Plant FIBer expression Database

External link	JGI Phytozome v13 [genome browser]
Symbol
Arabidopsis homologues Show only best Show top 10	Locus ID BLAST score/e-value TF class Alias TAIR10 short description AT4G13930 561 / 0 SHM4 serine hydroxymethyltransferase 4 (.1) AT4G13890 499 / 1e-176 SHM5, EDA36, EDA37 SERINE HYDROXYMETHYLTRANSFERASE 5, EMBRYO SAC DEVELOPMENT ARREST 36, EMBRYO SAC DEVELOPMENT ARREST 37, Pyridoxal phosphate (PLP)-dependent transferases superfamily protein (.1) AT1G22020 392 / 1e-132 SHM6 serine hydroxymethyltransferase 6 (.1) AT1G36370 391 / 2e-132 SHM7 serine hydroxymethyltransferase 7 (.1) AT4G37930 336 / 7e-112 SHMT1, STM, SHM1 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) AT4G32520 336 / 1e-111 AtSHMT3, SHM3 serine hydroxymethyltransferase 3 (.1.2) AT5G26780 332 / 4e-110 SHM2 serine hydroxymethyltransferase 2 (.1.2.3)
Paralogs Show only best Show top 10	Gene ID BLAST score/e-value At best hit BLAST score/e-value TAIR10 short description Lus10043157 [exp] 637 / 0 AT4G13930 865 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10022557 [exp] 566 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10015471 [exp] 408 / 5e-139 AT1G36370 819 / 0.0 serine hydroxymethyltransferase 7 (.1) Lus10019942 [exp] 407 / 2e-138 AT1G36370 817 / 0.0 serine hydroxymethyltransferase 7 (.1) Lus10028218 [exp] 343 / 1e-114 AT5G26780 903 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Lus10042923 [exp] 338 / 1e-112 AT4G37930 881 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10022391 [exp] 325 / 2e-107 AT4G32520 828 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10005916 [exp] 323 / 2e-106 AT4G32520 823 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10029559 [exp] 315 / 6e-104 AT4G37930 900 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1)
Poplar homologues Show only best Show top 10	Locus ID BLAST score/e-value At best hit BLAST score/e-value TAIR10 short description Potri.001G320400 [exp] 567 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.017G059300 [exp] 566 / 0 AT4G13930 868 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.002G090200 [exp] 405 / 3e-138 AT1G36370 809 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.005G170800 [exp] 404 / 4e-138 AT1G36370 837 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.001G212000 [exp] 404 / 9e-138 AT1G36370 798 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.002G109200 [exp] 338 / 7e-113 AT5G26780 904 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Potri.010G254700 [exp] 329 / 4e-109 AT4G37930 918 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Potri.006G232300 [exp] 328 / 2e-108 AT4G32520 869 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Potri.008G002900 [exp] 325 / 2e-107 AT4G37930 933 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1)
PFAM info	Clan ID Clan name Pfam ID Pfam name Pfam description CL0061 [flax] [poplar] PLP_aminotran PF00464 [flax] [poplar] SHMT Serine hydroxymethyltransferase
Representative CDS sequence Show only first row Show all	>Lus10032592 pacid=23146341 polypeptide=Lus10032592 locus=Lus10032592.g ID=Lus10032592.BGIv1.0 annot-version=v1.0 ATGGATCCAGTGAAGGTGTGGGGAAACACTCCTTTGCAAACCGTGGACCCTGAGATCCACGACCTCATCGAGAAGGAGAAGCGCCGTCAATGCCGCGGGA TCGAGCTCATCGCTTCCGAGAACTTCACTTCCTTTGCCGTCATCGAAGCCCTCGGCAGCGCCCTCACCAACAAGTACTCCGAGGGCATGCCCGGTGAATT CCAGCACTGCTACATCGACTACGATAAGCTGGAAGAGAAGGCTTTGGATTTCAGGCCACGGTTGATCATCTGTGGTGGCAGTGCTTACCCTAGGGACTGG GATTACGCTAGGTTCAGGGCTATTGCTGATAAATGCGGCGCACTTTTGCTCTGCGATATGGCTCACATTAGCGGCCTAGTTGCTGCTCAGGAAGCTGCCA ACCCCTTTGAGTTCTGTGACATTGTCACAACCACCACCCACAAGAGTTTGAGGGGTCCCAGAGCTGGTATGATCTTCTACCGCAAGGGACCTAAGCCAGC CAACAAGAAGGGTCAGCCTCAAGGAAACTATGAATTCGAGGACAACATCAACTTCTCTGTCTTCCCTGCCCTCCAGGGAGGCCCCCATAATCACCAGATC GGTGCCCTTGCTGTTGCATTGAAGCAGGCTGCAACCCCTGCATTCAAGGCCTACGCCAAGCAAGTGAAGGCCAATGCTGTTGCTGTTGGAAACTATTTGA TGAGCAAAGGCTACACCTTGGTTACTGGAGGAACTGAGAACCACCTTGTTCTGTGGGATCTGAGACCTCTTGGGTTGACTGGCAACAAGGTCGAGAAGGT TTGCGATCTCTGTAACATCACTGTGAACAAGAATGCAGTGTTCGGAGACAGCAGTGCTTTGTCCCCGGGAGGCGTGAGAGTTGGTGCACCTGCCATGACT TCAAGAGGGTTGTTGGAGAAAGACTTTGAGCAAATCGGAGAGTTCCTCCACCGTGCTGTCGCCTTGACACTGAGCATCCAGAAGGAGTATGGGAAGTTGC TGAAGGACTTCAACAAGGGGCTGGAGAACAACAAGGAGATTGAGGCATTGAAAGCTGATGTTGAGAAATTTGCAGGTTCCTTCGATATGCCCGGTTTCCT CATGTCTGAGATGAAGTACCAGGAGTAA
AA sequence Show only first row Show all	>Lus10032592 pacid=23146341 polypeptide=Lus10032592 locus=Lus10032592.g ID=Lus10032592.BGIv1.0 annot-version=v1.0 MDPVKVWGNTPLQTVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGEFQHCYIDYDKLEEKALDFRPRLIICGGSAYPRDW DYARFRAIADKCGALLLCDMAHISGLVAAQEAANPFEFCDIVTTTTHKSLRGPRAGMIFYRKGPKPANKKGQPQGNYEFEDNINFSVFPALQGGPHNHQI GALAVALKQAATPAFKAYAKQVKANAVAVGNYLMSKGYTLVTGGTENHLVLWDLRPLGLTGNKVEKVCDLCNITVNKNAVFGDSSALSPGGVRVGAPAMT SRGLLEKDFEQIGEFLHRAVALTLSIQKEYGKLLKDFNKGLENNKEIEALKADVEKFAGSFDMPGFLMSEMKYQE

