OakRootRNADB Database

Transcript: MSTRG.3.1

You can find all information about transcript in the cards below

Transcript summary

Feature	Description
Transcript name	MSTRG.3.1
Gene name	MSTRG.3
Transcript biotype	lncRNA
Coding potential	Low
Transcript localization	Cytoplasm
Transcript localization (score)	0.331933
Chromosome	Qrob_Chr01
Start	22746
End	28649
Strand	-
Length	800
Exon count	2
Exon coordinates	22746-23358, 28463-28649

Transcript sequence

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>MSTRG.3.1
CGGTAATAACTCTTTCTATAACGTATTCCGAATTTCTGACAACACTACCCCTCTCTCTGTATCAACAATTGAATAAAAATGACAACAACGAAGAAGAAGAAGTTGATGTCATCGGCGCCATAGAGGGGCAAAGAGGAAGCCACTGAACAGTTCCAAGACGATAACGATTGATGATTCCCTCGTCGAGATATAGTTTCATATGAAACATTTCCCTTAATCTCAAGACCCTGGCCTTGCTATCAGAGTATCTAGAAGGGGTGGGGAAGAAGAAGAAACAACCTAAGAAAGGGAGGCAAAAGAAGCAAAATAGTCGGAAATGAGGAAACTCAATGTCTTCATCCAAAATAATGTAAAAGGAAGATTTACTTTCACAACAAAATATGTGTTCTCTTAAAACAAAGATCATTTTGTGTTTTTTTCGTGTTTCATTAAATATTGTTTACGAGGCAATCATATGAATTCTACAAGTTGTGATTGTGTCTAGTGGACGCCCTCTTATGTGAACTTAATATTTTCTTTTGTTTTTGTTCCCTCTTTAGGTCACGTGGACAATATAAATAGACTAAAATTATTAACCTATAGTTTATCATCTAATTAAACTCTATTGACGAACCGTCTCACATGTGCCTGTACCATGTGACTCGATGTAAGTATTACATATCATACAGCGTGTCTCCACCGCAGAATATTTTGTAGGATCTTTCTTTTCTTCTTTTCTTTTTGTAATTTGAGATGCACTATTTGCTGCCAATAGCTGTAAACTTACCCATCTATAATATATTATTATATATATAAAAGCA

Peptide sequence

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>MSTRG.3.1_peptide
MIFVLREHIFCCESKSSFYIILDEDIEFPHFRLFCFFCLPFLGCFFFFPTPSRYSDSKARVLRLREMFHMKLYLDEGIINRYRLGTVQWLPLCPSMAPMTSTSSSSLLSFLFNC*

Regulation

Family	Family type	Domains
Unknown

Libraries description

Harvest date	Type of root	Root length	Root vitality	Type of cultivation	Biological replicates
1/2/3	K/KB	kr/sr/dl	NN/NT/TN/TT	kon/rh	1/2/3
1 – First harvest date – 7-weeks old plant (sown in early spring)	K – meristematic zone of the taproot	kr – short root (5 – 9 cm)	NN – normal condition roots	kon – growing in containers	1 – first biological replicate
2 – Second harvest date – 8-weeks old plant (sown in early spring)	KB – lateral root	sr – medium root (9,5 – 15 cm)	NT - dying root	rh – growing in rhizotron	2 – second biological replicate
3 – Third harvest date – 8-weeks old plant (sown in early summer)		dl – long root (15,5 – 35 cm)	TN – thick root		3 – third biological replicate
			TT – thick and dying root

