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 AT4G32520 811 / 0 AtSHMT3, SHM3 serine hydroxymethyltransferase 3 (.1.2) AT4G37930 580 / 0 SHMT1, STM, SHM1 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) AT5G26780 574 / 0 SHM2 serine hydroxymethyltransferase 2 (.1.2.3) AT4G13930 548 / 0 SHM4 serine hydroxymethyltransferase 4 (.1) AT4G13890 538 / 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 490 / 1e-168 SHM6 serine hydroxymethyltransferase 6 (.1) AT1G36370 479 / 2e-164 SHM7 serine hydroxymethyltransferase 7 (.1)
Paralogs Show only best Show top 10	Gene ID BLAST score/e-value At best hit BLAST score/e-value TAIR10 short description Lus10022391 [exp] 1021 / 0 AT4G32520 828 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10039629 [exp] 578 / 0 AT4G37930 933 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10029559 [exp] 577 / 0 AT4G37930 900 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10028218 [exp] 562 / 0 AT5G26780 903 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Lus10042923 [exp] 559 / 0 AT4G37930 881 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10043157 [exp] 553 / 0 AT4G13930 865 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10022557 [exp] 540 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10019942 [exp] 479 / 3e-164 AT1G36370 817 / 0.0 serine hydroxymethyltransferase 7 (.1) Lus10015471 [exp] 476 / 4e-163 AT1G36370 819 / 0.0 serine hydroxymethyltransferase 7 (.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.006G232300 [exp] 877 / 0 AT4G32520 869 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Potri.002G109200 [exp] 578 / 0 AT5G26780 904 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Potri.010G254700 [exp] 578 / 0 AT4G37930 918 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Potri.008G002900 [exp] 573 / 0 AT4G37930 933 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Potri.017G059300 [exp] 556 / 0 AT4G13930 868 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.001G320400 [exp] 551 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.005G170800 [exp] 501 / 2e-173 AT1G36370 837 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.002G090200 [exp] 498 / 2e-172 AT1G36370 809 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.001G212000 [exp] 479 / 2e-164 AT1G36370 798 / 0.0 serine hydroxymethyltransferase 7 (.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	>Lus10005916 pacid=23140113 polypeptide=Lus10005916 locus=Lus10005916.g ID=Lus10005916.BGIv1.0 annot-version=v1.0 ATGCAGACTTGCGCCGGAACTGCACTCACCGGTTCTCTACAACAGCCCATTTGGAGCAATGGAACAAGGCTTGTCGTTCCCAAAAATTCTGGCTTTGGTC TGTTCCGAAACCAGGTTAAGCTCAAATCCCTGAAACCCTGCAAATCTTCCAACCTTGAAGGCAGCTTTGTGACTGGCAGGCCTCCCTCTTCCGTATCTGT TCCAATTCCGGAAATTGAAGGAGGTCATAAGAGTGGGTTCCAGGACCATGCCCTCAGTAATGCTGATCCAGCTGTTCATGAGATTATCAGTAAGGAAAAA GATAGGCAATTCAAAAGCCTTGCGCTCATTGCCTCCGAGAATTTTACTTCTCGGGCGGTTATGGAAGCTGTTGGCTCATGTCTGACCAACAAGTACTCTG AAGGACTGCCTGGTAAAAGATACTATGGTGGAAATGAATTTATTGATGAGCTTGAAACACTTTGTCAAGAAAGAGCTTTAGCTGCTTTTCACTTGGATGG CAACAAGTGGGGTGTCAATGTACAACCATTGTCTGGCTCACCTGCTAATTTTGAGGTTTACACGGCAATTCTTAAGCCACACGATCGAATCATGGGTTTG GATTTGCCTCATGGAGGTCATTTAACTCATGGGTTCATGACTCGTACGAGGAGGGTGTCTGCCACTTCGGTATATTTCGAGTCCATGCCATACCGGCTTG ATGAGTCTACAGGTCTGATTGATTATGATAAGCTTGAAGAGAATGCTAATCTGTTTCGACCTAAACTTATTATTGTGGGAGCTAGTGCTTATCCCCGAGA TTTTGATTATCCTCGCATGAGGAAAATAGCGGATTCTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATAAGTGGACTAGTTGCTGCGTCTGTCATT GCTGATCCTTTTGAATACTGCGACATTGTAACGACAACCACACACAAGTCGCTACGAGGTCCAAGAGGTGGAATGATTTTCTTCAGAAGAGATCCTGTTC TTGGTGTTGATTTGGAAACGGCCATCAACAATTCTGTTTTCCCAGGCTTGCAGGGCGGTCCCCATAACCACACGATCGGAGCACTAGCTGTTTGCTTGAA GCATGCTCAATCCCCTTCATTCCAAACCTATCAGAAGCAGGTCATTTCTAATTGTAGGGCGCTTGCACAACGATTGGGTGAATTGGGATATAAGCTTGTT TCTGGTGGCAGTGACAACCATCTTGTTCTTGTAGATCTCAGGCCAATGGGAGTTGATGGAGCTCGGGTCGAAAAGATTCTTGACATGGCATTTATTACAC TCAACAAGAACTCGGTGCCTGGTGATAAGAGTGCGCTGATGCCGGGTGGAATTCGTATTGGATCGCCTGCCATGACTACAAGGGGATTCAAGGAGAGGGA ATTCGTGGCAACAGCTGACTTGATTCATGAGGGCGTGCGGATAACACTGGAAGCTAAATCACTAGCATCAGGGTCAAAGCTGCAGGACTTCTTGAAGTTT GTTTCGTCTCCAGAGTTCCCGCTGAAAGATAAGTTGTTGGATCTCCAGAAACGTGTTGAAGCGCTTACAACCCAGTTTCCTATTCCCGGGATATGA
AA sequence Show only first row Show all	>Lus10005916 pacid=23140113 polypeptide=Lus10005916 locus=Lus10005916.g ID=Lus10005916.BGIv1.0 annot-version=v1.0 MQTCAGTALTGSLQQPIWSNGTRLVVPKNSGFGLFRNQVKLKSLKPCKSSNLEGSFVTGRPPSSVSVPIPEIEGGHKSGFQDHALSNADPAVHEIISKEK DRQFKSLALIASENFTSRAVMEAVGSCLTNKYSEGLPGKRYYGGNEFIDELETLCQERALAAFHLDGNKWGVNVQPLSGSPANFEVYTAILKPHDRIMGL DLPHGGHLTHGFMTRTRRVSATSVYFESMPYRLDESTGLIDYDKLEENANLFRPKLIIVGASAYPRDFDYPRMRKIADSVGAFLMMDMAHISGLVAASVI ADPFEYCDIVTTTTHKSLRGPRGGMIFFRRDPVLGVDLETAINNSVFPGLQGGPHNHTIGALAVCLKHAQSPSFQTYQKQVISNCRALAQRLGELGYKLV SGGSDNHLVLVDLRPMGVDGARVEKILDMAFITLNKNSVPGDKSALMPGGIRIGSPAMTTRGFKEREFVATADLIHEGVRITLEAKSLASGSKLQDFLKF VSSPEFPLKDKLLDLQKRVEALTTQFPIPGI

