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 AT5G26780 872 / 0 SHM2 serine hydroxymethyltransferase 2 (.1.2.3) AT4G37930 867 / 0 SHMT1, STM, SHM1 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) AT4G32520 561 / 0 AtSHMT3, SHM3 serine hydroxymethyltransferase 3 (.1.2) AT4G13930 542 / 0 SHM4 serine hydroxymethyltransferase 4 (.1) AT4G13890 518 / 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 467 / 7e-160 SHM7 serine hydroxymethyltransferase 7 (.1) AT1G22020 460 / 6e-157 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 Lus10042923 [exp] 994 / 0 AT4G37930 881 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10039629 [exp] 832 / 0 AT4G37930 933 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10029559 [exp] 819 / 0 AT4G37930 900 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Lus10022391 [exp] 551 / 0 AT4G32520 828 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10005916 [exp] 550 / 0 AT4G32520 823 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Lus10043157 [exp] 547 / 0 AT4G13930 865 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10022557 [exp] 534 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Lus10019942 [exp] 474 / 1e-162 AT1G36370 817 / 0.0 serine hydroxymethyltransferase 7 (.1) Lus10015471 [exp] 473 / 2e-162 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.002G109200 [exp] 916 / 0 AT5G26780 904 / 0.0 serine hydroxymethyltransferase 2 (.1.2.3) Potri.010G254700 [exp] 888 / 0 AT4G37930 918 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Potri.008G002900 [exp] 882 / 0 AT4G37930 933 / 0.0 SERINE HYDROXYMETHYLTRANSFERASE 1, serine transhydroxymethyltransferase 1 (.1) Potri.006G232300 [exp] 559 / 0 AT4G32520 869 / 0.0 serine hydroxymethyltransferase 3 (.1.2) Potri.001G320400 [exp] 548 / 0 AT4G13930 874 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.017G059300 [exp] 545 / 0 AT4G13930 868 / 0.0 serine hydroxymethyltransferase 4 (.1) Potri.005G170800 [exp] 481 / 4e-166 AT1G36370 837 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.002G090200 [exp] 480 / 1e-165 AT1G36370 809 / 0.0 serine hydroxymethyltransferase 7 (.1) Potri.001G212000 [exp] 477 / 4e-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	>Lus10028218 pacid=23166488 polypeptide=Lus10028218 locus=Lus10028218.g ID=Lus10028218.BGIv1.0 annot-version=v1.0 ATGGCGTCCATGGCTCTTCGCAGGCTCTCCTACTCTCCCATCAGACCTTACTGCAATGGCGGTTCCCTGTATTCCATGTCTTCCTTGCCTAATCAGGCAG TTTCCGACAAAGACTCTGCTCGCGCCACCTGGATAAAGCAATTGAATGCACCGCTGGAGGAAATCGATCCGGAAATAGCTGACATTATTGAGCATGAGAA AGCCAGACAATGGAAGGGACTTGAACTCATCCCTTCAGAAAATTTCACATCAGTTTCCGTGATGCAAGCTGTAGGTTCTGTTATGACCAATAAATACAGT GAGGGTTACCCTGGAGCAAGATACTATGGTGGAAACGAGTACATTGATATGGCTGAGAGATTGTGCCAAAAGCGTGCTTTAGAAGCCTTTGAGCTGGATC CTGAAAAATGGGGAGTTAATGTCCAGTCACTATCTGGGTCTCCAGCCAATTTTCAAGTTTACACTGCCTTGTTGAAACCGCATGAGAGAATCATGGCATT GGATCTACCTCATGGAGGCCATCTTTCACATGGTTATCAGACTGATACGAAGAAGATATCTGCTGTGTCCATATTTTTTGAGACAATGCCCTATAGATTA AACGAGACAACAGGTTATATTGACTATGATCAGTTAGAGAAAAGTGCTGCACTCTTTAGACCAAAACTTGTAGTTGCTGGTGCAAGCGCTTATGCACGTC TTTACGACTATGCTCGCATCCGCGAAGTCTGCGACAAGCAAAAAGCTATCTTGTTAGCCGATATGGCACACATTAGTGGGTTGGTAGCAGGTGGTGTCAT CCCATCTCCTTTCGAATATGCTGATGTTGTGACCACCACAACTCACAAGTCACTTCGTGGTCCTCGTGGAGCTATGATATTCTTCAGGAAAGGGTTAAAA GAAGTTAACAAAAAAGGGCAAGAAGTGATGTATGATTATGAAGATAAAATTAACGCAGCGGTCTTTCCTGGACTTCAAGGAGGTCCACACAATCACACAA TTACCGCATTGGCAGTTGCACTGAAGCAGGTCAAAAGCCCCGAATATAAAGCCTACCAAGAGCAAGTCCTCAGTAACAGTTCAAAGTTTGCACAGAGCTT GCTAGATAAAGGTTATGACATTGTATCTGGTGGGACAGAGAACCATTTAGTCTTGGTGAATCTGAAAAATAAGGGCATTGATGGATCCAGAGTTGAAAAG GTCATGGAATCAGTTCATATTGCAGCAAATAAGAACACAGTCCCTGGGGATGTGTCAGCCATGGTTCCGGGCGGTGTTCGTATGGGAACTCCGGCTCTGA CATCAAGGGGCTTCGTTGAGAAAGACTTTGAGAAAGTAGCAGAGTTCTTTGATGCAGCTGTAAAGTTGGCCTTGAAGATCAAAGCTGAATCCAAAGGACC GAAGCTGAAGGATTTCAGTGCCGCTCTAACGTCAGATGCATTCAAATCCGAGATCTCTAACCTGCGCGGAGATGTTGAGGAGTACGCTAAGCAGTTTCCC ACAGTTGGGTTCGAGAAGGAAACAATGAAATACAAAGACTAA
AA sequence Show only first row Show all	>Lus10028218 pacid=23166488 polypeptide=Lus10028218 locus=Lus10028218.g ID=Lus10028218.BGIv1.0 annot-version=v1.0 MASMALRRLSYSPIRPYCNGGSLYSMSSLPNQAVSDKDSARATWIKQLNAPLEEIDPEIADIIEHEKARQWKGLELIPSENFTSVSVMQAVGSVMTNKYS EGYPGARYYGGNEYIDMAERLCQKRALEAFELDPEKWGVNVQSLSGSPANFQVYTALLKPHERIMALDLPHGGHLSHGYQTDTKKISAVSIFFETMPYRL NETTGYIDYDQLEKSAALFRPKLVVAGASAYARLYDYARIREVCDKQKAILLADMAHISGLVAGGVIPSPFEYADVVTTTTHKSLRGPRGAMIFFRKGLK EVNKKGQEVMYDYEDKINAAVFPGLQGGPHNHTITALAVALKQVKSPEYKAYQEQVLSNSSKFAQSLLDKGYDIVSGGTENHLVLVNLKNKGIDGSRVEK VMESVHIAANKNTVPGDVSAMVPGGVRMGTPALTSRGFVEKDFEKVAEFFDAAVKLALKIKAESKGPKLKDFSAALTSDAFKSEISNLRGDVEEYAKQFP TVGFEKETMKYKD

