Plant FIBer expression Database

External link	JGI Phytozome v13 [genome browser] Popgenie AspWood
Symbol	SHMT2,SHM1.2
Arabidopsis homologues Show only best Show top 10	Locus ID BLAST score/e-value TF class Alias TAIR10 short description AT4G37930 933 / 0 SHMT1, STM, SHM1 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) AT5G26780 907 / 0 SHM2 serine hydroxymethyltransferase 2 (.1.2.3) AT4G32520 592 / 0 AtSHMT3, SHM3 serine hydroxymethyltransferase 3 (.1.2) AT4G13930 543 / 0 SHM4 serine hydroxymethyltransferase 4 (.1) AT4G13890 516 / 0 SHM5, EDA36, EDA37 SERINE HYDROXYMETHYLTRANSFERASE 5, EMBRYO SAC DEVELOPMENT ARREST 36, EMBRYO SAC DEVELOPMENT ARREST 37, Pyridoxal phosphate (PLP)-dependent transferases superfamily protein (.1) AT1G36370 476 / 4e-163 SHM7 serine hydroxymethyltransferase 7 (.1) AT1G22020 468 / 6e-160 SHM6 serine hydroxymethyltransferase 6 (.1)
Paralogs Show only best Show top 10	Gene ID BLAST score/e-value At best hit BLAST score/e-value TAIR10 short description Potri.010G254700 [exp] 1024 / 0 AT4G37930 918 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Potri.002G109200 [exp] 932 / 0 AT5G26780 904 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Potri.006G232300 [exp] 583 / 0 AT4G32520 869 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Potri.001G320400 [exp] 545 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.017G059300 [exp] 543 / 0 AT4G13930 868 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.005G170800 [exp] 497 / 5e-172 AT1G36370 837 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.002G090200 [exp] 492 / 5e-170 AT1G36370 809 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.001G212000 [exp] 481 / 2e-165 AT1G36370 798 / 0.0 serine hydroxymethyltransferase 7 (.1)
Flax homologues Show only best Show top 10	Locus ID BLAST score/e-value At best hit BLAST score/e-value TAIR10 short description Lus10039629 [exp] 920 / 0 AT4G37930 933 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10028218 [exp] 904 / 0 AT5G26780 903 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Lus10029559 [exp] 895 / 0 AT4G37930 900 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10042923 [exp] 887 / 0 AT4G37930 881 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10005916 [exp] 573 / 0 AT4G32520 823 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10022391 [exp] 572 / 0 AT4G32520 828 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10043157 [exp] 552 / 0 AT4G13930 865 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10022557 [exp] 532 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10015471 [exp] 489 / 3e-168 AT1G36370 819 / 0.0 serine hydroxymethyltransferase 7 (.1) Lus10019942 [exp] 488 / 5e-168 AT1G36370 817 / 0.0 serine hydroxymethyltransferase 7 (.1)
