Gene detail

Detail information of GWHGAAZE028417

Functional Annotation

Database	Orthologs	E value	Annotation
Nr	XP_002309513.1	0	glycine hydroxymethyltransferase family protein [Populus trichocarpa]
COG	YP_003321776.1	8E-136	glycine hydroxymethyltransferase
Swissprot	tr\|Q94JQ3\|GLYP3_ARATH	0	Serine hydroxymethyltransferase 3, chloroplastic (Precursor)
trEMBL	tr\|B9HDQ7\|B9HDQ7_POPTR	0	Serine hydroxymethyltransferase {ECO:0000256\|RuleBase:RU000585}
TAIR10	AT4G32520.2	0	serine hydroxymethyltransferase 3

Location And Transcript Sequence (JBrowse)

Scaffold	Type	Start	End	Strand
GWHAAZE00000008	gene	55489616	55497345	+
GWHAAZE00000008	mRNA	55489616	55497345	+
GWHAAZE00000008	exon	55489616	55489826	+
GWHAAZE00000008	exon	55491981	55492167	+
GWHAAZE00000008	exon	55492267	55492441	+
GWHAAZE00000008	exon	55492945	55493062	+
GWHAAZE00000008	exon	55493161	55493273	+
GWHAAZE00000008	exon	55493410	55493532	+
GWHAAZE00000008	exon	55494698	55494802	+
GWHAAZE00000008	exon	55495400	55495486	+
GWHAAZE00000008	exon	55495582	55495689	+
GWHAAZE00000008	exon	55496428	55496500	+
GWHAAZE00000008	exon	55497071	55497345	+
GWHAAZE00000008	CDS	55489616	55489826	+
GWHAAZE00000008	CDS	55491981	55492167	+
GWHAAZE00000008	CDS	55492267	55492441	+
GWHAAZE00000008	CDS	55492945	55493062	+
GWHAAZE00000008	CDS	55493161	55493273	+
GWHAAZE00000008	CDS	55493410	55493532	+
GWHAAZE00000008	CDS	55494698	55494802	+
GWHAAZE00000008	CDS	55495400	55495486	+
GWHAAZE00000008	CDS	55495582	55495689	+
GWHAAZE00000008	CDS	55496428	55496500	+
GWHAAZE00000008	CDS	55497071	55497345	+

Transcript Sequence
>GWHTAAZE028451 ATGCAGGCTTGTAGTGGAACTGCGTTAATGGGTTCTCTTAAACAACCCCATTGGACTAAGTTGCCGAGTCTTCCGACTAAAGGGTCCTGTATTACTCGATTCCCTCATCAAGTTAAACTCAGCTTGGTGAAGCCTTGTAGATCATCTCAACTTGAAGATAACTTAGTCACTGGGAAGCCACCCTCTTCCTTGTCTGCTCCTCTGCTCGAAGGTAGCTTTGAAGACTATGGGTTGAGTACAGCCGATCCTGAAGTGCGTGAAATTATTGACCAAGAAAAGCAACGCCAGTTTAGAAGCTTAGAGCTTATTGCTTCTGAGAACTTCACTTCCCGAGCTGTGATGGAAGCAGTTGGTTCTTGCCTTACAAATAAGTACTCTGAAGGACTCCCAGGCAAAAGGTACTATGGTGGGAATGAGTACATTGATGAACTGGAAACTCTGTGTCAGCAAAGGGCTTTAGCAGCATTTCACTTGGATGGCAAGAAATGGGGTGTAAACGTCCAGCCTTTGTCGGGTTCTCCTGCTAATTTTGAGGTTTACACGGCAATTCTTAAACCGCATGACCGCATAATGGGGCTGGACTTGCCACATGGAGGACACTTGTCCCATGGGTTCATGACGCCTAAGAGACGGGTATCGGGGACATCTATTTATTTTGAATCCATGCCCTATCGGCTTGACGAATCTACAGGCCTAGTTGATTATGACATGCTTGAGAAAACTGCTATCCTCTTTCGGCCGAAACTTATTATTGCTGGTGCTAGTGCTTATCCTCGAGATTTTGACTATCCTCGTATGAGGAAGATTGCAGATGCTGTTGGGGCATTTCTTATGATGGATATGGCACACATAAGCGGACTTGTTGCTGCTTCTGTGGTTGGTAATCCTTTTGACTACTGCGATATTGTAACAACAACAACACACAAGTCCTTGAGAGGGCCTAGAGGTGGCATGATCTTCTTCAAGAAGGATAATGTTTTGGGTGTTGATTTAGAGTCTGCCATCAACAATGCTGTTTTCCCAGGTTTACAGGGCGGTCCACACAACCACACGATTGGGGGACTTGCTGTGTGCCTGAAACATGCTCAGTCTCCCGAGTTTAAGGATTATCAAAACAAGGTTGTATCTAATTGTCGAGCTCTTGCAAGCCGATTGACTGAGCTGGGATACAAGCTGGTCTCCGGAGGGAGTGATAATCATTTAGTTCTTGTGGATCTCAGGCCACTGGGTATTGACGGTGCTAGGGTGGAGACAATTCTTGACATGGCATCCATCACCCTAAATAAAAATTCAGTTCCTGGCGATAAAAGTGCGCTAATGCCAGGCGGCATACGCATTGGGTCACCTGCTATGACGACCCGAGGGTTCATGGAGAAGGAATTCATATCAACTGCTGACCTCATTCATGAGGGCGTCCAGATAACCCTTGAAGCGAAACGGGCCGCTTCGGGTCCGAAGCTTCAAGATTTTATGAAGTTCGTAAAATCTCCGGATTTCTCCTTGAAGGATCGGATCTCTGATCTTCGGGAGAGGGTGGAAAATTTGACAACCCAGTTTCCTTTGCCTGGTTTATGA

