCATTAAACCCACTTCAGTGCAGGTCCAGAAGGAAGAGAAGTGCTTCATATTACCTCCCCGTTACTCCCAGTAACGTCTGCAAACCCAGAAGGCTCTATATTGATTTCAAAGATGTAGGCTGGCAGGATTGGATCATTGCACCTCAGGGATATTTAGCTAATTATTGTCATGGAGAGTGTCCTTTTCCTCTGAGCGAGAGTTTGAATGGGACTAACCATGCTATCCTGCAGACGCTGGTCCATTCGTTTGATCCTAAAGGAACACCTCAGCCCTGTTGCGTTCCCATCAAACTGTCCCCCATCTCCATGCTCTACTATGACA
>TCONS_00023431
ATCCGAAGGGGAAGGTAAACACTGAAAGCCGATCCTTTCGCGGTTTAATTGTGTCAAAATCCCCGTCACGCTGCATATATTTTCATCTCAAGTGAAAGACGAGGTTGTGAAGAACTGAAACCCGTGAAACTGAAGAGCCAGGAGGGAAAACCTCAGAGCACAACGTGTGTTTGTGATGAATGAAGACGAACACAATGTCATGTTATTCAGACGGCCATATTTCATCTCCTGACTAGACCACACACTGGATTGGGTTTCATTCACAATGCAGACACTGTGCGGAGGTAAATGAGGTATTCTTACGCCATAGACATGCAGAGACTAGAAAGATGATGGTCTTGTGCAAGAAAAGCTGTTTTTGAGCTCTATGGGACTCTGGAGTCGACCCAAACCATCGCATCATGCCGCAGTGCCATCACAGATGTGGAAAATCTTTAAACAGGCCAGCAAACAGACCGTTAATGACCCATGTGTGGTGTCTGAATATGGGGTACGAGGAAACATCGTGAGGTTTATGCAGGATCAAGGTAGTCTGATATCAGCGCCGGCCGTCCACAGCTTTAACTGTGTGCGAAAGCATCTGTTTTTCAACATGTCTGTGCTGGAGGAGGTTGAGCAACTCTCGTTGGCGCAGCTGGAAATGAAGTTCAAACAGGATCTGCTTCTCCTGGGCCCGCATGTGTTCAGCGTCGACCTGTACAGAGTGTTAAAAACCACACTGAAGGGAGTAACGCATGAATCCAGCCGAAAACTCCTCCAATCTCAAACGCTCAGTCCTGGAGCTCACGCTTCAGTGCTGGTCA
>TCONS_00024522
GTTCAGGGGCGGATGATGACAGTCGTAATCCGAAGGGGAAGGTAAACACTGAAAGCCGATCCTTTCGCGGTTTAATTGTGTCAAAATCCCCGTCACGCTGCATATATTTTCATCTCAAGTGAAAGACGAGGTTGTGAAGAACTGAAACCCGTGAAACTGAAGAGCCAGGAGGGAAAACCTCAGAGCACAACGTGTGTTTGTGATGAATGAAGACGAACACAATGTCATGTTATTCAGACGGCCATATTTCATCTCCTGACTAGACCACACACTGGATTGGGTTTCATTCACAATGCAGACACTGTGCGGAGGTAAATGAGGTATTCTTACGCCATAGACATGCAGAGACTAGAGAATGCAGCAGGATGCAGTTATCAGTGAAGGCCTGATGGATTAGCTCAGAGTCTTGAAGATTGTGTCTGATGAAGAACAGGAGCAGAAGAAGCTCTTTAGTCTGAGCAGTGTGAAC
>TCONS_00024810
TGACAGTCGTAATCCGAAGGGGAAGGTAAACACTGAAAGCCGATCCTTTCGCGGTTTAATTGTGTCAAAATCCCCGTCACGCTGCATATATTTTCATCTCAAGTGAAAGACGAGGTTGTGAAGAACTGAAACCCGTGAAACTGAAGAGCCAGGAGGGAAAACCTCAGAGCACAACGTGTGTTTGTGATGAATGAAGACGAACACAATGTCATGTTATTCAGACGGCCATATTTCATCTCCTGACTAGACCACACACTGGATTGGGTTTCATTCACAATGCAGACACTGTGCGGAGGTAAATGAGGTATTCTTACGCCATAGACATGCAGAGACTAGAatgcccttttatccgcaacccagtactgggaaacccagaagcactcaaaggaaacccatgccaatagggg
>TCONS_00024811
TGACAGTCGTAATCCGAAGGGGAAGGTAAACACTGAAAGCCGATCCTTTCGCGGTTTAATTGTGTCAAAATCCCCGTCACGCTGCATATATTTTCATCTCAAGTGAAAGACGAGGTTGTGAAGAACTGAAACCCGTGAAACTGAAGAGCCAGGAGGGAAAACCTCAGAGCACAACGTGTGTTTGTGATGAATGAAGACGAACACAATGTCATGTTATTCAGACGGCCATATTTCATCTCCTGACTAGACCACACACTGGATTGGGTTTCATTCACAATGCAGACACTGTGCGGAGGTAAATGAGGTATTCTTACGCCATAGACATGCAGAGACTAGAGTAAGCCGCATCCTTATATAGGTCTATATAGTGTGTTATTGATTGCATTGAAGACTCGAATATTTAATGGTTTTGGGATAACTTTTGATGAAtgattttgatccactttaaatgttatgtgtgtaatatttttactactgtaaataaataattactgtgtgtgtatgtatataattttGTGAACATTTCCATAACTAAAGTTGTATTTAAC

