Gene detail

CRO_T001171's detailed information

Annotation (DRYAD)

Gene ID	Functional Annotation
CRO_T001171	chlorophyll A/B binding protein

Blast top3 hits

Species	Gene ID	E-value	Annotation
Arabidopsis thaliana	AT1G29910	2.00E-135	CAB3\|chlorophyll A/B binding protein 3;LHCB1.2\|LIGHT HARVESTING CHLOROPHYLL A/B BINDING PROTEIN 1.2
Arabidopsis thaliana	AT1G19150	4.00E-27	Lhca6\|photosystem I light harvesting complex gene 6
Arabidopsis thaliana	AT1G15820	1.00E-16	LHCB6\|light harvesting complex photosystem II subunit 6

Network

Network Category	Global Network	Tissue Preferential Network	Treat Response Network
Coexpression Positive	Top300 PCC Genelist	Top300 PCC Genelist	Top300 PCC Genelist
Coexpression Negative	Top300 PCC Genelist	Top300 PCC Genelist	Top300 PCC Genelist
PPI Relationship	Null
miRNA-Target Relationship	Null

Functional module

Module ID	Function Annotation	Category
TissueCFM000370	benzoate biosynthesis III (CoA-dependent, non-β-oxidative) Protein_kinases_phosphatases, PPC:4.1.5.1: WNK like kinase - with no lysine kinase Protein_kinases_phosphatases, PPC:4.5.1: MAPK Family chloroplast photosystem II chloroplast thylakoid membrane photosystem I reaction center chloroplast thylakoid lumen response to wounding response to ozone photosynthesis, light harvesting mitochondrial translational elongation response to UV-B Glycolysis / Gluconeogenesis Photosynthesis - antenna proteins MAPK cascade protein-chromophore linkage photosystem I	tissue preferential network

Location

Gene	Assembly	Scaffold	Start	End	Strand
CRO_T001171	scaffolds.min_1000bp	scaffold_3012443	5106	5938	+

