Gene detail

Detail information of GWHGAAZE028414

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	55313011	55323484	+
GWHAAZE00000008	mRNA	55313011	55323484	+
GWHAAZE00000008	exon	55313011	55313221	+
GWHAAZE00000008	exon	55315372	55315558	+
GWHAAZE00000008	exon	55315660	55315834	+
GWHAAZE00000008	exon	55319077	55319194	+
GWHAAZE00000008	exon	55319292	55319404	+
GWHAAZE00000008	exon	55319540	55319662	+
GWHAAZE00000008	exon	55320804	55320908	+
GWHAAZE00000008	exon	55321532	55321618	+
GWHAAZE00000008	exon	55321714	55321821	+
GWHAAZE00000008	exon	55322564	55322636	+
GWHAAZE00000008	exon	55323210	55323484	+
GWHAAZE00000008	CDS	55313011	55313221	+
GWHAAZE00000008	CDS	55315372	55315558	+
GWHAAZE00000008	CDS	55315660	55315834	+
GWHAAZE00000008	CDS	55319077	55319194	+
GWHAAZE00000008	CDS	55319292	55319404	+
GWHAAZE00000008	CDS	55319540	55319662	+
GWHAAZE00000008	CDS	55320804	55320908	+
GWHAAZE00000008	CDS	55321532	55321618	+
GWHAAZE00000008	CDS	55321714	55321821	+
GWHAAZE00000008	CDS	55322564	55322636	+
GWHAAZE00000008	CDS	55323210	55323484	+

Transcript Sequence
>GWHTAAZE028448 ATGCAGGCTTGTAGTGGAACTGCGGTAATGGGTTCTCTTAAACAACCCCATTGGACTAAGTTGCCGAGTCTTCCGACTAAAGGGTCCTGTATTACTCGATTCCCTCATCAAGTTAAACTCAGCTCGGTGAAGCCTTGTAGATCATCTCAACTTGAAGATAACTTAGTCACTGGGAAGCCACCCTCTTCCTTTTCTGCTCCTGTGCTCGAAGGTAGCTTTGAAGACTATGGGTTGAGTACAGCCGATCCTGAAGTGCGTGAAATTATTGACCAAGAAAAGCAACGCCAGTTTAGAAGCTTAGAGCTTATTGCTTCTGAGAACTTCACTTCCCGAGCTGTGATGGAAGCAGTTGGTTCTTGCCTTACAAATAAGTACTCTGAAGGACTCCCGGGCAAAAGGTACTATGGTGGGAATGAGTACATTGATGAACTGGAAACTCTGTGTCAGCAAAGGGCTTTAGCAGCATTTCACTTGGATGGCAAGAAATGGGGTGTAAACGTCCAACCTTTGTCGGGTTCTCCTGCTAATTTTGAGGTTTACACGGCAATTCTTAAACCGCATGACCGCATAATGGGGCTGGACTTGCCACATGGAGGACACTTGTCCCATGGGTTCATGACGCCTAAGAGACGGGTATCGGGGACATCTATTTATTTTGAATCCATGCCCTATCGGCTTGACGAATCTACAGGCCTAGTTGATTATGACATGCTTGAGAAAACTGCTATCCTCTTTCGGCCAAAACTTATTATTGCTGGTGCTAGTGCTTATCCTCGAGATTTTGACTATCCTCGTATGAGGAAGATTGCAGATGCTGTTGGGGCATTTCTTATGATGGATATGGCACACATAAGCGGACTTGTTGCTGCTTCTGTGGTTGGTAATCCTTTTGACTACTGCGATATTGTAACAACAACAACACACAAGTCCTTGAGAGGGCCTAGAGGTGGCATGATCTTCTTCAAGAAGGATAATGTTTTGGGTGTTGATTTAGAGTCTGCCATCAACAATGCTGTTTTCCCAGGTTTACAGGGCGGTCCACACAACCACACGATTGGGGGACTTGCTGTGTGCCTGAAACATGCTCAGTCTCCCGAGTTTAAGGATTATCAAAACAAGGTTGTATCTAATTGTGGAGCTCTTGCAAGCCGATTGACTGAGCTGGGATACAAGCTGGTCTCTGGTGGGAGTGATAATCATTTAGTTCTTGTGGATCTCAGGCCACTGGGTATTGACGGTGCTAGGGTGGAGACAATTCTTGACATGGCATCTATCACCCTAAATAAAAATTCAGTTCCTGGCGATAAAAGTGCGCTAATGCCAGGCGGCATACGCATTGGGTCACCTGCTATGACGACCCGAGGGTTCACGGAGAAGGAATTCATATCAACTGCTGACCTCATTCATGAGGGCGTCCAGATAACCCTTGAAGCGAAACGGGCCGCTTCGGGTCCGAAGCTTCAAGATTTTATGAAGTTCGTAAAATCTCCGGATTTCTCCTTGAAGGATCGGATCTCTGATCTTCGGGAGAGGGTGGAAAATTTGACAACCCAGTTTCCTTTGCCTGGTTTATGA