Transcript expression table

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Name	TPM
1K_dl_NN_kon1	0.34
1K_dl_NN_kon2	0.15
1K_dl_NN_kon3	0.68
1K_dl_NT_kon1	0.63
1K_dl_NT_kon2	0.56
1K_dl_NT_kon3	1.71
1K_kr_NN_kon1	0.00
1K_kr_NN_kon2	0.52
1K_kr_NN_kon3	0.11
1K_sr_NN_kon1	0.41
1K_sr_NN_kon2	0.54
1K_sr_NN_kon3	0.44
1KB_dl_NN_kon1	0.69
1KB_dl_NN_kon2	1.03
1KB_dl_NN_kon3	0.90
1KB_sr_NN_kon1	1.55
1KB_sr_NN_kon2	0.86
1KB_sr_NN_kon3	0.73
2K_dl_NN_kon1	0.59
2K_dl_NN_kon2	0.50
2K_dl_NN_kon3	0.96
2K_dl_NN_rh1	0.00
2K_dl_NN_rh2	0.19
2K_dl_NN_rh3	0.31
2K_dl_NT_kon1	0.38
2K_dl_NT_kon2	0.46
2K_dl_NT_kon3	0.41
2K_kr_NN_kon1	0.75
2K_kr_NN_kon2	0.79
2K_kr_NN_kon3	0.00
2K_sr_NN_kon1	1.06
2K_sr_NN_kon2	0.91
2K_sr_NN_kon3	0.12
2K_sr_NN_rh1	0.30
2K_sr_NN_rh2	0.00
2K_sr_NN_rh3	0.58
2K_sr_NT_rh1	0.00
2K_sr_NT_rh2	2.81
2K_sr_NT_rh3	0.00
2K_sr_TN_kon1	0.88
2K_sr_TN_kon2	0.80
2K_sr_TN_kon3	0.34
2KB_dl_NN_kon1	0.38
2KB_dl_NN_kon2	0.00
2KB_dl_NN_kon3	0.14
2KB_dl_NN_rh1	0.00
2KB_dl_NN_rh2	0.31
2KB_dl_NN_rh3	0.00
2KB_sr_NN_kon1	0.12
2KB_sr_NN_kon2	0.54
2KB_sr_NN_kon3	1.32
2KB_sr_NN_rh1	0.36
2KB_sr_NN_rh2	0.00
2KB_sr_NN_rh3	0.43
2KB_sr_TN_kon1	0.10
2KB_sr_TN_kon2	0.51
2KB_sr_TN_kon3	0.33
2KB_sr_TN_rh1	0.00
2KB_sr_TN_rh2	0.00
2KB_sr_TN_rh3	0.00
3K_dl_NN_kon1	0.46
3K_dl_NN_kon2	0.62
3K_dl_NN_kon3	0.48
3K_dl_NN_rh1	1.49
3K_dl_NN_rh2	0.80
3K_dl_NN_rh3	0.66
3K_dl_TN_kon1	1.24
3K_dl_TN_kon2	0.78
3K_dl_TN_kon3	2.47
3K_dl_TN_rh1	1.10
3K_dl_TN_rh2	1.02
3K_dl_TN_rh3	0.15
3KB_dl_NN_kon1	0.71
3KB_dl_NN_kon2	0.63
3KB_dl_NN_kon3	0.80

Libraries description

Type of root	Root length	Root vitality	Type of cultivation	Biological replicates
K/KB/SW	kr/sr/dl	NN/NT/TN/TT	kon/rh/krh	1/2/3
K – meristematic zone of the taproot	kr – short root (5 – 9 cm)	NN – normal condition roots	kon – growing in containers	1 – first biological replicate
KB – lateral root	sr – medium root (9,5 – 15 cm)	NT - dying root	rh – growing in rhizotron	2 – second biological replicate
SW – elongation zone of taproot	dl – long root (15,5 – 35 cm)	TN – thick root	krh - growing in a container and then transferred to a rhizotron	3 – third biological replicate
		TT – thick and dying root

