Plant FIBer expression Database

External link	JGI Phytozome v13 [genome browser] Popgenie AspWood
Symbol	SHM4.2
Arabidopsis homologues Show only best Show top 10	Locus ID BLAST score/e-value TF class Alias TAIR10 short description AT4G13930 868 / 0 SHM4 serine hydroxymethyltransferase 4 (.1) AT4G13890 774 / 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) AT1G22020 620 / 0 SHM6 serine hydroxymethyltransferase 6 (.1) AT1G36370 618 / 0 SHM7 serine hydroxymethyltransferase 7 (.1) AT4G32520 571 / 0 AtSHMT3, SHM3 serine hydroxymethyltransferase 3 (.1.2) AT4G37930 555 / 0 SHMT1, STM, SHM1 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) AT5G26780 545 / 0 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.001G320400 [exp] 917 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.002G090200 [exp] 634 / 0 AT1G36370 809 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.005G170800 [exp] 631 / 0 AT1G36370 837 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.001G212000 [exp] 619 / 0 AT1G36370 798 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.006G232300 [exp] 557 / 0 AT4G32520 869 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Potri.002G109200 [exp] 553 / 0 AT5G26780 904 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Potri.010G254700 [exp] 541 / 0 AT4G37930 918 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Potri.008G002900 [exp] 535 / 0 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 Lus10043157 [exp] 868 / 0 AT4G13930 865 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10022557 [exp] 862 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10015471 [exp] 618 / 0 AT1G36370 819 / 0.0 serine hydroxymethyltransferase 7 (.1) Lus10019942 [exp] 618 / 0 AT1G36370 817 / 0.0 serine hydroxymethyltransferase 7 (.1) Lus10028218 [exp] 559 / 0 AT5G26780 903 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Lus10005916 [exp] 555 / 0 AT4G32520 823 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10022391 [exp] 555 / 0 AT4G32520 828 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10032592 [exp] 548 / 0 AT4G13930 561 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10042923 [exp] 547 / 0 AT4G37930 881 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10029559 [exp] 535 / 0 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.017G059300.1 pacid=42813534 polypeptide=Potri.017G059300.1.p locus=Potri.017G059300 ID=Potri.017G059300.1.v4.1 annot-version=v4.1 ATGGATCCAGTAACTGTGTGGGGAAACTCCTCCCTCCAAACAGTTGACCCAGAAATCCACGACTTAATCGAGAAGGAAAAACGCCGCCAATGCAAAGGAA TCGAACTGATCGCATCAGAAAACTTCACTTCTTTCGCCGTTATAGAGGCTCTTGGAAGCGCTCTCACCAACAAGTACTCTGAGGGTATGCCAGGTAACCG CTACTACGGCGGTAATGAATATATTGATGAGATTGAAAATCTCTGCAGAGCTCGGGCCCTTCAAGCTTTTCATTTAGACCCCACTAAATGGGGTGTAAAT GTCCAGCCCTATTCTGGTTCCCCTGCAAATTTCGCTGCGTACACAGCAGTTCTCCAGCCCCATGACAGAATCATGGGCTTGGATTTGCCTTCAGGGGGGC ATTTGACTCATGGGTATTACACATCTGGGGGTAAAAAGATTTCAGCTACCAGTATTTATTTTGAGAGTTTGCCTTACAAGGTGAACCCGCAAACTGGGTT TCTTGATTATGATAGGTTGGAAGAAAAGGCTTTGGATTTTAGGCCTAAGCTTATTATTTGTGGTGGAAGTGCTTATCCTAGAGACTGGGATTATAAGAAG TTTAGATCTGTTGCTGATAAGTGTGGTGCTCTTTTGCTTTGTGACATGGCTCACATCAGTGGCCTTGTTGCTGCTCAGGAAGCTGCCAACCCGTTTGAGT ACTGTGACATAGTCACCACCACTACCCACAAAAGTTTGAGGGGTCCCAGGGCTGGTATGATCTTCTACCGCAAGGGCCCTAAGCCACCCAAGAAGGGTCA GCCGGAGGATGCAGTTTATGACTTTGAAGACAAGATCAACTTTGCAGTTTTCCCATCTCTTCAGGGTGGTCCTCACAACCACCAGATTGGTGCTCTGGCT GTTGCATTGAAACAGGCCCAGAGCCCTGGGTTCAAGGCCTATGCTAAGCAAGTCAAGGCCAATGCAGTTGCCCTTGGAAACTACTTGATGAGCAAGGGAT ACAAGCTTGTTACTGAAGGCACCGAGAACCACCTTGTTCTGTGGGATCTTAGGCCCCTTGGGTTGACAGGCAACAAGGTTGAAAAACTATGTGACCTTGC AAACATCACTGTGAACAAGAATGCCGTGTTTGGTGACAGCAGTGCTTTGGCACCTGGTGGAGTGAGAATCGGTGCCCCCGCCATGACTTCTAGAGGTTTG GTTGAGAAGGATTTCGAGCAGATTGGAGAATTCCTCCACCGTGCTGTGACCATCACACTGAGCATCCAAAAGGAACATGGAAAGCTCTTGAAGGACTTCA ACAAGGGTCTGGTGAACAACAAGGAAATCGAGGCCCTCAAGGCTGATGTTGAACAGTTCTCAGGCTCCTTTGAGATGCCTGGCTTTCTGATGTCTGAGAT GAAGTATAAGGATTAG
AA sequence Show only first row Show all	>Potri.017G059300.1 pacid=42813534 polypeptide=Potri.017G059300.1.p locus=Potri.017G059300 ID=Potri.017G059300.1.v4.1 annot-version=v4.1 MDPVTVWGNSSLQTVDPEIHDLIEKEKRRQCKGIELIASENFTSFAVIEALGSALTNKYSEGMPGNRYYGGNEYIDEIENLCRARALQAFHLDPTKWGVN VQPYSGSPANFAAYTAVLQPHDRIMGLDLPSGGHLTHGYYTSGGKKISATSIYFESLPYKVNPQTGFLDYDRLEEKALDFRPKLIICGGSAYPRDWDYKK FRSVADKCGALLLCDMAHISGLVAAQEAANPFEYCDIVTTTTHKSLRGPRAGMIFYRKGPKPPKKGQPEDAVYDFEDKINFAVFPSLQGGPHNHQIGALA VALKQAQSPGFKAYAKQVKANAVALGNYLMSKGYKLVTEGTENHLVLWDLRPLGLTGNKVEKLCDLANITVNKNAVFGDSSALAPGGVRIGAPAMTSRGL VEKDFEQIGEFLHRAVTITLSIQKEHGKLLKDFNKGLVNNKEIEALKADVEQFSGSFEMPGFLMSEMKYKD

