Plant FIBer expression Database

External link	JGI Phytozome v13 [genome browser] Popgenie AspWood
Symbol	SHMT4
Arabidopsis homologues Show only best Show top 10	Locus ID BLAST score/e-value TF class Alias TAIR10 short description AT1G36370 810 / 0 SHM7 serine hydroxymethyltransferase 7 (.1) AT1G22020 781 / 0 SHM6 serine hydroxymethyltransferase 6 (.1) AT4G13930 615 / 0 SHM4 serine hydroxymethyltransferase 4 (.1) AT4G13890 600 / 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) AT4G32520 488 / 2e-168 AtSHMT3, SHM3 serine hydroxymethyltransferase 3 (.1.2) AT4G37930 487 / 4e-168 SHMT1, STM, SHM1 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) AT5G26780 480 / 2e-165 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 Potri.005G170800 [exp] 1035 / 0 AT1G36370 837 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.001G212000 [exp] 793 / 0 AT1G36370 798 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.001G320400 [exp] 624 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.017G059300 [exp] 624 / 0 AT4G13930 868 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.006G232300 [exp] 493 / 3e-170 AT4G32520 869 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Potri.002G109200 [exp] 481 / 5e-166 AT5G26780 904 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Potri.010G254700 [exp] 478 / 1e-164 AT4G37930 918 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Potri.008G002900 [exp] 477 / 3e-164 AT4G37930 933 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.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 Lus10015471 [exp] 773 / 0 AT1G36370 819 / 0.0 serine hydroxymethyltransferase 7 (.1) Lus10019942 [exp] 771 / 0 AT1G36370 817 / 0.0 serine hydroxymethyltransferase 7 (.1) Lus10022557 [exp] 623 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10043157 [exp] 621 / 0 AT4G13930 865 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10022391 [exp] 482 / 5e-166 AT4G32520 828 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10005916 [exp] 482 / 6e-166 AT4G32520 823 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10028218 [exp] 481 / 8e-166 AT5G26780 903 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Lus10042923 [exp] 473 / 1e-162 AT4G37930 881 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10039629 [exp] 468 / 1e-160 AT4G37930 933 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10029559 [exp] 467 / 2e-160 AT4G37930 900 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.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.002G090200.1 pacid=42779483 polypeptide=Potri.002G090200.1.p locus=Potri.002G090200 ID=Potri.002G090200.1.v4.1 annot-version=v4.1 ATGGATTTAACACAAGCAGCGCAATCAGGTCTCTCGCTTCGATTTCACTCAAGTTCAATTCCAATTCAACTGCAATTACTCGATCAAAAACAAGAGACCC ACATCGATAACGAAGAAAACCAAACAGAAGATGAACAATTTAGCATTTTGGGTCATCAAGTGTGTATAAAGAGACCAAGAGATAACAGTTCTCAATCATC ATCTTCATCATCGACGACAAGTTCTTCCAAACGGGTTGCTATGGATCCGGGTTTGGAGTCTCGTCGGGCCATGGTTCGGGCATGGGGTAACCACCGTCTT CCCGTCGCGGATCCTGAAATTCATGAGATTATGGAGAAAGAGAAGCAAAGGCAGTTTAAAGGTATTGAATTGATTGCATCTGAGAATTTTGTTTGCCGTG CAGTTATGGAAGCTCTTGGTAGTCATTTAACTAATAAATATTCGGAGGGATTGCCTGGTTCCAGATACTATACGGGAAATCAATATATTGATCAAATTGA ATTGATTTGTTGGAGCCGCGCGCTGGCAGCTTTTGGACTTGATTCTGATAAATGGGGTGTTAATGTGCAGCCATATTCGTGTACTTCAGCGAATTTTTCT GTTTTCACTGGGCTTTTATTGCCTGGGGATAGGATCATGGGGTTAGACTCGCCTTCTGGAGGGCATTTAAGTCATGGGTATTATACACCTGGAGGGAAGA ATGTGTCAGCTTCGTCAATATTTTTTGAGAGTCTGCCATATAAAGTGAATCCACAAACCGGGTATATTGATTATGATAAGATGGAGGAGAAGGCTATGGA TTTTAGACCTAAGATACTGATCTGTGGTGGGAGTTCGTACCCGAGGGAGTGGGATTATGCGAGGTTTAGACAAGTTGCTGATAAGATTGGTGCTGTTTTG ATGTGTGATATGGCTCACATTAGCGGGCTCGTAGCAGCTAAGGAATGTGTAAGTCCATTTGAATATTGTGATATTGTTACCTCTACAACACACAAAAGTC TTCGAGGTCCTAGAGGGGGGATTATTTTTTATAGGAAAGGCCCAAAATTGAGGAAGCAGGGCATGCTTCTTAGTCATGGTGATGGTATCAGCCATTATGA TTTTGAAGAAAAGATAAATTTTGCAGTCCATCCATCAACACAAGGGGGTCCTCACAATAATCACATCGCTGCTCTTGCCATAGCCTTAAAACAAGTGGCC ACACCAGAGTACAAAGCATATATGCAACAGGTGAGGAAAAATGCTCAGGCATTAGCATCTGCTTTGTTGAGAAGAAAATGCAGACTCGTGACTGGTGGGA CTGATAACCATTTGTTGCTGTGGGATCTAACTACTTGGGGATTAACAGGCAAGTGTTATGAGAAGGTGTGTGAAATGTGCCACATCACTCTAAATAAAAG TGCCATATTTGGTGACAATGGTGCGATCTGTCCTGGAGGAGTGAGAATTGGTGCTCCTGCTATGACATCAAGAGGTTGCATAGAGGCTGATTTTGAGACG ATTGCTGACTTTCTTCTTAAGGCTGCTCAGATTACTACTGTTGTGCAGAGGGAACATGGAAAAAAGGATTTCCTCAAAGGTCTTCATAACAATAGAGATA TTGTTGAGCTTCGAAACCGGGTTGAGATTTTTGCTTCTCAGTTTGCCATGCCAGGATTTGACATTTGA
AA sequence Show only first row Show all	>Potri.002G090200.1 pacid=42779483 polypeptide=Potri.002G090200.1.p locus=Potri.002G090200 ID=Potri.002G090200.1.v4.1 annot-version=v4.1 MDLTQAAQSGLSLRFHSSSIPIQLQLLDQKQETHIDNEENQTEDEQFSILGHQVCIKRPRDNSSQSSSSSSTTSSSKRVAMDPGLESRRAMVRAWGNHRL PVADPEIHEIMEKEKQRQFKGIELIASENFVCRAVMEALGSHLTNKYSEGLPGSRYYTGNQYIDQIELICWSRALAAFGLDSDKWGVNVQPYSCTSANFS VFTGLLLPGDRIMGLDSPSGGHLSHGYYTPGGKNVSASSIFFESLPYKVNPQTGYIDYDKMEEKAMDFRPKILICGGSSYPREWDYARFRQVADKIGAVL MCDMAHISGLVAAKECVSPFEYCDIVTSTTHKSLRGPRGGIIFYRKGPKLRKQGMLLSHGDGISHYDFEEKINFAVHPSTQGGPHNNHIAALAIALKQVA TPEYKAYMQQVRKNAQALASALLRRKCRLVTGGTDNHLLLWDLTTWGLTGKCYEKVCEMCHITLNKSAIFGDNGAICPGGVRIGAPAMTSRGCIEADFET IADFLLKAAQITTVVQREHGKKDFLKGLHNNRDIVELRNRVEIFASQFAMPGFDI