Gene detail image

more details in UCSC

Sequences

Genome:
CRO_T001171
ACCAATTCTCACTTCCACTTTCATTCTTAATCCCCATGGCTGCTTCAACAATGGCTCTTTCCTCCCCATCTTTTGCCGGAAAGGCAGTTAAACTTTCCCCTTCTGCCCCTGAATTAATGGGAAATGGCAGAGTTTCAATGAGGAAATCCACCGTCAAGCAAGTTTCTTCCGGCAGCCCATGGTACGGTCCAGACCGTGTTAAATACTTGGGTCCATTCTCCGGTGAACCCCCAAGCTACCTCACCGGTGAATTCCCCGGCGATTACGGCTGGGACACTGCCGGACTTTCAGCCGATCCCGAGACATTCGCCAAAAACCGTGAACTCGAGGTCATCCACTGCAGATGGGCTATGCTCGGAGCTCTCGGATGCGTTTTCCCTGAGCTATTGGCACGTAACGGCGTCAAATTCGGGGAAGCTGTCTGGTTCAAGGCCGGATCTCAGATCTTCAGCGAAGGAGGGCTTGATTATTTGGGAAACCCTAGCTTGATCCACGCACAGAGCATATTGGCAATTTGGGCATGTCAAGTTGTGTTGATGGGAGCCGTTGAGGGTTACCGTATTGCTGGAGGACCTCTCGGAGAAGTTACCGACCCGCTTTACCCAGGTGGTAGCTTTGACCCGTTGGGTCTAGCCGATGACCCGGAAGCATTTGCAGAGCTGAAGGTGAAGGAAATTAAGAACGGAAGATTGGCTATGTTCTCAATGTTCGGATTCTTCGTTCAGGCAATTGTTACAGGTAAAGGTCCATTGGAGAACCTTGCTGACCACCTTGCAGATCCAGTTAACAACAACGCATGGGCTTACGCCACCAACTTTGTTCCCGGAAAGTGA
CDS:
CRO_T001171
ATGGCTGCTTCAACAATGGCTCTTTCCTCCCCATCTTTTGCCGGAAAGGCAGTTAAACTTTCCCCTTCTGCCCCTGAATTAATGGGAAATGGCAGAGTTTCAATGAGGAAATCCACCGTCAAGCAAGTTTCTTCCGGCAGCCCATGGTACGGTCCAGACCGTGTTAAATACTTGGGTCCATTCTCCGGTGAACCCCCAAGCTACCTCACCGGTGAATTCCCCGGCGATTACGGCTGGGACACTGCCGGACTTTCAGCCGATCCCGAGACATTCGCCAAAAACCGTGAACTCGAGGTCATCCACTGCAGATGGGCTATGCTCGGAGCTCTCGGATGCGTTTTCCCTGAGCTATTGGCACGTAACGGCGTCAAATTCGGGGAAGCTGTCTGGTTCAAGGCCGGATCTCAGATCTTCAGCGAAGGAGGGCTTGATTATTTGGGAAACCCTAGCTTGATCCACGCACAGAGCATATTGGCAATTTGGGCATGTCAAGTTGTGTTGATGGGAGCCGTTGAGGGTTACCGTATTGCTGGAGGACCTCTCGGAGAAGTTACCGACCCGCTTTACCCAGGTGGTAGCTTTGACCCGTTGGGTCTAGCCGATGACCCGGAAGCATTTGCAGAGCTGAAGGTGAAGGAAATTAAGAACGGAAGATTGGCTATGTTCTCAATGTTCGGATTCTTCGTTCAGGCAATTGTTACAGGTAAAGGTCCATTGGAGAACCTTGCTGACCACCTTGCAGATCCAGTTAACAACAACGCATGGGCTTACGCCACCAACTTTGTTCCCGGAAAGTGA
Transcript:
CRO_T001171
ACCAATTCTCACTTCCACTTTCATTCTTAATCCCCATGGCTGCTTCAACAATGGCTCTTTCCTCCCCATCTTTTGCCGGAAAGGCAGTTAAACTTTCCCCTTCTGCCCCTGAATTAATGGGAAATGGCAGAGTTTCAATGAGGAAATCCACCGTCAAGCAAGTTTCTTCCGGCAGCCCATGGTACGGTCCAGACCGTGTTAAATACTTGGGTCCATTCTCCGGTGAACCCCCAAGCTACCTCACCGGTGAATTCCCCGGCGATTACGGCTGGGACACTGCCGGACTTTCAGCCGATCCCGAGACATTCGCCAAAAACCGTGAACTCGAGGTCATCCACTGCAGATGGGCTATGCTCGGAGCTCTCGGATGCGTTTTCCCTGAGCTATTGGCACGTAACGGCGTCAAATTCGGGGAAGCTGTCTGGTTCAAGGCCGGATCTCAGATCTTCAGCGAAGGAGGGCTTGATTATTTGGGAAACCCTAGCTTGATCCACGCACAGAGCATATTGGCAATTTGGGCATGTCAAGTTGTGTTGATGGGAGCCGTTGAGGGTTACCGTATTGCTGGAGGACCTCTCGGAGAAGTTACCGACCCGCTTTACCCAGGTGGTAGCTTTGACCCGTTGGGTCTAGCCGATGACCCGGAAGCATTTGCAGAGCTGAAGGTGAAGGAAATTAAGAACGGAAGATTGGCTATGTTCTCAATGTTCGGATTCTTCGTTCAGGCAATTGTTACAGGTAAAGGTCCATTGGAGAACCTTGCTGACCACCTTGCAGATCCAGTTAACAACAACGCATGGGCTTACGCCACCAACTTTGTTCCCGGAAAGTGA
Protein:
CRO_T001171
MAASTMALSSPSFAGKAVKLSPSAPELMGNGRVSMRKSTVKQVSSGSPWYGPDRVKYLGPFSGEPPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLIHAQSILAIWACQVVLMGAVEGYRIAGGPLGEVTDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWAYATNFVPGK*