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DESeq2's median of ratios [FLAX]

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	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
AT4G32520		AtSHMT3, SHM3	serine hydroxymethyltransferas...		Lus10005916 [exp]	0	1
AT5G14520			pescadillo-related (.1)		Lus10002201 [exp]	2.2	0.9126
AT3G16260		TRZ4	tRNAse Z4 (.1)		Lus10038290 [exp]	3.0	0.9066
AT3G12270		ATPRMT3	ARABIDOPSIS THALIANA PROTEIN A...		Lus10026158 [exp]	3.5	0.9139
AT2G34357			ARM repeat superfamily protein...		Lus10041231 [exp]	4.2	0.9111
AT2G21440			RNA-binding (RRM/RBD/RNP motif...		Lus10022044 [exp]	4.4	0.9229
AT5G52820			WD-40 repeat family protein / ...		Lus10029493 [exp]	4.6	0.9106
AT1G24090			RNase H family protein (.1)		Lus10020869 [exp]	4.6	0.9136
AT4G30930		WRKY32, NFD1	NUCLEAR FUSION DEFECTIVE 1, Ri...		Lus10011178 [exp]	5.3	0.8986
AT2G44040			Dihydrodipicolinate reductase,...		Lus10041701 [exp]	6.9	0.8967
AT4G35910			Adenine nucleotide alpha hydro...		Lus10018066 [exp]	7.2	0.9003

Compare expression of checked genes

Lus10005916 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.