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Orthologous genes in OrthoFinder**

Species Gene Description
 ath-m.4.lig   PHYD   phytochrome D 
 ath-u.5   PHYD   phytochrome D 
 ath-r.7   PHYD   phytochrome D 
 ath-m.9   PHYD   phytochrome D 
 ath-e.2   PHYD   phytochrome D 
 ath-m.4.bio   PHYD   phytochrome D 
 ath-m.4.hor   PHYD   phytochrome D 
 ath-m.4.str   PHYD   phytochrome D 
 ath-m.4.tis   PHYD   phytochrome D 
 ath-u.5   PHYB   phytochrome B 
 ath-u.5   PHYE   phytochrome E 
 bra-r.6   103869720   phytochrome B 
 bna-r.1   125606336   phytochrome B 
 bna-r.1   106400775   phytochrome B-like 
 bna-r.1   106391876   phytochrome E 
 ghi-r.1   107935905   phytochrome E 
 ghi-r.1   107896595   phytochrome B 
 ghi-r.1   107916208   phytochrome B 
 cit-r.1   102608760   phytochrome E 
 cit-r.1   102618185   phytochrome B 
 gma-u.5   PHYE1   phytochrome E-like 
 gma-u.5   PHYE2   phytochrome E-like 
 gma-u.5   PHYB   phytochrome B-like 
 vvi-u.5   100261882   phytochrome B 
 vvi-u.5   PHYE   phytochrome E 
 ppo-u.5   7485902   phytochrome B 
 ppo-u.5   7485825   phytochrome B 
 mtr-u.5   11420025   phytochrome B-2 
 sly-u.5   PHYE   phytochrome E 
 sly-u.5   PHYB1   phytochrome B1 
 sly-u.5   PHYB2   phytochrome B2 
 sot-r.1   102577925   phytochrome B 
 sot-r.1   102580316   phytochrome B-like 
 sot-r.1   102588382   phytochrome E 
 nta-r.1   107825586   phytochrome E-like 
 nta-r.1   107809873   phytochrome E-like 
 nta-r.1   107780828   phytochrome B 
 osa-u.5   4332623   phytochrome B-like 
 zma-u.5   100381811   phytochromeB2 
 zma-u.5   100383702   Phytochrome B 
 tae-r.2   123097663   phytochrome B 
 tae-r.2   123092340   phytochrome B 
 tae-r.2   100137004   phytochrome B 
 hvu-r.1   123448812   phytochrome B 
 sbi-r.1   8081072   phytochrome B 
 bdi-r.1   100829838   phytochrome B 

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Top 50 coexpressed genes to PHYD (ath-m.4.lig coexpression data)

 KEGG ID   Pathway name   #genes in coex list   #genes in genome   -log10(p)   Link to the KEGG* map 
(Multiple genes)

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Top 50 enrichment test to PHYD (ath-m.4.lig coexpression data)

CoexMap"827319"


athPHYD | Entrez gene ID : 827319      
Species ath bra bna ghi cit gma vvi ppo mtr sly sot nta osa zma tae hvu sbi bdi cre
Paralog 11 1 3 3 2 3 2 2 1 3 3 3 1 2 3 1 1 1 0
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CoexMap
Chloroplast
Nucleus

