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 AT5G27720 188 / 1e-57 LSM4, EMB1644 SM-like protein 4, embryo defective 1644, Small nuclear ribonucleoprotein family protein (.1) AT3G11530 171 / 2e-51 Vacuolar protein sorting 55 (VPS55) family protein (.1), Vacuolar protein sorting 55 (VPS55) family protein (.2) AT5G06210 129 / 3e-35 RNA binding (RRM/RBD/RNP motifs) family protein (.1) AT5G06220 125 / 5e-30 LETM1-like protein (.1.2) AT1G32410 113 / 2e-29 Vacuolar protein sorting 55 (VPS55) family protein AT3G11560 119 / 6e-28 LETM1-like protein (.1.2.3.4) AT3G46020 81 / 2e-18 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) AT4G13860 80 / 4e-18 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) AT2G27330 79 / 9e-18 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) AT4G20030 80 / 2e-17 RNA-binding (RRM/RBD/RNP motifs) family protein (.1)
Paralogs Show only best Show top 10	Gene ID BLAST score/e-value At best hit BLAST score/e-value TAIR10 short description Lus10004221 [exp] 397 / 1e-135 AT5G27720 182 / 2e-57 SM-like protein 4, embryo defective 1644, Small nuclear ribonucleoprotein family protein (.1) Lus10004224 [exp] 149 / 2e-43 AT5G06210 96 / 1e-26 RNA binding (RRM/RBD/RNP motifs) family protein (.1) Lus10021329 [exp] 144 / 5e-36 AT3G11560 976 / 0.0 LETM1-like protein (.1.2.3.4) Lus10017005 [exp] 141 / 4e-35 AT3G11560 975 / 0.0 LETM1-like protein (.1.2.3.4) Lus10006605 [exp] 110 / 3e-27 AT1G32410 202 / 4e-67 Vacuolar protein sorting 55 (VPS55) family protein Lus10013306 [exp] 84 / 4e-19 AT5G06210 94 / 3e-25 RNA binding (RRM/RBD/RNP motifs) family protein (.1) Lus10003980 [exp] 81 / 8e-18 AT2G37510 169 / 1e-54 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) Lus10023758 [exp] 80 / 2e-17 AT2G37510 164 / 9e-53 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) Lus10025835 [exp] 84 / 1e-16 AT1G52155 353 / 2e-114 unknown protein
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.002G205700 [exp] 184 / 7e-56 AT5G27720 179 / 5e-59 SM-like protein 4, embryo defective 1644, Small nuclear ribonucleoprotein family protein (.1) Potri.014G130700 [exp] 181 / 1e-54 AT5G27720 176 / 7e-58 SM-like protein 4, embryo defective 1644, Small nuclear ribonucleoprotein family protein (.1) Potri.006G209100 [exp] 173 / 3e-52 AT3G11530 210 / 3e-72 Vacuolar protein sorting 55 (VPS55) family protein (.1), Vacuolar protein sorting 55 (VPS55) family protein (.2) Potri.006G208500 [exp] 142 / 5e-40 AT5G06210 160 / 1e-51 RNA binding (RRM/RBD/RNP motifs) family protein (.1) Potri.001G146600 [exp] 116 / 1e-30 AT1G32410 176 / 6e-58 Vacuolar protein sorting 55 (VPS55) family protein Potri.016G074900 [exp] 125 / 3e-30 AT3G11560 1033 / 0.0 LETM1-like protein (.1.2.3.4) Potri.006G208300 [exp] 124 / 7e-30 AT3G11560 1056 / 0.0 LETM1-like protein (.1.2.3.4) Potri.003G087500 [exp] 113 / 1e-29 AT1G32410 180 / 1e-59 Vacuolar protein sorting 55 (VPS55) family protein Potri.015G057400 [exp] 84 / 6e-18 AT5G61030 157 / 8e-47 glycine-rich RNA-binding protein 3 (.1) Potri.009G160300 [exp] 79 / 8e-18 AT2G27330 98 / 1e-27 RNA-binding (RRM/RBD/RNP motifs) family protein (.1)
PFAM info	Clan ID Clan name Pfam ID Pfam name Pfam description CL0527 [flax] [poplar] Sm-like PF01423 [flax] [poplar] LSM LSM domain CL0221 [flax] [poplar] RRM PF00076 [flax] [poplar] RRM_1 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) CL0221 [flax] [poplar] PF04133 [flax] [poplar] Vps55 Vacuolar protein sorting 55
Representative CDS sequence Show only first row Show all	>Lus10029426 pacid=23139935 polypeptide=Lus10029426 locus=Lus10029426.g ID=Lus10029426.BGIv1.0 annot-version=v1.0 ATGGTCGTGGAGGAGTTTGTTCCGTCGCCGTCGAAGAAACGGCCGCTGGCTGAGGGGTGGATGGGGGTCCACACGGGGGATCTGAGTTTATGTTTATGGG AATTGGGGAATGTTTCTGACGGCGAGAAAGAAAACATGCACACGTGTGGGTCATCAGCCGCCGGCAAAATAACCGCCGGGGTCAGAGGACCTGATTTGGA AGACCCCACCTTTTCCAACTTCGCTTGTGCAATATACAACAACTGGTGGCCGATGTTATCAGCTCTTATGTACGTGGTAGTGCCTATGCCCTGTCTATTC TTCGGAGGAGGGTCCACTCAATTCCTCACTAGTCGAGACGGTGGCGGTTGGATAGATGCTGCTAAGTTCATGACCGGAGCATCTGCAGTAGGGAGCCTGG CCATTCCTATCATCCTCAGGCACGCTAACATGATCGAAACAGGAGCCATGTTCATCGAGTTCACGTCTTTCTTCATATTCCTTCCTCTTTCTCTGTTGAA GACTGCACAGGGCCATCCAATGTTGGTTGAGCTTAAGAACGGTGAAACTTACAATGGGCATCTGGTCAATTGTGATACTTGGATGAACATTCATCTCCGA GAAGTTATCTGCACCGCAAAGGATGGAGACCGGTTTTGGCGTATGCCTGAATGCTACATTCGTGGGAATACCATCAAGTATCTCAGAGTTCCTGACGAGG TGATTGATAAAGTTCAGGAAGACAAAAGTCGCTCAGGCCACCCTAGTTTATTGTTGGCTTTTCTAATGACTGGTTGCTTTTACGCAGATCGAAAGCCTCC TGGTGTTGGACGTGGCAGAGGAAGGGGCAGAGAAGATGGTCCAGCAGGTGGTAGGGGACCAAACCGCGGTGGAAGCTTTGATGATGGAGCTAATAAAGGT CCGGGTGGAGGCCGTGGCAGAGGTGGTCCTTCTGGTGGGAAGAACAGAGGACTGTCATTTTACACAACCGAGGATGGATTATCCGAGTCGTTTTCTCAGT ATGGTCAAGTTGTCGAAGCCAAGGTTATAACGGACAGAGTCACCAACAAATCAAAGGGGTTTGGTTTCGTAACTTTTGCTTCTGCCAATGAAGCCGAGAA AGCCATAACCGAGATGGACGGGAAGAGTCTGAATGGTCGGGTCATTTTTGTCGATTTCGCGAAAGCTAAATCTAGCTTTGGAGAAGGAATTCCAATCGCT AGAGGACCTCCGGAAGGGCTTCAAACCAACAACAACCCATTGCTGACTTCTGAAACAAATGTGTTGCAAGGAACACAGTTCCTAGTCATTGATATTGGTG CAGCGATGGGGCTGCTTCGACGAGCCTTGATTCGAGATGAGCCGAAAGACAAAGAGAAACGTACTCTTAAAAGAAATGTGACCGATGTTGCATTTGTGGT TCCTATTAGCATTCGCATGCTTCTTCCTCAGAACGTTTATTTAATCTGGGAAAGGTTTGATGCTCGACAGGTTACTGCAGTTGGGCATGCAGCAATGTTA GCTGCAATTCAGCGATATGTACCGGGTTTGGTTAGGTTATATCTGTTGAGACAGCTTGAGAAAGTGAAGCAAATGGATGCCATCGAATCCAATCCCAACG AAAGTGCCGAGACATCTGCTTGA
AA sequence Show only first row Show all	>Lus10029426 pacid=23139935 polypeptide=Lus10029426 locus=Lus10029426.g ID=Lus10029426.BGIv1.0 annot-version=v1.0 MVVEEFVPSPSKKRPLAEGWMGVHTGDLSLCLWELGNVSDGEKENMHTCGSSAAGKITAGVRGPDLEDPTFSNFACAIYNNWWPMLSALMYVVVPMPCLF FGGGSTQFLTSRDGGGWIDAAKFMTGASAVGSLAIPIILRHANMIETGAMFIEFTSFFIFLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLR EVICTAKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQEDKSRSGHPSLLLAFLMTGCFYADRKPPGVGRGRGRGREDGPAGGRGPNRGGSFDDGANKG PGGGRGRGGPSGGKNRGLSFYTTEDGLSESFSQYGQVVEAKVITDRVTNKSKGFGFVTFASANEAEKAITEMDGKSLNGRVIFVDFAKAKSSFGEGIPIA RGPPEGLQTNNNPLLTSETNVLQGTQFLVIDIGAAMGLLRRALIRDEPKDKEKRTLKRNVTDVAFVVPISIRMLLPQNVYLIWERFDARQVTAVGHAAML AAIQRYVPGLVRLYLLRQLEKVKQMDAIESNPNESAETSA

