Transcript

Sequence

>Osa04LNT0284200.1

GGTAAACCTCACAAACGTTCTAAGCTGACGGTGGTCGATGCCACTGATGCACGCCCTCCTTATGGGCCACTGCTGCAGGTCCTATCCACTCTCAGGTTAGTTATCCAATATCCATGTAATTAATCACTAAGTAAACCATTGTAGTAGCGGTAGTACTATATGTGCCAACAACTAGTATTCTTCTGTCATCACTGATCCCTTCTCTACACTATTGATGAATGTGCTCACGAAAATCATTTTGTACTGTGGCAAGCTGGCAATGAACTCTCCTGAGTCACATAAATGCCTTTGTACCGGCTGGTTTTAATTGCATCGGTTGGTGACGCTTCTGGATCAAAGTGATAGGTTCAATGTCAATGGGCTTCCACTATTGGAGCTGACACAGAAGCTTTTGAAGTGGTAGGTACAAAGAGAGTGGAACAGAACAAGCTTCACTATATCCTTTACTTTCTTTTCTGAGCTGAGCATCGCTTTCTGCATTGAAAGGAAAATGATATTATGGTTAGCTGATGAAGAAACTTATTAATCATGAATAGTAGATTAGATAGTGGTCAATTTCTATTAACATGGCAGATAATTAACAGTACTTTACTTCTGAACAATCATTGGTTAACAAAATACTTGCTGAGCTGGCATACGCCAGCCAAAGTTTTTATTAAGCTTAGAAAGTGTTCAAAGGGATTTCTTTGTTTTAGTCCACGAGTCCAAATTCTTGTATTTTTCAACCTTGTCTCATGGAATAAAAAACTAACGTGTATACGATATAATTATATGAATTTAACTGGGATAAAATACAACTTGCTTTCAGATTATGTTAGCTTGGGATAGTTTTGCAAAGATGACTTGATACACACAATTTCAGTTTCTTAATAGAATAGCACCCAAGGAAATGTTCTGTCTGTATCCACCTTTTGTACAATTTGGTGGGAATATATCTTACTAACATTTATATTTCTTATTAATTTCTAGGGAGTTTAGAACGGCGTTGAATATTGATAGATATTTAGCATCTCACTAATGGATAATAAAACATGGCTTTGGAGAAAAAAATCCTCAGAAAGGACAATTTCAACGAAGAACAAAGCCAATATATCAGAGAGGGAACAGGAGGTACATCACTTATCTCTTTAACATTATTAAGAAGCCTTATGAATTATGATATGTTCCTATCTGGATTTTCAACTTTTCCTTCCCTAGTGACCTCTCATCTTGATCGTGTGCTCGGTGTCGCGGACGCGGACGAGCGCGGGGGGAGACTCTCCTGGGTCGTCGGCAGTCGCGCGCGCGTGATTCCGCGGTGGTCGGGCGCCGGCCGGGATTTCGTGCGGGCGAGAGGGGCGGGGCGCAGGCGGCGGAGGGGATCGGTTTGGGAGGGAAGGGTTTGGG

Coding Potentia

Explanation	CPC Score
noncoding (weak)	-0.370867

Genome Browser

Expression

Axis x: Treatment
Axis y: FPKM
Value above bar: Standard deviation

Variation

Transcript ID	Chromosome	Locus	Ref	Alt
Osa04LNT0284200.1	4	33084827	C	G
Osa04LNT0284200.1	4	33081024	G	T
Osa04LNT0284200.1	4	33083637	T	C
Osa04LNT0284200.1	4	33084202	T	C
Osa04LNT0284200.1	4	33086358	C	T

Transposon

Transcript ID	Transposon ID	Chromosome	Strand	Start	End	Counts

small RNA targets

Transcript ID	MiRNA ID	Inhibition	Expectation	Score	Binding Start	Binding End
Osa04LNT0284200.1	osa-miR5079b	Cleavage	4.0	20.345	1	22
Osa04LNT0284200.1	osa-miR393b-3p	Cleavage	5.0	15.553	1	21
Osa04LNT0284200.1	osa-miR1849	Translation	4.5	8.751	1	21
Osa04LNT0284200.1	osa-miR2093-3p	Translation	5.0	16.986	1	20
Osa04LNT0284200.1	osa-miR2121a	Translation	5.0	15.629	1	24
Osa04LNT0284200.1	osa-miR2121b	Translation	5.0	15.629	1	24
Osa04LNT0284200.1	osa-miR5079a	Cleavage	4.0	20.345	1	22
Osa04LNT0284200.1	osa-miR5515	Cleavage	4.5	14.98	1	21

QTL

Transcript ID	Chr	QTL Gene	Character Major	Character Minor	Marker Interval1	Marker Interval2
Osa04LNT0284200.1	4	nan	Morphological trait	Panicle/flower	RG620	RG214
Osa04LNT0284200.1	4	QGn4	Morphological trait	Panicle/flower	RG143	RG214
Osa04LNT0284200.1	4	QGwp4	Physiological trait	Source activity	RG143	RG214
Osa04LNT0284200.1	4	rpf4.1	Resistance or Tolerance	Drought tolerance	RG214	RG620
Osa04LNT0284200.1	4	nan	Morphological trait	Root	RG214	C1016
Osa04LNT0284200.1	4	OsAOX1a	Resistance or Tolerance	Cold tolerance	R2737	R740
Osa04LNT0284200.1	4	gpps4.1	Resistance or Tolerance	Drought tolerance	RG214	RG620
Osa04LNT0284200.1	4	nan	Morphological trait	Panicle/flower	RM303	RM348
Osa04LNT0284200.1	4	qSN-4b	Resistance or Tolerance	Drought tolerance	RM255	RM349
Osa04LNT0284200.1	4	Xa2	Resistance or Tolerance	Bacterial blight resistance	RM317	RM349
Osa04LNT0284200.1	4	tgwt4	Morphological trait	Seed	RG143	RG214
Osa04LNT0284200.1	4	rfw4a	Resistance or Tolerance	Drought tolerance	RM349	RM1136
Osa04LNT0284200.1	4	nan	Morphological trait	Root	RM3276	RM3335
Osa04LNT0284200.1	4	np4	Morphological trait	Panicle/flower	RG143	RG214
Osa04LNT0284200.1	4	nan	Morphological trait	Panicle/flower	RG143	RG214
Osa04LNT0284200.1	4	tgwt4	Morphological trait	Seed	RG143	RG214
Osa04LNT0284200.1	4	np4	Morphological trait	Seed	RG143	RG214
Osa04LNT0284200.1	4	nan	Physiological trait	Source activity	RG143	RG329
Osa04LNT0284200.1	4	gpp4	Morphological trait	Seed	RZ569	RZ565

pre-miRNA

Transcript ID	Pre-miRNA	Identity(%)	Alignment Length	Pre-miRNA start	Pre-miRNA end	E-value	Bitscore

GWAS

Transcript ID	Chromosome	Locus	Trait	Value	Plus Minus