functional annotation
KEGG
GO BP
GO:0009584 [list] [network] detection of visible light  (5 genes)  IEA  
GO:0009585 [list] [network] red, far-red light phototransduction  (20 genes)  IEA  
GO:0010017 [list] [network] red or far-red light signaling pathway  (53 genes)  IGI  
GO:0006355 [list] [network] regulation of DNA-templated transcription  (1618 genes)  IEA  
GO CC
GO:0005886 [list] [network] plasma membrane  (2598 genes)  ISM  
GO:0005634 [list] [network] nucleus  (10367 genes)  IDA  
GO MF
GO:0009883 [list] [network] red or far-red light photoreceptor activity  (3 genes)  IGI  
GO:0000155 [list] [network] phosphorelay sensor kinase activity  (9 genes)  IEA  
GO:0042803 [list] [network] protein homodimerization activity  (237 genes)  IEA  
GO:0042802 [list] [network] identical protein binding  (414 genes)  IPI  
GO:0005515 [list] [network] protein binding  (5363 genes)  IPI  
Protein NP_193360.1 [sequence] [blastp]
Subcellular
localization
wolf
chlo 6,  nucl 1,  cyto 1,  mito 1,  cysk 1,  nucl_plas 1  (predict for NP_193360.1)
Subcellular
localization
TargetP
chlo 7,  mito 3  (predict for NP_193360.1)
Gene expression
All samples [Expression pattern]
Tissue specificity*
Show Coexpressed Genes
Gene Function KEGG Entrez
Gene
ID		 Other ID Link Target Condition-specific* Reference

ath-m.4.lig
for
PHYD
ath-u.5
for
PHYD
ath-r.7
for
PHYD
ath-m.9
for
PHYD
ath-e.2
for
PHYD
ath-m.4.bio
for
PHYD
ath-m.4.hor
for
PHYD
ath-m.4.str
for
PHYD
ath-m.4.tis
for
PHYD
ath-u.5
for
PHYB
ath-u.5
for
PHYE
bra-r.6
for
103869720
bna-r.1
for
125606336
bna-r.1
for
106400775
bna-r.1
for
106391876
ghi-r.1
for
107935905
ghi-r.1
for
107896595
ghi-r.1
for
107916208
cit-r.1
for
102608760
cit-r.1
for
102618185
gma-u.5
for
PHYE1
gma-u.5
for
PHYE2
gma-u.5
for
PHYB
vvi-u.5
for
100261882
vvi-u.5
for
PHYE
ppo-u.5
for
7485902
ppo-u.5
for
7485825
mtr-u.5
for
11420025
sly-u.5
for
PHYE
sly-u.5
for
PHYB1
sly-u.5
for
PHYB2
sot-r.1
for
102577925
sot-r.1
for
102580316
sot-r.1
for
102588382
nta-r.1
for
107825586
nta-r.1
for
107809873
nta-r.1
for
107780828
osa-u.5
for
4332623
zma-u.5
for
100381811
zma-u.5
for
100383702
tae-r.2
for
123097663
tae-r.2
for
123092340
tae-r.2
for
100137004
hvu-r.1
for
123448812
sbi-r.1
for
8081072
bdi-r.1
for
100829838


Ortholog ID: 3650
Species ath ath ath bra bna bna bna ghi ghi ghi cit cit gma gma gma vvi vvi ppo ppo mtr sly sly sly sot sot sot nta nta nta osa zma zma tae tae tae hvu sbi bdi
Symbol PHYD PHYB PHYE LOC103869720 LOC106400775 LOC106391876 LOC106360866 LOC107935905 LOC107896595 LOC121202968 LOC102608760 LOC102618185 PHYE1 PHYE2 PHYB LOC100261882 PHYE LOC7485902 LOC7485825 LOC11420025 PHYE PHYB1 PHYB2 LOC102577925 LOC102580316 LOC102588382 LOC107809873 LOC107767359 LOC107782401 LOC4332623 LOC100381811 LOC100383702 LOC123097663 LOC123092340 LOC100137004 LOC123448812 LOC8081072 LOC100829838
Function* phytochrome D phytochrome B phytochrome E phytochrome B phytochrome B-like phytochrome E phytochrome E phytochrome E phytochrome B phytochrome E phytochrome E phytochrome B phytochrome E-like phytochrome E-like phytochrome B-like phytochrome B phytochrome E phytochrome B phytochrome B phytochrome B-2 phytochrome E phytochrome B1 phytochrome B2 phytochrome B phytochrome B-like phytochrome E phytochrome E-like phytochrome B phytochrome B phytochrome B-like phytochromeB2 Phytochrome B phytochrome B phytochrome B phytochrome B phytochrome B phytochrome B phytochrome B
Coexmap

