Plant FIBer expression Database

External link	JGI Phytozome v13 [genome browser] Popgenie AspWood
Symbol
Arabidopsis homologues Show only best Show top 10	Locus ID BLAST score/e-value TF class Alias TAIR10 short description AT3G52660 422 / 2e-144 RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2) AT4G00830 404 / 7e-137 LIF2 LHP1-Interacting Factor 2, RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2), RNA-binding (RRM/RBD/RNP motifs) family protein (.3), RNA-binding (RRM/RBD/RNP motifs) family protein (.4) AT5G28390 137 / 3e-38 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) AT2G44710 119 / 2e-28 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) AT4G34110 81 / 6e-16 PABP2, PAB2, ATPAB2 ARABIDOPSIS POLY\(A\) BINDING 2, poly(A) binding protein 2 (.1) AT4G36960 74 / 4e-14 RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2) AT5G54900 74 / 5e-14 ATRBP45A RNA-binding protein 45A (.1) AT3G16380 72 / 4e-13 PAB6 poly(A) binding protein 6 (.1) AT4G19610 72 / 4e-13 nucleotide binding;nucleic acid binding;RNA binding (.1) AT1G71770 72 / 5e-13 PAB5 poly(A)-binding protein 5 (.1), poly(A)-binding protein 5 (.2)
Paralogs Show only best Show top 10	Gene ID BLAST score/e-value At best hit BLAST score/e-value TAIR10 short description Potri.009G163400 [exp] 717 / 0 AT3G52660 400 / 9e-136 RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2) Potri.006G212400 [exp] 479 / 8e-167 AT3G52660 473 / 1e-164 RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2) Potri.016G079200 [exp] 469 / 2e-162 AT3G52660 449 / 4e-155 RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2) Potri.014G104500 [exp] 397 / 2e-134 AT4G00830 574 / 0.0 LHP1-Interacting Factor 2, RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2), RNA-binding (RRM/RBD/RNP motifs) family protein (.3), RNA-binding (RRM/RBD/RNP motifs) family protein (.4) Potri.002G178200 [exp] 389 / 2e-131 AT4G00830 558 / 0.0 LHP1-Interacting Factor 2, RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2), RNA-binding (RRM/RBD/RNP motifs) family protein (.3), RNA-binding (RRM/RBD/RNP motifs) family protein (.4) Potri.002G139700 [exp] 138 / 9e-35 AT2G44710 585 / 0.0 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) Potri.005G116400 [exp] 136 / 5e-34 AT2G44710 325 / 1e-98 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) Potri.007G014100 [exp] 132 / 1e-32 AT2G44710 322 / 8e-98 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) Potri.014G051500 [exp] 129 / 2e-31 AT2G44710 627 / 0.0 RNA-binding (RRM/RBD/RNP motifs) family protein (.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 Lus10034195 [exp] 516 / 0 AT3G52660 444 / 7e-154 RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2) Lus10043390 [exp] 506 / 2e-177 AT3G52660 444 / 7e-154 RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2) Lus10021351 [exp] 438 / 2e-150 AT3G52660 478 / 3e-166 RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2) Lus10002689 [exp] 374 / 1e-125 AT4G00830 591 / 0.0 LHP1-Interacting Factor 2, RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2), RNA-binding (RRM/RBD/RNP motifs) family protein (.3), RNA-binding (RRM/RBD/RNP motifs) family protein (.4) Lus10030207 [exp] 369 / 1e-123 AT4G00830 601 / 0.0 LHP1-Interacting Factor 2, RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2), RNA-binding (RRM/RBD/RNP motifs) family protein (.3), RNA-binding (RRM/RBD/RNP motifs) family protein (.4) Lus10017026 [exp] 305 / 2e-99 AT3G52660 320 / 2e-105 RNA-binding (RRM/RBD/RNP motifs) family protein (.1), RNA-binding (RRM/RBD/RNP motifs) family protein (.2) Lus10028162 [exp] 132 / 2e-32 AT2G44710 675 / 0.0 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) Lus10033990 [exp] 113 / 2e-26 AT2G44710 301 / 2e-88 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) Lus10012785 [exp] 112 / 6e-26 AT2G44710 305 / 4e-92 RNA-binding (RRM/RBD/RNP motifs) family protein (.1) Lus10002835 [exp] 77 / 1e-14 AT4G34110 918 / 0.0 ARABIDOPSIS POLY\(A\) BINDING 2, poly(A) binding protein 2 (.1)
PFAM info	Clan ID Clan name Pfam ID Pfam name Pfam description CL0221 [poplar] [flax] RRM PF00076 [poplar] [flax] RRM_1 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
Representative CDS sequence Show only first row Show all	>Potri.004G201900.2 pacid=42794175 polypeptide=Potri.004G201900.2.p locus=Potri.004G201900 ID=Potri.004G201900.2.v4.1 annot-version=v4.1 ATGCCAAGTACAAAAGGAAATGCATCTGCAGCTGCTGAGGAAGCAGAATCTGAAAAGCCGGTTGAGTCCGATGAGAAAGTTGATTTTGATGAAGACTATG ATCCTGAGGAAATGATGGATGAGGAGGTTGAGTATGAAGTAGAGGAAATAGTGGAAGAAGTGGAAGAAGAGGAAATAATAGAAGAGGAAGTGGAGGTGGA GGAAGAAGAGGAGGAAAATGCTAGTAATGCTAATGGGGGTGATATCCAAAGTAGCCATCAAGGTGATGAGGCAAAGGTTGAAGATGAGGATGAGAAGAAA AAACATGCTGAGCTTCTTGCCCGTCCTCCTCATGGTTCTGAAGTATATATTGGTGGTGTTCCTAATGATGCTTCTGAGGAGGACTTGAAGGATTTTTGCG AGTCTGTTGGAGAAGTTACGGAGGTACGTATGATGAAAGGAAAAGATTCAAGTGACAATAAGGGCTTTGCATTTGTGACTTTTAGAAGTGTTGATTTGGC TACTAAAGCAATTGGTGAGCTGAATAATACTGAATTCAAGGGTAAAAGAATCAAATGCTCAACATCTCAGGCAAAGCACCGGTTGTTCCTTAGCAACATT CCTAGAAGTTGGGGAGAGGAAGATCTTAGCAAGTTTGTGGCTGAGGTTGGGCCTGGTACAACCAATGTGCAATTGGTGAAGGAGAAGAGCTCAAGCAATA ACAGGGGCTATGCTTTTGTTGAGTACTACAATAATGCTTGCGCTGAATATTCGAGGCAGAAGATGATAGATCCAAAATTTAAGCTGGGTGATAATGCCCC AAGTGTGAGCTGGGCTGACCCTAAAAATGCTGACTCTTCCACTTCTTCACAGGTTAAGGCAATATATGTGAAGAATTTACCAAAGACTGTTACCCAAGAT CAGTTGAAGAAGCTATTTGAACGACATGGAAAAATCACAAAAGTGGTTTTGCCTCCAGCAAAATCTGGACAAGAGAAAAATAGAATTGGTTTTGTGCATT TTGCTGAGAGGTCTAGTGCTATGAAAGCTCTGAAAGATACTGAAAAATATGAACTAAATGGCCAAAGTGTCGAGTGTGCACTTGCAAAACCTCAGTCAGA GCAGAAGCCTGCTGGAGGGTCAAACTTGCAGAGGGCTGGTTTGTTACCAGCTTACCCACCTGGTGTTGGTTATGGTATGATGGGGAGTGCCTATGGTGCT CTTGGTGCAGGATATGTTGCAACAGGCTTTACACAGCCATTGATCTATGGAAGTGGACCAGCCCCTGCTGGCATGGCAATGATGCCAATGCTTCTACCTG ATGGGCAGTTCGGATATGTCCTGCAACAGCCAGGAGTACAGCTACACTCCCCAACTTCATATCAAAGAAATGATAGTAGGAGTGGAAGTGGGCGTGGCAA CAAAATGGTTGGCAGTTCAAGTAGGGGTAGACAGCGCAGTGATGCCAGCCATGGTCGCAGATTTCGTCCGTACTAA
AA sequence Show only first row Show all	>Potri.004G201900.2 pacid=42794175 polypeptide=Potri.004G201900.2.p locus=Potri.004G201900 ID=Potri.004G201900.2.v4.1 annot-version=v4.1 MPSTKGNASAAAEEAESEKPVESDEKVDFDEDYDPEEMMDEEVEYEVEEIVEEVEEEEIIEEEVEVEEEEEENASNANGGDIQSSHQGDEAKVEDEDEKK KHAELLARPPHGSEVYIGGVPNDASEEDLKDFCESVGEVTEVRMMKGKDSSDNKGFAFVTFRSVDLATKAIGELNNTEFKGKRIKCSTSQAKHRLFLSNI PRSWGEEDLSKFVAEVGPGTTNVQLVKEKSSSNNRGYAFVEYYNNACAEYSRQKMIDPKFKLGDNAPSVSWADPKNADSSTSSQVKAIYVKNLPKTVTQD QLKKLFERHGKITKVVLPPAKSGQEKNRIGFVHFAERSSAMKALKDTEKYELNGQSVECALAKPQSEQKPAGGSNLQRAGLLPAYPPGVGYGMMGSAYGA LGAGYVATGFTQPLIYGSGPAPAGMAMMPMLLPDGQFGYVLQQPGVQLHSPTSYQRNDSRSGSGRGNKMVGSSSRGRQRSDASHGRRFRPY