---

DESeq2's median of ratios [POPLAR]

Mapped by: StringTie Salmon 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	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
AT4G13930		SHM4	serine hydroxymethyltransferas...		Potri.017G059300 [exp]	0	1	SHM4.2
AT2G32720		B5 #4, B5#4, AT...	ARABIDOPSIS CYTOCHROME B5 ISOF...		Potri.002G242500 [exp]	1.73	0.9389
AT3G57690		AGP23, ATAGP23	ARABINOGALACTAN-PROTEIN 23, ar...		Potri.016G052001 [exp]	4.69	0.8897
AT1G18290			unknown protein		Potri.015G036800 [exp]	4.89	0.8947
AT3G17390		MAT4, SAMS3, MT...	S-ADENOSYLMETHIONINE SYNTHETAS...		Potri.013G004100 [exp]	5.29	0.8954	AdoMet_e2,Pt-SAMS.1
AT3G03550			RING/U-box superfamily protein...		Potri.013G073500 [exp]	5.74	0.9046
AT1G52150	HD	ATHB15, ICU4, C...	INCURVATA 4, CORONA, Homeobox-...		Potri.001G188800 [exp]	5.91	0.8969	ATHB.12
AT4G27880			Protein with RING/U-box and TR...		Potri.012G015500 [exp]	6.48	0.9062	SINAT4.2
AT3G12955			SAUR-like auxin-responsive pro...		Potri.011G143400 [exp]	7.07	0.8909	SAUR5
AT2G28310			Protein of unknown function (D...		Potri.009G011000 [exp]	10.19	0.9045
AT5G03530		ATRABALPHA, AtR...	ARABIDOPSIS THALIANA RAB GTPAS...		Potri.010G229600 [exp]	10.81	0.8937	RAB1.1

Compare expression of checked genes

Potri.017G059300 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.