Network for GWHGAAZE028414

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	5.30E-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:0003824	molecular_function	catalytic activity
GO:0030170	molecular_function	pyridoxal phosphate binding
GO:0004372	molecular_function	glycine hydroxymethyltransferase activity

Expression pattern

Expression pattern detail

SRP	Sample	Description	TPM
SRP075780	SRR3591705	youngest leaf	3.654
	SRR3591706	second leaf	1.091
	SRR3591707	mature leaf	2.411
	SRR3591708	Shoot apex	2.785
	SRR3591709	Stem	2.500
	SRR3591710	White floral bud	2.533
	SRR3591711	White flower	3.251
	SRR3591712	Green floral bud	3.334
	SRR3591713	Yellow flower	3.452
SRP173429	SRR8316895	Juvenile bud stage	11.302
	SRR8316896	Juvenile bud stage	13.847
	SRR8316897	Juvenile bud stage	3.348
	SRR8316894	Third green stage	6.541
	SRR8316900	Third green stage	23.911
	SRR8316901	Third green stage	19.729
	SRR8316898	Complete white stage	5.101
	SRR8316899	Complete white stage	15.942
	SRR8316903	Complete white stage	5.877
	SRR8316902	Silver flowering stage	6.328
	SRR8316904	Silver flowering stage	6.664
	SRR8316905	Silver flowering stage	3.023
	SRR8316906	Gold flowering stage	9.989
	SRR8316907	Gold flowering stage	12.192
	SRR8316908	Gold flowering stage	7.706
SRP132670	SRR6706286	Control	20.047
	SRR6706287	Light intensity 50%	21.205
	SRR6706288	Light intensity 20%	23.145
CNP0000432	CNS0095592	Slightly white alabastrum(diploid) 1	9.902
	CNS0095593	Slightly white alabastrum(diploid) 2	9.367
	CNS0095594	Slightly white alabastrum(diploid) 3	11.057
	CNS0095595	Whole white alabastrum(diploid) 2	10.158
	CNS0095596	Whole white alabastrum(diploid) 3	12.028
	CNS0095597	Whole white alabastrum(diploid) 4	6.748
	CNS0095598	Silvery flower (diploied) 1	11.803
	CNS0095599	Silvery flower (diploied) 2	8.409
	CNS0095600	Silvery flower (diploied) 3	12.075
	CNS0095601	Golden flower (diploid) 1	9.677
	CNS0095602	Golden flower (diploid) 2	10.877
	CNS0095603	Golden flower (diploid) 3	12.118
	CNS0095604	Slightly white alabastrum(tetraploid) 1	4.158
	CNS0095605	Slightly white alabastrum(tetraploid) 2	4.506
	CNS0095606	Slightly white alabastrum(tetraploid) 3	8.518
	CNS0095607	Whole white alabastrum(tetraploid) 1	2.719
	CNS0095608	Whole white alabastrum(tetraploid) 2	2.630
	CNS0095609	Whole white alabastrum(tetraploid) 3	7.032
	CNS0095610	Silvery flower (tetraploid) 1	5.208
	CNS0095611	Silvery flower (tetraploid) 2	4.900
	CNS0095612	Silvery flower (tetraploid) 3	4.325
	CNS0095613	Golden flower (tetraploid) 1	3.065
	CNS0095614	Golden flower (tetraploid) 2	4.366
	CNS0095615	Golden flower (tetraploid) 3	2.511
CRA001975	CRR073297	Stem 1	17.904
	CRR073298	Stem 2	15.351
	CRR073299	Stem 3	17.781
	CRR073300	Leaf 1	14.783
	CRR073301	Leaf 2	17.559
	CRR073302	Leaf 3	20.064
	CRR073303	Juvenile bud 1	17.179
	CRR073304	Juvenile bud 2	11.364
	CRR073305	Juvenile bud 3	18.996
	CRR073306	Third green 1	6.263
	CRR073307	Third green 2	4.451
	CRR073308	Third green 3	6.460
	CRR073309	Second white 1	10.946
	CRR073310	Second white 2	9.933
	CRR073311	Second white 3	11.395
	CRR073312	Silver flowering 1	9.888
	CRR073313	Silver flowering 2	10.007
	CRR073314	Silver flowering 3	10.162
	CRR073315	Gold flowering 1	12.796
	CRR073316	Gold flowering 2	17.293
	CRR073317	Gold flowering 3	12.073
	CRR073318	Tawny withering 1	12.736
	CRR073319	Tawny withering 2	12.327
	CRR073320	Tawny withering 3	15.375