---

DESeq2's median of ratios [FLAX]

Order by: Tissue Experiment Show only core collection Show again Show schematic diagram

---

Coexpressed genes

Compare expression of checked genes Schematic diagram [FLAX] Schematic diagram [POPLAR]

*If you select 4 or less genes and then press "compare expression", expression will be shown as a graph. If you select more than 4 genes, expresion will be shown as a heat map.
*Color represents relative expression level among samples for each gene.

At best	At TF class	At alias	At description		Locus	MR	r	Symbol	HYP	R_s2_CTR	R_s2_Fox	R_s4_CTR	R_s4_Fox	R_r1_CTR	R_r1_Fox	R_r3_CTR	R_r3_Fox	R_r1s2_CTR	R_r1s2_Fox	R_r3s2_CTR	R_r3s2_Fox	R_s6_CTR	R_s6_Al4	R_s6_Al12	R_s6_Al24	R_s8_CTR	R_s8_Al4	R_s8_Al12	R_s8_Al24	R_r5_CTR	R_r5_Al4	R_r5_Al12	R_r5_Al24	R_r7_CTR	R_r7_Al4	R_r7_Al12	R_r7_Al24	LEAF_N	LEAF_P	LEAF_NPK	SAM	AR_Bet	AR_rdf	cPAR	TOP_Bet	TOP_rdf	iFIBa	iFIBb	MID_Bet	MID_rdf	tFIBa	tFIB_Gr	tFIB_Li	tFIB_Bi	tFIBb	tFIBb_PUL8	tFIBb_PUL24	tFIBb_PUL96	tFIBb_OPP8	tFIBb_OPP24	tFIBb_OPP96	sXYLa	sXYLb	sXYLb_PUL8	sXYLb_PUL24	sXYLb_PUL96	sXYLb_OPP8	sXYLb_OPP24	sXYLb_OPP96
AT4G13930		SHM4	serine hydroxymethyltransferas...		Lus10032592 [exp]	0	1
AT5G17920		ATCIMS, ATMETS,...	methionine synthesis 1, COBALA...		Lus10002620 [exp]	1.0	0.9818
AT3G59970		MTHFR1	methylenetetrahydrofolate redu...		Lus10027078 [exp]	1.4	0.9769
AT5G11890		EMB3135	EMBRYO DEFECTIVE 3135, unknown...		Lus10024987 [exp]	2.2	0.9725
AT4G34050		CCoAOMT1	caffeoyl coenzyme A O-methyltr...		Lus10027888 [exp]	5.7	0.9752
AT5G61840		GUT1, IRX10-L	Exostosin family protein (.1)		Lus10043209 [exp]	7.0	0.9698
AT1G26570		UGD1, ATUGD1	UDP-glucose dehydrogenase 1 (....		Lus10026656 [exp]	7.2	0.9641
AT5G60020		LAC17, ATLAC17	laccase 17 (.1)		Lus10024378 [exp]	7.7	0.9609
AT1G19940		ATGH9B5	glycosyl hydrolase 9B5 (.1)		Lus10033156 [exp]	7.9	0.9605
AT3G42950			Pectin lyase-like superfamily ...		Lus10027646 [exp]	9.2	0.9750
AT1G19300		ATGATL1, GATL1,...	PARVUS, GAOLAOZHUANGREN 1, GAL...		Lus10016301 [exp]	13.0	0.9648

Compare expression of checked genes

Lus10032592 coexpression network

*The number of genes in the network is adjusted within 50 genes.
*Gene name represents symbol(s) of closest Arabidopsis gene if symbol(s) for the gene itself doesn't exist.
*Circle diameter represents the number of connection with other genes within this network.
*Color for gene name represents subnetwork based on the result of network clustering.