Gene Ontology

GO term	Description	Category
GO:0009522	photosystem I	cellular_component
GO:0009535	chloroplast thylakoid membrane	cellular_component
GO:0009765	photosynthesis, light harvesting	biological_process
GO:0016021	integral component of membrane	cellular_component
GO:0016168	chlorophyll binding	molecular_function
GO:0018298	protein-chromophore linkage	biological_process
GO:0046872	metal ion binding	molecular_function

Gene family

Gene family	subfamily
--	--

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Pathway ID
K08912	LHCB1	-	Photosynthesis - antenna proteins	ko00196

PlantCyC

Gene	Enzyme ID	Description	Pathway	Pathway id
--	--	--	--	--

Pfam domain

Pfam accession	Pfam name	Alignment start	Alignment end	E-value
PF00504.18	Chloroa_b-bind	65	231	1.6e-50

Expression pattern

SRA Experiment	Description	FPKM
ERR364390	mixed tissue CK	33.5532
SRR122236	mixed tissue RA CK	0.22082905
SRR122237	mixed tissue RB CK	0
SRR122250	callus YE 0.3mg/ml CK	12.6278
SRR122247	callus YE 0.3mg/ml 6h	5.29339
SRR122248	callus YE 0.3mg/ml 12h	8.20725
SRR122249	callus YE 0.3mg/ml 24h	20.3071
SRR122242	callus MeJA 100um 0h	8.78904
SRR122246	callus MeJA 100um 6h	0.888247
SRR122240	callus MeJA 100um 12h	0.294823
SRR122241	callus MeJA 100um 24h	2.47601
SRR122239	flower CK 1	56.2549
SRR1271859	flower CK 2	14.60295
SRR1144633	healthy flowers CK	137.4405
SRR1144634	flowers PnWB infected	115.9595
SRR122257	hairy root CK	0.179678
SRR122258	hairy root MeJA 250um CK	0.135838
SRR122259	hairy root MeJA 250um 24h	0.152445
SRR122256	hairy root RebH F CK	2.64787
SRR122255	hairy root TDCi CK	0.201959
SRR122260	hairy root TDCi MeJA 250um CK	0
SRR122261	hairy root TDCi MeJA 250um 24h	0
SRR1820161	Hairy roots CK BAI1 14	37.524
SRR1820157	Hairy roots CK BAI1 18	46.7104
SRR1820149	Hairy roots CK BAI1 19	66.5672
SRR1820238	Hairy roots CK GUS 3	18.9538
SRR1820233	Hairy roots CK GUS 4	25.4164
SRR1820326	Hairy roots CK GUS 5	27.4557
SRR2098821	hairy roots OE AS CK rep1	0
SRR2099440	hairy roots OE AS CK rep2	0.0725455
SRR122252	immature leaf CK	877.953
SRR342023	leaf CK 1	346.9855
SRR342022	leaf CK 2	348.633
SRR342019	leaf CK 3	229.455
SRR342017	leaf CK 4	314.8125
SRR1271857	leaf CK 5	103.9093
SRR122251	mature leaf CK	511.559
SRR648705	root CK 1	44.34195
SRR1271858	root CK 2	0.1903635
SRR122254	root CK 3	132.523
SRR648707	root MeJA 24h	21.64685
SRR648709	root MeJA 24h DSN normalized	17.9324
SRR837772	seedling CK	367.6065
SRR122243	sterile seedlings AE CK 1	142.83
SRR122245	sterile seedlings AE CK 2	88.358
SRR122244	sterile seedlings AF MeJA 6um 12d	30.7712
SRR122253	stem CK	2.688
SRR646572	shoots CK	517.834
SRR647068	shoots MeJA 6h 1	296.831
SRR646596	shoots MeJA 6h 2	59.48155
SRR646604	shoots MeJA 24h	694.3515
SRR924147	suspension cells EX ORCA2 CK	40.25635
SRR924148	suspension cells EX ORCA3 CK	40.35885

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