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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
AT5G27720		LSM4, EMB1644	SM-like protein 4, embryo defe...		Lus10029426 [exp]	0	1
AT5G27720		LSM4, EMB1644	SM-like protein 4, embryo defe...		Lus10004221 [exp]	1.4	0.9283
AT1G28490		OSM1, ATSYP61, ...	syntaxin of plants 61 (.1.2)		Lus10017686 [exp]	2.8	0.9356
AT2G27490		ATCOAE	dephospho-CoA kinase family (....		Lus10013897 [exp]	3.2	0.9140
AT1G64750		DSS1(I), ATDSS1...	deletion of SUV3 suppressor 1(...		Lus10030906 [exp]	4.5	0.9020
AT3G16640		TCTP	translationally controlled tum...		Lus10002877 [exp]	4.9	0.9114
AT3G48140			B12D protein (.1)		Lus10042151 [exp]	5.7	0.9204
AT5G53045			unknown protein		Lus10017942 [exp]	5.8	0.8898
AT3G19130		ATRBP47B	RNA-binding protein 47B (.1)		Lus10014029 [exp]	6.0	0.8976
AT5G57860			Ubiquitin-like superfamily pro...		Lus10035816 [exp]	6.3	0.8853
AT3G61113			Ubiquitin related modifier 1 (...		Lus10036551 [exp]	6.5	0.8940

Compare expression of checked genes

Lus10029426 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.