ATTED-II : GeneCoexpression result

Species	Gene	Description
vvi-u.5	PHYA	phytochrome A
vvi-r.5	PHYA	phytochrome A
vvi-u.5	100258014	phytochrome C
ath-u.5	PHYC	phytochrome C
ath-u.5	PHYA	phytochrome A
gma-u.5	E4	phytochrome A
gma-u.5	PHYA	phytochrome A
gma-u.5	PHYA3	phytochrome A-2-like
ppo-u.5	7482219	phytochrome A
mtr-u.5	11405950	phytochrome A
sly-u.5	PHYF	phytochrome F
sly-u.5	phyA	Phytochrome A
osa-u.5	4334135	phytochrome C-like
osa-u.5	4333930	phytochrome A-like
zma-u.5	103643916	phytochrome A-like
zma-u.5	115101004	uncharacterized LOC115101004
zma-u.5	103644014	phytochrome C

functional annotation

KEGG

vvi04712 [list] [network] Circadian rhythm - plant (44 genes)

GO BP

GO:0009584 [list] [network] detection of visible light	(4 genes)	IEA
GO:0009585 [list] [network] red, far-red light phototransduction	(4 genes)	IEA
GO:0017006 [list] [network] protein-tetrapyrrole linkage	(6 genes)	IEA
GO:0006355 [list] [network] regulation of DNA-templated transcription	(1359 genes)	IEA

GO CC

GO:0005634 [list] [network] nucleus

(2597 genes)

IEA

GO MF

GO:0009881 [list] [network] photoreceptor activity	(6 genes)	IEA
GO:0042803 [list] [network] protein homodimerization activity	(9 genes)	IEA
GO:0000155 [list] [network] phosphorelay sensor kinase activity	(14 genes)	IEA

Protein

XP_002278610.1 [sequence] [blastp]
XP_010659783.1 [sequence] [blastp]

Subcellular
localization
wolf

nucl 4, chlo 3, mito 3, chlo_mito 3	(predict for XP_002278610.1)
nucl 4, chlo 3, mito 3, chlo_mito 3	(predict for XP_010659783.1)

Subcellular
localization
TargetP

mito 6, chlo 4	(predict for XP_002278610.1)
mito 6, chlo 4	(predict for XP_010659783.1)

Gene expression

All samples

[Expression pattern]

Tissue specificity^*

	Gene	Function	KEGG					Entrez Gene ID	Other ID	Link	Target		Reference
	Gene	Function	KEGG					Entrez Gene ID	Other ID	Link	vvi-u.5 for PHYA	vvi-r.5 for PHYA	vvi-u.5 for 100258014	ath-u.5 for PHYC	ath-u.5 for PHYA	gma-u.5 for E4	gma-u.5 for PHYA	gma-u.5 for PHYA3	ppo-u.5 for 7482219	mtr-u.5 for 11405950	sly-u.5 for PHYF	sly-u.5 for phyA	osa-u.5 for 4334135	osa-u.5 for 4333930	zma-u.5 for 103643916	zma-u.5 for 115101004	zma-u.5 for 103644014

Ortholog ID: 3383

Species

vvi

ath

gma

bra

ppo

mtr

ghi

bna

cit

sly

sot

nta

osa

zma

tae

hvu

sbi

bdi

Symbol

PHYA

LOC100258014

PHYC

PHYA

PHYA3

PHYA

PHYF

phyA

C-PHYA

Function^*

phytochrome A

phytochrome C

phytochrome A

phytochrome A-2-like

phytochrome A

phytochrome C

phytochrome A

phytochrome C-like

phytochrome C

phytochrome A

phytochrome C

phytochrome A-2

phytochrome F

Phytochrome A

type A phytochrome

phytochrome C

phytochrome A1-like

phytochrome C-like

phytochrome A-like

uncharacterized LOC115101004

phytochrome C

phytochrome A type 3

phytochrome a

phytochrome C

phytochrome A type 3

Coexmap

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Coexpression

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KEGG Info

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
vvi04120	Ubiquitin mediated proteolysis	3

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
gma03082	ATP-dependent chromatin remodeling	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
gma04712	Circadian rhythm - plant	4

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
bra04712	Circadian rhythm - plant	2
bra02010	ABC transporters	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
bra00500	Starch and sucrose metabolism	7

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
mtr04712	Circadian rhythm - plant	5

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
ghi04075	Plant hormone signal transduction	6

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
ghi04075	Plant hormone signal transduction	6

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)
bna04712	Circadian rhythm - plant	4

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
cit04120	Ubiquitin mediated proteolysis	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
cit03040	Spliceosome	4

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
sly04120	Ubiquitin mediated proteolysis	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
sot03040	Spliceosome	3
sot04712	Circadian rhythm - plant	2
sot04146	Peroxisome	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
sot04120	Ubiquitin mediated proteolysis	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
nta04712	Circadian rhythm - plant	4

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
nta00520	Amino sugar and nucleotide sugar metabolism	2
nta04148	Efferocytosis	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
osa03040	Spliceosome	3
osa03082	ATP-dependent chromatin remodeling	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
osa04075	Plant hormone signal transduction	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
zma04712	Circadian rhythm - plant	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
zma04712	Circadian rhythm - plant	2
zma04146	Peroxisome	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
tae00040	Pentose and glucuronate interconversions	3
tae00310	Lysine degradation	3

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
tae00040	Pentose and glucuronate interconversions	2

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
hvu00052	Galactose metabolism	3

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
sbi00460	Cyanoamino acid metabolism	4
sbi00500	Starch and sucrose metabolism	4
sbi00999	Biosynthesis of various plant secondary metabolites	4

KEGG^* ID	Title	#genes	Link to the KEGG^* map (Multiple genes)
bdi04120	Ubiquitin mediated proteolysis	2
bdi00020	Citrate cycle (TCA cycle)	2
bdi00785	Lipoic acid metabolism	2
bdi01200	Carbon metabolism	2
bdi01210	2-Oxocarboxylic acid metabolism	2

Expression

Expression pattern

Entrez Gene ID^*

100240824

100258014

833570

837483

100791098

547810

103843346

103868296

7482219

11405950

107923974

107912456

106346267

106417700

102618478

102616503

101259349

544176

102577627

102595581

107773723

107827766

4334135

4333930

103643916

115101004

123105051

123113346

123452263

123447547

8059991

8086232

100834357

100836209

Select Species^**

Orthologous genes in OrthoFinder^**

Top 50 coexpressed genes to PHYA (vvi-u.5 coexpression data)

Top 50 enrichment test to PHYA (vvi-u.5 coexpression data)


Species	vvi	ath	gma	ppo	mtr	sly	osa	zma	bdi	hvu	bra	cit	bna	sbi	ghi	sot	nta	cre	tae
Paralog	3	2	3	1	1	2	2	3	0	0	0	0	0	0	0	0	0	0	0

Select Species**

Orthologous genes in OrthoFinder**

Top 50 coexpressed genes to PHYA (vvi-u.5 coexpression data)

Top 50 enrichment test to PHYA (vvi-u.5 coexpression data)

Select Species^**

Orthologous genes in OrthoFinder^**