Function

symbol description
gdf3 Predicted to enable cytokine activity. Involved in regulation of epiboly involved in gastrulation with mouth forming second. Acts upstream of or within with a positive effect on nodal signaling pathway. Acts upstream of or within with a negative effect on BMP signaling pathway. Acts upstream of or within several processes, including embryonic morphogenesis; left/right pattern formation; and regulation of nodal signaling pathway involved in determination of left/right asymmetry. Part of protein-containing complex. Is expressed in several structures, including heart primordium; mesoderm; oocyte; somite; and tail bud. Human ortholog(s) of this gene implicated in Klippel-Feil syndrome 3; dextro-looped transposition of the great arteries 3; isolated microphthalmia 7; and visceral heterotaxy. Orthologous to several human genes including GDF3 (growth differentiation factor 3).

GO:

id name namespace
GO:0060395 SMAD protein signal transduction biological_process
GO:0051781 positive regulation of cell division biological_process
GO:0030509 BMP signaling pathway biological_process
GO:1904086 regulation of epiboly involved in gastrulation with mouth forming second biological_process
GO:0048666 neuron development biological_process
GO:0060027 convergent extension involved in gastrulation biological_process
GO:1900145 regulation of nodal signaling pathway involved in determination of left/right asymmetry biological_process
GO:0001947 heart looping biological_process
GO:0010862 positive regulation of pathway-restricted SMAD protein phosphorylation biological_process
GO:0005576 extracellular region cellular_component
GO:0005615 extracellular space cellular_component
GO:0005125 cytokine activity molecular_function
GO:0008083 growth factor activity molecular_function

KEGG:

id description
ko04060 Cytokine-cytokine receptor interaction
ko04052 Cytokines and growth factors

ZFIN:

id description
ZDB-GENE-980526-389 Predicted to enable cytokine activity. Involved in regulation of epiboly involved in gastrulation with mouth forming second. Acts upstream of or within with a positive effect on nodal signaling pathway. Acts upstream of or within with a negative effect on BMP signaling pathway. Acts upstream of or within several processes, including embryonic morphogenesis; left/right pattern formation; and regulation of nodal signaling pathway involved in determination of left/right asymmetry. Part of protein-containing complex. Is expressed in several structures, including heart primordium; mesoderm; oocyte; somite; and tail bud. Human ortholog(s) of this gene implicated in Klippel-Feil syndrome 3; dextro-looped transposition of the great arteries 3; isolated microphthalmia 7; and visceral heterotaxy. Orthologous to several human genes including GDF3 (growth differentiation factor 3).

Ensembl:

ensembl_id ENSDARG00000037995

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00023429 False 1255 mRNA 0.44 2 4239437 4245311
TCONS_00023430 False 1519 mRNA 0.41 3 4239671 4245902
TCONS_00023431 False 803 mRNA 0.48 4 4240139 4252221
TCONS_00024522 False 469 lncRNA 0.46 3 4247891 4252248
TCONS_00024810 False 407 lncRNA 0.46 3 4250902 4252232
TCONS_00024811 True 548 lncRNA 0.38 2 4251579 4252232
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Neighbor

gene id symbol gene type direction distance location
XLOC_011850 bmp2a coding downstream 7905 4227254 ~ 4231532 (-)
XLOC_011849 PLCB1 coding downstream 253201 3841012 ~ 3986236 (-)
XLOC_011848 NA coding downstream 409611 3823109 ~ 3829826 (-)
XLOC_011847 PLCB4 coding downstream 423744 3717384 ~ 3815693 (-)
XLOC_011846 WSCD1 coding downstream 935632 3281440 ~ 3303805 (-)
XLOC_011852 napba coding upstream 44828 4297076 ~ 4318428 (-)
XLOC_011853 klhl10a coding upstream 134401 4386649 ~ 4396692 (-)
XLOC_011854 NA coding upstream 890137 5142385 ~ 5143041 (-)
XLOC_011855 NA coding upstream 905123 5157371 ~ 5426458 (-)
XLOC_011856 NA coding upstream 1200065 5452313 ~ 5564131 (-)
XLOC_011844 NA non-coding downstream 1188341 3020946 ~ 3051096 (-)
XLOC_011835 NA non-coding downstream 1803159 2430899 ~ 2436278 (-)
XLOC_011834 CABZ01058452.1 non-coding downstream 1817408 2401258 ~ 2422029 (-)
XLOC_011832 CABZ01052589.1 non-coding downstream 2073667 2165656 ~ 2165770 (-)
XLOC_011859 NA non-coding upstream 1398863 5651111 ~ 5654012 (-)
XLOC_011864 NA non-coding upstream 1628829 5881077 ~ 5884928 (-)

Expression

Expression of XLOC_011851(gdf3) in the Zebrafish Sample from each Developmental Stage of PRJEB12982

Boxplot with 18 boxes. Box plot charts are typically used to display groups of statistical data. Each data point in the chart can have up to 5 values: minimum, lower quartile, median, upper quartile, and maximum.
The chart has 1 X axis displaying categories.
The chart has 1 Y axis displaying Expression. Range: 0 to 1000.
End of interactive chart.

Expression of XLOC_011851(gdf3) in the Zebrafish Sample of PRJEB12982

Bar chart with 360 bars.
The chart has 1 X axis displaying categories.
The chart has 1 Y axis displaying Expression. Range: 0 to 1000.
End of interactive chart.

Co-expression Network