PFAM info	Clan ID Clan name Pfam ID Pfam name Pfam description CL0061 [poplar] [flax] PLP_aminotran PF00464 [poplar] [flax] SHMT Serine hydroxymethyltransferase
Representative CDS sequence Show only first row Show all	>Potri.008G002900.16 pacid=42808574 polypeptide=Potri.008G002900.16.p locus=Potri.008G002900 ID=Potri.008G002900.16.v4.1 annot-version=v4.1 ATGGCAATGGCAATAGCCATGGCCCTTCGCAGGCTCCCCTCTTCCTTTGACAAGCCCCTTCGCCCCGCTCTCTTCAAAGCCACCTCCCTCTATTATATGT CTTCCTTGCCGGATGAAGCTGTATACGAGAAGGAGAAACCTGGTGTCACTTGGCCAAAGCAGCTAAATGCACCCTTAGAGGTTGTTGACCCACAAATTGC TGATATTATTGAGCTCGAGAAAGCTAGGCAATGGAAGGGGCTTGAGCTTATACCCTCAGAGAACTTCACCTCCGTATCAGTGATGCAAGCCGTGGGTTCT GTCATGACCAACAAGTACAGTGAAGGATATCCAGGTGCAAGATACTACGGTGGAAACGAGTTTATTGACATGGCAGAATCATTATGTCAGAAGCGTGCTC TGGAAGCATTTCGCCTGGATCCTGCTAAATGGGGAGTCAACGTGCAATCTTTATCTGGATCTCCATCTAATTTTCAAGTCTACACTGCATTGTTAAAACC TCATGAAAGAATCATGGCACTTGATCTTCCTCACGGAGGCCATCTTTCTCATGGCTATCAGACAGACACCAAAAAAATATCTGCAGTGTCAATATTTTTT GAGACAATGCCATACAGATTGAATGAGAGCACTGGCTATATTGACTATGATCAGCTGGAGAAAAGTGCCACTCTTTTCAGACCAAAATTAATAGTAGCTG GTGCTAGTGCTTATGCACGTCTATATGATTATGCACGCATTCGCAAGGTTTGCGACAAACAAAAAGCTATACTGTTGGCCGATATGGCGCACATTAGTGG ATTGGTTGCAGCTGGTGTCATCCCATCGCCTTTTGAGTATGCAGATGTAGTGACCACCACAACTCACAAGTCACTTCGTGGGCCACGTGGGGCCATGATT TTCTTCAGGAAGGGGCTGAAAGAGGTTAACAAACAAGGGAAAGAGGTCTTTTATGACTATGAGGACAAAATCAATCAAGCTGTCTTTCCTGGGCTTCAAG GTGGTCCACACAACCACACAATTGCTGGTTTAGCAGTTGCTTTGAAACAGGCTACAACTCTGGAGTACAAAGCGTATCAAGAGCAGGTTCTTAGTAATTG CTCAAAATTTGCTCAGAGTCTAGTTGAGAAAGGCTATGAACTTGTTTCTGGTGGAACTGAGAACCATTTAGTTTTGGTGAACCTGAAGAACAAGGGTATT GATGGCTCCAGAGTTGAAAAGGTGCTCGAATCTGTTCACATTGCTGCAAACAAAAACACTGTTCCTGGTGATGTGTCTGCCATGGTTCCTGGTGGCATCA GGATGGGAACACCGGCTCTTACTTCTAGGGGGTTCGTGGAAGAGGATTTTGCTAAGGTGGCAGATTTCTTTGATGCTTCGGTGAAGTTGGCAGTGAAGAT GAAGGCTGAAACCAAAGGGACAAAGTTGAAGGATTTCTTGGTTACAATGCAGTCTGCTCACTTTCAATCTGAGATTTCAAAACTCCGTCATGAAGTGGAA GAATATGCTAAGCAATTCCCAACAATTGGATTTAACAAAGAAACCATGAAGTACAAGAATTGA
AA sequence Show only first row Show all	>Potri.008G002900.16 pacid=42808574 polypeptide=Potri.008G002900.16.p locus=Potri.008G002900 ID=Potri.008G002900.16.v4.1 annot-version=v4.1 MAMAIAMALRRLPSSFDKPLRPALFKATSLYYMSSLPDEAVYEKEKPGVTWPKQLNAPLEVVDPQIADIIELEKARQWKGLELIPSENFTSVSVMQAVGS VMTNKYSEGYPGARYYGGNEFIDMAESLCQKRALEAFRLDPAKWGVNVQSLSGSPSNFQVYTALLKPHERIMALDLPHGGHLSHGYQTDTKKISAVSIFF ETMPYRLNESTGYIDYDQLEKSATLFRPKLIVAGASAYARLYDYARIRKVCDKQKAILLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPRGAMI FFRKGLKEVNKQGKEVFYDYEDKINQAVFPGLQGGPHNHTIAGLAVALKQATTLEYKAYQEQVLSNCSKFAQSLVEKGYELVSGGTENHLVLVNLKNKGI DGSRVEKVLESVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFVEEDFAKVADFFDASVKLAVKMKAETKGTKLKDFLVTMQSAHFQSEISKLRHEVE EYAKQFPTIGFNKETMKYKN