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Coexpression

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KEGG Info
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
ath03040 Spliceosome 3
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
ath00020 Citrate cycle (TCA cycle) 2
ath04144 Endocytosis 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
ath04120 Ubiquitin mediated proteolysis 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
bna04712 Circadian rhythm - plant 4
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
bna00906 Carotenoid biosynthesis 2
bna00562 Inositol phosphate metabolism 2
bna04070 Phosphatidylinositol signaling system 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
bna00906 Carotenoid biosynthesis 2
bna00562 Inositol phosphate metabolism 2
bna04070 Phosphatidylinositol signaling system 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
ghi03060 Protein export 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
ghi04712 Circadian rhythm - plant 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
ghi03060 Protein export 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
cit03040 Spliceosome 3
cit00500 Starch and sucrose metabolism 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
gma03040 Spliceosome 2
gma00760 Nicotinate and nicotinamide metabolism 2
gma01240 Biosynthesis of cofactors 2
gma04712 Circadian rhythm - plant 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
vvi03040 Spliceosome 2
vvi00562 Inositol phosphate metabolism 2
vvi04070 Phosphatidylinositol signaling system 2
vvi04712 Circadian rhythm - plant 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
vvi01200 Carbon metabolism 3
vvi00460 Cyanoamino acid metabolism 2
vvi00630 Glyoxylate and dicarboxylate metabolism 2
vvi00910 Nitrogen metabolism 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
ppo04712 Circadian rhythm - plant 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
ppo04712 Circadian rhythm - plant 2
ppo03015 mRNA surveillance pathway 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
mtr03040 Spliceosome 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
sly03040 Spliceosome 3
sly00906 Carotenoid biosynthesis 2
sly03013 Nucleocytoplasmic transport 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
sly00500 Starch and sucrose metabolism 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
sly00860 Porphyrin metabolism 3
sly01240 Biosynthesis of cofactors 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
sot04712 Circadian rhythm - plant 4
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
sot04712 Circadian rhythm - plant 5
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
sot03040 Spliceosome 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
nta00905 Brassinosteroid biosynthesis 2
nta04712 Circadian rhythm - plant 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
nta04712 Circadian rhythm - plant 5
nta04517 IgSF CAM signaling 2
nta04518 Integrin signaling 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
nta04712 Circadian rhythm - plant 5
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
zma04075 Plant hormone signal transduction 2
zma00010 Glycolysis / Gluconeogenesis 2
zma00030 Pentose phosphate pathway 2
zma00051 Fructose and mannose metabolism 2
zma00710 Carbon fixation by Calvin cycle 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
zma04075 Plant hormone signal transduction 2
zma04712 Circadian rhythm - plant 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
tae04136 Autophagy - other 3
tae04712 Circadian rhythm - plant 3
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
tae04136 Autophagy - other 3
tae03082 ATP-dependent chromatin remodeling 3
tae04712 Circadian rhythm - plant 3
tae04146 Peroxisome 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
tae04136 Autophagy - other 3
tae03082 ATP-dependent chromatin remodeling 3
tae04712 Circadian rhythm - plant 3
tae04146 Peroxisome 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
hvu04712 Circadian rhythm - plant 2
KEGG* ID Title #genes Link to the KEGG* map
(Multiple genes)
bdi00190 Oxidative phosphorylation 2
bdi00020 Citrate cycle (TCA cycle) 2
bdi01200 Carbon metabolism 2
bdi01210 2-Oxocarboxylic acid metabolism 2
bdi01230 Biosynthesis of amino acids 2
Expression Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern Expression pattern
Entrez Gene ID* 827319 816394 827538 103869720 106400775 106391876 106360866 107935905 107896595 121202968 102608760 102618185 100808192 100800339 100799831 100261882 100264019 7485902 7485825 11420025 101253446 101262847 101264523 102577925 102580316 102588382 107809873 107767359 107782401 4332623 100381811 100383702 123097663 123092340 100137004 123448812 8081072 100829838
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