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Orthologous genes in OrthoFinder**

Species Gene Description
 ath-u.5   PHYB   phytochrome B 
 ath-r.7   PHYB   phytochrome B 
 ath-m.9   PHYB   phytochrome B 
 ath-e.2   PHYB   phytochrome B 
 ath-m.4.bio   PHYB   phytochrome B 
 ath-m.4.hor   PHYB   phytochrome B 
 ath-m.4.lig   PHYB   phytochrome B 
 ath-m.4.str   PHYB   phytochrome B 
 ath-m.4.tis   PHYB   phytochrome B 
 ath-u.5   PHYD   phytochrome D 
 ath-u.5   PHYE   phytochrome E 
 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 
 osa-u.5   4332623   phytochrome B-like 
 zma-u.5   100381811   phytochromeB2 
 zma-u.5   100383702   Phytochrome B 

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Top 50 coexpressed genes to PHYB (ath-u.5 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 PHYB (ath-u.5 coexpression data)

CoexMap"816394"


athPHYB | Entrez gene ID : 816394      
Species ath gma vvi ppo mtr sly osa zma sot hvu tae cit sbi ghi cre bna nta bdi bra
Paralog 11 3 2 2 1 3 1 2 0 0 0 0 0 0 0 0 0 0 0
Show/Hide Columns:        



CoexMap
Chloroplast
Nucleus

functional annotation
KEGG ath04712 [list] [network] Circadian rhythm - plant (43 genes)
GO BP
GO:0017012 [list] [network] protein-phytochromobilin linkage  (1 genes)  IDA  
GO:0010202 [list] [network] response to low fluence red light stimulus  (2 genes)  IMP  
GO:0010617 [list] [network] circadian regulation of calcium ion oscillation  (3 genes)  IMP  
GO:0071588 [list] [network] hydrogen peroxide mediated signaling pathway  (4 genes)  IMP  
GO:0009584 [list] [network] detection of visible light  (5 genes)  IEA  
GO:0010148 [list] [network] transpiration  (6 genes)  IMP  
GO:0010244 [list] [network] response to low fluence blue light stimulus by blue low-fluence system  (9 genes)  IDA  
GO:0010161 [list] [network] red light signaling pathway  (10 genes)  IMP  
GO:0009643 [list] [network] photosynthetic acclimation  (11 genes)  IMP  
GO:0009649 [list] [network] entrainment of circadian clock  (12 genes)  IMP  
GO:0009687 [list] [network] abscisic acid metabolic process  (21 genes)  IMP  
GO:0009638 [list] [network] phototropism  (26 genes)  IMP  
GO:0010218 [list] [network] response to far red light  (57 genes)  IMP  
GO:0010374 [list] [network] stomatal complex development  (68 genes)  IMP  
GO:0009867 [list] [network] jasmonic acid mediated signaling pathway  (74 genes)  IMP  
GO:0009640 [list] [network] photomorphogenesis  (77 genes)  IMP  
GO:0009630 [list] [network] gravitropism  (101 genes)  IMP  
GO:2000028 [list] [network] regulation of photoperiodism, flowering  (101 genes)  IMP  
GO:0010029 [list] [network] regulation of seed germination  (105 genes)  IMP  
GO:0015979 [list] [network] photosynthesis  (154 genes)  IMP  
GO:0045892 [list] [network] negative regulation of DNA-templated transcription  (200 genes)  IDA  
GO:0006325 [list] [network] chromatin organization  (231 genes)  IMP  
GO:0009408 [list] [network] response to heat  (271 genes)  IMP  
GO:0031347 [list] [network] regulation of defense response  (290 genes)  IMP  
GO:0042742 [list] [network] defense response to bacterium  (363 genes)  IMP  
GO:0009409 [list] [network] response to cold  (436 genes)  IMP  
GO:0009266 [list] [network] response to temperature stimulus  (682 genes)  IMP  
GO:0009416 [list] [network] response to light stimulus  (776 genes)  IMP  
GO CC
GO:0016604 [list] [network] nuclear body  (91 genes)  IDA  
GO:0005829 [list] [network] cytosol  (2593 genes)  IDA  
GO:0005886 [list] [network] plasma membrane  (2598 genes)  ISM  
GO:0005634 [list] [network] nucleus  (10367 genes)  IDA  
GO MF
GO:0031517 [list] [network] red light photoreceptor activity  (1 genes)  IDA  
GO:0031516 [list] [network] far-red light photoreceptor activity  (2 genes)  IDA  
GO:0009883 [list] [network] red or far-red light photoreceptor activity  (3 genes)  IMP  
GO:0000155 [list] [network] phosphorelay sensor kinase activity  (9 genes)  IEA  
GO:1990841 [list] [network] promoter-specific chromatin binding  (15 genes)  IDA  
GO:0004673 [list] [network] protein histidine kinase activity  (17 genes)  ISS  
GO:0042803 [list] [network] protein homodimerization activity  (237 genes)  IDA  
GO:0042802 [list] [network] identical protein binding  (414 genes)  IPI  
GO:0043565 [list] [network] sequence-specific DNA binding  (875 genes)  IDA  
GO:0005515 [list] [network] protein binding  (5363 genes)  IPI  
Protein NP_001325249.1 [sequence] [blastp]
NP_179469.1 [sequence] [blastp]
Subcellular
localization
wolf
nucl 3,  plas 2,  vacu 1,  cysk_plas 1,  E.R._plas 1,  cyto_plas 1  (predict for NP_001325249.1)
nucl 5,  plas 2,  chlo 1,  cyto_plas 1  (predict for NP_179469.1)
Subcellular
localization
TargetP
chlo 6,  other 6  (predict for NP_001325249.1)
chlo 6,  other 6  (predict for NP_179469.1)
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-u.5
for
PHYB