Network for GWHGAAZE028417

Network category	Network	Top300 PCC genelist
Coexpression Positive	Network	Top300 PCC genelist
Coexpression Negative	Network	Top300 PCC genelist

Functional Module

Module ID	Function Annotation

Protein Structure

Pfam accession	Pfam name	Alignment start	Alignment end	E-value
PF00464.20	SHMT	78	467	1.10E-192

Protein Sequence

Gene family

Gene family	subfamily
--	--

KEGG pathway

KO	Enzyme	pathway	mapID
K00600	glyA, SHMT	Metabolic pathways	map01100
		Biosynthesis of secondary metabolites	map01110
		Microbial metabolism in diverse environments	map01120
		Carbon metabolism	map01200
		Biosynthesis of amino acids	map01230
		Glyoxylate and dicarboxylate metabolism	map00630
		Methane metabolism	map00680
		Glycine, serine and threonine metabolism	map00260
		Cyanoamino acid metabolism	map00460
		One carbon pool by folate	map00670

Gene Ontology

GO term	Ontology	Name
GO:0019264	biological_process	glycine biosynthetic process from serine
GO:0035999	biological_process	tetrahydrofolate interconversion
GO:0030170	molecular_function	pyridoxal phosphate binding
GO:0003824	molecular_function	catalytic activity
GO:0004372	molecular_function	glycine hydroxymethyltransferase activity

Expression pattern

Expression pattern detail

SRP	Sample	Description	TPM
SRP075780	SRR3591705	youngest leaf	19.078
	SRR3591706	second leaf	9.993
	SRR3591707	mature leaf	13.662
	SRR3591708	Shoot apex	17.575
	SRR3591709	Stem	18.248
	SRR3591710	White floral bud	13.793
	SRR3591711	White flower	18.898
	SRR3591712	Green floral bud	16.992
	SRR3591713	Yellow flower	21.810
SRP173429	SRR8316895	Juvenile bud stage	10.623
	SRR8316896	Juvenile bud stage	13.589
	SRR8316897	Juvenile bud stage	10.190
	SRR8316894	Third green stage	5.769
	SRR8316900	Third green stage	21.486
	SRR8316901	Third green stage	18.062
	SRR8316898	Complete white stage	5.285
	SRR8316899	Complete white stage	14.294
	SRR8316903	Complete white stage	5.870
	SRR8316902	Silver flowering stage	5.414
	SRR8316904	Silver flowering stage	5.397
	SRR8316905	Silver flowering stage	2.820
	SRR8316906	Gold flowering stage	11.331
	SRR8316907	Gold flowering stage	11.837
	SRR8316908	Gold flowering stage	17.110
SRP132670	SRR6706286	Control	13.137
	SRR6706287	Light intensity 50%	13.594
	SRR6706288	Light intensity 20%	14.650
CNP0000432	CNS0095592	Slightly white alabastrum(diploid) 1	7.753
	CNS0095593	Slightly white alabastrum(diploid) 2	9.570
	CNS0095594	Slightly white alabastrum(diploid) 3	9.444
	CNS0095595	Whole white alabastrum(diploid) 2	8.269
	CNS0095596	Whole white alabastrum(diploid) 3	9.965
	CNS0095597	Whole white alabastrum(diploid) 4	8.223
	CNS0095598	Silvery flower (diploied) 1	11.101
	CNS0095599	Silvery flower (diploied) 2	7.182
	CNS0095600	Silvery flower (diploied) 3	12.087
	CNS0095601	Golden flower (diploid) 1	8.712
	CNS0095602	Golden flower (diploid) 2	12.233
	CNS0095603	Golden flower (diploid) 3	10.719
	CNS0095604	Slightly white alabastrum(tetraploid) 1	15.805
	CNS0095605	Slightly white alabastrum(tetraploid) 2	12.353
	CNS0095606	Slightly white alabastrum(tetraploid) 3	20.095
	CNS0095607	Whole white alabastrum(tetraploid) 1	11.277
	CNS0095608	Whole white alabastrum(tetraploid) 2	11.800
	CNS0095609	Whole white alabastrum(tetraploid) 3	20.163
	CNS0095610	Silvery flower (tetraploid) 1	16.455
	CNS0095611	Silvery flower (tetraploid) 2	19.473
	CNS0095612	Silvery flower (tetraploid) 3	13.353
	CNS0095613	Golden flower (tetraploid) 1	8.962
	CNS0095614	Golden flower (tetraploid) 2	12.684
	CNS0095615	Golden flower (tetraploid) 3	8.420
CRA001975	CRR073297	Stem 1	17.182
	CRR073298	Stem 2	13.145
	CRR073299	Stem 3	16.039
	CRR073300	Leaf 1	13.578
	CRR073301	Leaf 2	17.059
	CRR073302	Leaf 3	17.892
	CRR073303	Juvenile bud 1	15.962
	CRR073304	Juvenile bud 2	9.826
	CRR073305	Juvenile bud 3	14.869
	CRR073306	Third green 1	5.226
	CRR073307	Third green 2	3.323
	CRR073308	Third green 3	4.676
	CRR073309	Second white 1	9.637
	CRR073310	Second white 2	6.152
	CRR073311	Second white 3	7.585
	CRR073312	Silver flowering 1	7.665
	CRR073313	Silver flowering 2	10.528
	CRR073314	Silver flowering 3	7.627
	CRR073315	Gold flowering 1	10.647
	CRR073316	Gold flowering 2	16.283
	CRR073317	Gold flowering 3	10.824
	CRR073318	Tawny withering 1	14.387
	CRR073319	Tawny withering 2	8.817
	CRR073320	Tawny withering 3	13.560