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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
AT3G52660			RNA-binding (RRM/RBD/RNP motif...		Potri.004G201900 [exp]	0	1
AT3G05670			RING/U-box protein (.1)		Potri.005G021000 [exp]	2.23	0.8379
AT1G15280			CASC3/Barentsz eIF4AIII bindin...		Potri.003G056500 [exp]	2.44	0.8316
AT5G38880			unknown protein		Potri.004G114600 [exp]	2.64	0.8072
AT1G04300			TRAF-like superfamily protein ...		Potri.008G163300 [exp]	9.48	0.8206
AT2G23460		ATXLG1, XLG1	extra-large G-protein 1 (.1)		Potri.005G131200 [exp]	9.59	0.7676	XLG.1
AT2G25730			unknown protein		Potri.006G244900 [exp]	11.31	0.8254
AT5G42820	C3HZnF	ATU2AF35B	Zinc finger C-x8-C-x5-C-x3-H t...		Potri.006G116700 [exp]	13.03	0.6866
AT5G53430		SET29, ATX5, SD...	SET domain group 29 (.1)		Potri.012G013900 [exp]	15.96	0.7773	SDG914
AT5G67030		NPQ2, LOS6, IBS...	NON-PHOTOCHEMICAL QUENCHING 2,...		Potri.001G229100 [exp]	17.05	0.7132
AT5G04460			RING/U-box superfamily protein...		Potri.010G231100 [exp]	17.23	0.7493

Compare expression of checked genes

Potri.004G201900 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.