Transcript expression table

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Name	TPM
K_dl_NN_kon1	0.17
K_dl_NN_kon2	0.52
K_dl_NN_kon3	0.38
K_dl_NN_krh1	1.56
K_dl_NN_krh2	1.06
K_dl_NN_krh3	0.24
K_dl_NN_rh1	0.87
K_dl_NN_rh2	0.55
K_dl_NN_rh3	1.04
K_dl_NT_kon1	0.43
K_dl_NT_kon2	0.55
K_dl_NT_kon3	0.84
K_dl_NT_krh1	0.11
K_dl_NT_krh2	0.00
K_dl_NT_krh3	0.16
K_kr_NN_kon1	0.26
K_kr_NN_kon2	0.08
K_kr_NN_kon3	0.30
K_kr_NN_krh1	1.13
K_kr_NN_krh2	1.01
K_kr_NN_krh3	1.11
K_kr_NN_rh1	1.30
K_kr_NN_rh2	0.77
K_kr_NN_rh3	0.87
K_sr_NN_kon1	0.64
K_sr_NN_kon2	0.43
K_sr_NN_kon3	0.73
K_sr_NN_krh1	0.55
K_sr_NN_krh2	1.01
K_sr_NN_krh3	0.82
K_sr_NN_rh1	0.96
K_sr_NN_rh2	1.46
K_sr_NN_rh3	1.11
K_sr_TT_krh1	1.93
K_sr_TT_krh2	1.68
K_sr_TT_krh3	1.42
K_sr_TT_rh1	0.76
K_sr_TT_rh2	0.71
K_sr_TT_rh3	0.24
KB_dl_NN_kon1	0.57
KB_dl_NN_kon2	0.40
KB_dl_NN_kon3	0.47
KB_dl_NN_krh1	0.56
KB_dl_NN_krh2	0.52
KB_dl_NN_krh3	0.27
KB_dl_NN_rh1	0.16
KB_dl_NN_rh2	0.56
KB_dl_NN_rh3	0.16
KB_dl_NT_kon1	0.53
KB_dl_NT_kon2	0.61
KB_dl_NT_kon3	0.46
KB_sr_NN_kon1	0.21
KB_sr_NN_kon2	0.59
KB_sr_NN_kon3	0.22
KB_sr_NN_rh1	0.62
KB_sr_NN_rh2	0.50
KB_sr_NN_rh3	0.85
KB_sr_TT_krh1	1.97
KB_sr_TT_krh2	1.27
KB_sr_TT_krh3	2.03
SW_dl_NN_kon1	0.40
SW_dl_NN_kon2	0.55
SW_dl_NN_kon3	0.60
SW_dl_NN_krh1	2.12
SW_dl_NN_krh2	0.79
SW_dl_NN_krh3	0.96
SW_dl_NN_rh1	1.46
SW_dl_NN_rh2	0.84
SW_dl_NN_rh3	0.92
SW_dl_NT_kon1	0.81
SW_dl_NT_kon2	0.55
SW_dl_NT_kon3	0.38
SW_dl_NT_krh1	0.00
SW_dl_NT_krh2	0.59
SW_dl_NT_krh3	0.09
SW_sr_NN_kon1	0.31
SW_sr_NN_kon2	0.14
SW_sr_NN_kon3	0.93
SW_sr_NN_rh1	1.33
SW_sr_NN_rh2	1.67
SW_sr_NN_rh3	1.15
SW_sr_NT_rh1	0.93
SW_sr_NT_rh2	0.90
SW_sr_NT_rh3	0.53
SW_sr_TN_krh1	0.00
SW_sr_TN_krh2	1.66
SW_sr_TN_krh3	1.92
SW_sr_TT_krh1	1.91
SW_sr_TT_krh2	2.17
SW_sr_TT_krh3	1.71

Annotations in other databases

Unknown

miRNA

miRBase ID	E-value	Species	Clade
Unknown

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Description	Contents	Format
Transcript	Transcript sequence in fasta format	fasta
Peptide	Peptide sequence in fasta format	fasta
Expression Dataset 1	Two-collumn table with library name and TPM	TSV
Expression Dataset 2	Two-collumn table with library name and TPM	TSV