.
ath-r.7
for
PHYB

.
ath-m.9
for
PHYB

.
ath-e.2
for
PHYB

.
ath-m.4.bio
for
PHYB

.
ath-m.4.hor
for
PHYB

.
ath-m.4.lig
for
PHYB

.
ath-m.4.str
for
PHYB

.
ath-m.4.tis
for
PHYB

.
ath-u.5
for
PHYD

.
ath-u.5
for
PHYE

.
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

.
osa-u.5
for
4332623

.
zma-u.5
for
100381811

.
zma-u.5
for
100383702

.


Ortholog ID: 3650
Species ath ath gma gma sly sly osa zma zma bra vvi vvi ppo ppo mtr tae tae hvu ghi ghi bna bna sbi sot sot cit cit bdi nta nta
Symbol PHYB PHYE PHYE1 PHYE2 PHYE PHYB2 LOC4332623 LOC100381811 LOC100383702 LOC103869720 PHYE LOC100261882 LOC7485825 LOC7485902 LOC11420025 LOC100137004 LOC123097663 LOC123448812 LOC107896595 LOC121202968 LOC106400775 LOC106360866 LOC8081072 LOC102577925 LOC102580316 LOC102618185 LOC102608760 LOC100829838 LOC107782401 LOC107767359
Function* phytochrome B phytochrome E phytochrome E-like phytochrome E-like phytochrome E phytochrome B2 phytochrome B-like phytochromeB2 Phytochrome B phytochrome B phytochrome E phytochrome B phytochrome B phytochrome B phytochrome B-2 phytochrome B phytochrome B phytochrome B phytochrome B phytochrome E phytochrome B-like phytochrome E phytochrome B phytochrome B phytochrome B-like phytochrome B phytochrome E 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)
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)
sly03040 Spliceosome 3
sly00906 Carotenoid biosynthesis 2
sly03013 Nucleocytoplasmic transport 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)
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)
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)
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)
ppo04712 Circadian rhythm - plant 2
ppo03015 mRNA surveillance pathway 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)
mtr03040 Spliceosome 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)
tae04136 Autophagy - other 3
tae04712 Circadian rhythm - plant 3
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)
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)
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)
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)
cit03040 Spliceosome 3
cit00500 Starch and sucrose metabolism 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
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)
nta04712 Circadian rhythm - plant 5
nta04517 IgSF CAM signaling 2
nta04518 Integrin signaling 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
Entrez Gene ID* 816394 827538 100808192 100800339 101253446 101264523 4332623 100381811 100383702 103869720 100264019 100261882 7485825 7485902 11420025 100137004 123097663 123448812 107896595 121202968 106400775 106360866 8081072 102577925 102580316 102618185 102608760 100829838 107782401 107767359
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