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DESeq2's median of ratios [POPLAR]

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

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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	NWA:WT	NWB:WT	NWA:OE-ARK2	NWB:OE-ARK2	NWA:miRNA-ARK2	NWB:miRNA-ARK2	NW 0hr	WT H20	WT-NW	TUA1dEY NW	TUA1dEY+TUB15 NW	TUA1dY+TUB9 NW	Pde NW	NWA:WT GA	NWBWT GA	TW:WT	TW:WT GA	NWA:OE-ARK2 GA	NWB:OE-ARK2 GA	TW:OE-ARK2	TW:OE-ARK2 GA	NWA:miRNA-ARK2 GA	NWB:miRNA-ARK2 GA	TW:miRNA-ARK2	TW:miRNA-ARK2 GA	TW 2hr	TW 8hr	TW 24hr	TW 48hr	TW 96hr	TW 336hr	WT ACC	35S::etr1-1 H20	35S::etr1-1 ACC	LMX5::etr1-1 H20	LMX5::etr1-1 ACC	WT-TW	TUA1dEY TW	TUA1dEY+TUB15 TW	TUA1dY+TUB9 TW	Pde TW	OW:WT	OW:WT GA	OW:OE-ARK2	OW:OE-ARK2 GA	OW:miRNA-ARK2	OW:miRNA-ARK2 GA	OW 2hr	OW 8hr	OW 24hr	OW 48hr	OW 96hr	OW 336hr	Root CTR	Root LongCold	Root LongDrougt	Root LongHeat	Root LongSalt	Root ShortCold	Root ShortDrougt	Root ShortHeat	Root ShortSalt	Ptr root	Leaf CTR	Leaf LongCold	Leaf LongDrougt	Leaf LongHeat	Leaf LongSalt	Leaf ShortCold	Leaf ShortDrougt	Leaf ShortHeat	Leaf ShortSalt	Ptr leaf	Stem CTR	Stem LongCold	Stem LongDrougt	Stem LongHeat	Stem LongSalt	Stem ShortCold	Stem ShortDrougt	Stem ShortHeat	Stem ShortSalt	Ptr shoot	Ptr xylem	Ptr phloem	Ptr fiber	Ptr vessel	Ptr fiber vessel ray
AT4G37930		SHMT1, STM, SHM...	SERINE HYDROXYMETHYLTRANSFERAS...		Potri.008G002900 [exp]	0	1	SHMT2,SHM1.2
AT5G66190		ATLFNR1	ferredoxin-NADP\(+\)-oxidoredu...		Potri.005G112900 [exp]	1.00	0.9852
AT4G23420			NAD(P)-binding Rossmann-fold s...		Potri.015G146600 [exp]	3.16	0.9740
AT4G31530			NAD(P)-binding Rossmann-fold s...		Potri.001G253900 [exp]	3.46	0.9793
AT5G58330			lactate/malate dehydrogenase f...		Potri.008G031700 [exp]	5.19	0.9781
AT3G05270			Plant protein of unknown funct...		Potri.005G178100 [exp]	8.66	0.9544
AT3G02730		TRXF1, ATF1	thioredoxin F-type 1 (.1)		Potri.019G054800 [exp]	9.00	0.9740	PtrcTrxf
AT5G03880			Thioredoxin family protein (.1...		Potri.006G213000 [exp]	9.79	0.9742
AT2G28800		ABL3, ALB3	ALBINO 3, 63 kDa inner membran...		Potri.001G237800 [exp]	9.89	0.9751	ALB3.2
AT3G63490		EMB3126	EMBRYO DEFECTIVE 3126, Ribosom...		Potri.001G262400 [exp]	10.39	0.9760	RPL1.2
AT1G70760		NdhL, CRR23	NADH dehydrogenase-like comple...		Potri.010G110400 [exp]	10.72	0.9758

Compare expression of checked genes

Potri.008G002900 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.