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DESeq2's median of ratios [FLAX]

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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
AT5G26780		SHM2	serine hydroxymethyltransferas...		Lus10028218 [exp]	0	1
AT4G37930		SHMT1, STM, SHM...	SERINE HYDROXYMETHYLTRANSFERAS...		Lus10042923 [exp]	1.0	0.9588
AT5G50090			unknown protein		Lus10043461 [exp]	2.4	0.9146
AT3G23690	bHLH	bHLH077	basic helix-loop-helix (bHLH) ...		Lus10021968 [exp]	3.5	0.9207
AT3G06350		EMB3004, MEE32	MATERNAL EFFECT EMBRYO ARREST ...		Lus10033981 [exp]	4.7	0.8842
AT3G23090			TPX2 (targeting protein for Xk...		Lus10021223 [exp]	4.9	0.8946
AT3G23690	bHLH	bHLH077	basic helix-loop-helix (bHLH) ...		Lus10041261 [exp]	7.2	0.8946
AT4G19670			RING/U-box superfamily protein...		Lus10040616 [exp]	8.1	0.9084
AT5G03300		ADK2	adenosine kinase 2 (.1)		Lus10023532 [exp]	8.9	0.9143
AT1G10750			Protein of Unknown Function (D...		Lus10013046 [exp]	9.2	0.8297
AT5G06940			Leucine-rich repeat receptor-l...		Lus10040500 [exp]	9.5	0.8995

Compare expression of checked genes

Lus10028218 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.