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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
AT1G36370		SHM7	serine hydroxymethyltransferas...		Potri.002G090200 [exp]	0	1	SHMT4
AT2G36220			unknown protein		Potri.016G079500 [exp]	2.00	0.9178
AT1G36370		SHM7	serine hydroxymethyltransferas...		Potri.005G170800 [exp]	4.24	0.8901
AT5G60680			Protein of unknown function, D...		Potri.004G211100 [exp]	4.35	0.8716
AT2G31305		INH3	inhibitor-3 (.1)		Potri.005G067400 [exp]	7.14	0.9018
AT5G43210			Excinuclease ABC, C subunit, N...		Potri.001G260600 [exp]	8.06	0.8953
AT1G07310			Calcium-dependent lipid-bindin...		Potri.001G249300 [exp]	8.12	0.8870
AT2G32840			proline-rich family protein (....		Potri.001G229800 [exp]	8.94	0.8954
AT3G07790			DGCR14-related (.1)		Potri.014G164200 [exp]	10.19	0.8922
AT5G16220			Octicosapeptide/Phox/Bem1p fam...		Potri.017G119100 [exp]	11.18	0.8655
AT2G44200			CBF1-interacting co-repressor ...		Potri.006G000200 [exp]	11.83	0.8879

Compare expression of checked genes

Potri.002G090200 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.