OakRootRNADB Database

Transcript: MSTRG.1.1

You can find all information about transcript in the cards below

Transcript summary

Feature	Description
Transcript name	MSTRG.1.1
Gene name	MSTRG.1
Transcript biotype	lncRNA
Coding potential	Low
Transcript localization	Extracellular_region
Transcript localization (score)	1.0426
Chromosome	Qrob_Chr01
Start	670
End	1185
Strand	-
Length	516
Exon count	1
Exon coordinates	670-1185

Transcript sequence

Download

>MSTRG.1.1
TCTCTCTCATTCAGCCGCCCCGTCCTCTCTCTCTCTTTCCAAGTGAAGTGTACGACATAGAATGGGACTTGATCATGGTGGATGCAGCTACTGGGTACCATGATAATGCCCCAGGAAGAATGAGTGCTATATACACAGCTGGGTTGATGGCTAGGAATAGAGACTGATGTGTTTGAAGGGTATTTGACAGAACTTGTGTCAAATACCCTTCACTATCCCAAGTCACAGGGCTCGCCTTTTGTCCATAGAGGTTTCATTCTCTGTCCTTTTTTTTTTTGCCTGTATTTTTTTTTTTAACCACAATTCTTGTTTTGTCATAGATCTATTATTTACTTGTGAGAATTGGAGCTGGGATTTTCCTTTCATGTATATTTTCTGTTGTTACAAATTTTTTATTGGATGAATTATACTACTGAGAATTACTAAATAAACATAATGTGGGGTGACCATCTTTGGTCCTTGATACTACCAATTTGGGCAGAAAAGGTTTACTATCCAACTAAGTGCACTGCTGGG

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

Download

Name	TPM
1K_dl_NN_kon1	0.69
1K_dl_NN_kon2	2.37
1K_dl_NN_kon3	1.46
1K_dl_NT_kon1	2.29
1K_dl_NT_kon2	1.02
1K_dl_NT_kon3	1.87
1K_kr_NN_kon1	0.18
1K_kr_NN_kon2	0.36
1K_kr_NN_kon3	0.38
1K_sr_NN_kon1	0.00
1K_sr_NN_kon2	0.40
1K_sr_NN_kon3	1.45
1KB_dl_NN_kon1	2.84
1KB_dl_NN_kon2	1.15
1KB_dl_NN_kon3	0.97
1KB_sr_NN_kon1	0.20
1KB_sr_NN_kon2	1.24
1KB_sr_NN_kon3	0.62
2K_dl_NN_kon1	0.70
2K_dl_NN_kon2	3.07
2K_dl_NN_kon3	3.16
2K_dl_NN_rh1	0.96
2K_dl_NN_rh2	1.21
2K_dl_NN_rh3	2.39
2K_dl_NT_kon1	5.35
2K_dl_NT_kon2	2.12
2K_dl_NT_kon3	1.00
2K_kr_NN_kon1	1.63
2K_kr_NN_kon2	0.59
2K_kr_NN_kon3	1.08
2K_sr_NN_kon1	0.00
2K_sr_NN_kon2	1.83
2K_sr_NN_kon3	2.39
2K_sr_NN_rh1	1.28
2K_sr_NN_rh2	0.60
2K_sr_NN_rh3	0.71
2K_sr_NT_rh1	0.19
2K_sr_NT_rh2	1.89
2K_sr_NT_rh3	0.00
2K_sr_TN_kon1	2.14
2K_sr_TN_kon2	1.23
2K_sr_TN_kon3	0.95
2KB_dl_NN_kon1	2.23
2KB_dl_NN_kon2	0.86
2KB_dl_NN_kon3	2.88
2KB_dl_NN_rh1	0.57
2KB_dl_NN_rh2	0.40
2KB_dl_NN_rh3	0.79
2KB_sr_NN_kon1	0.66
2KB_sr_NN_kon2	0.00
2KB_sr_NN_kon3	0.21
2KB_sr_NN_rh1	0.75
2KB_sr_NN_rh2	1.37
2KB_sr_NN_rh3	2.34
2KB_sr_TN_kon1	2.04
2KB_sr_TN_kon2	1.96
2KB_sr_TN_kon3	1.73
2KB_sr_TN_rh1	0.00
2KB_sr_TN_rh2	0.00
2KB_sr_TN_rh3	0.00
3K_dl_NN_kon1	0.19
3K_dl_NN_kon2	0.20
3K_dl_NN_kon3	0.20
3K_dl_NN_rh1	0.20
3K_dl_NN_rh2	2.21
3K_dl_NN_rh3	1.55
3K_dl_TN_kon1	2.38
3K_dl_TN_kon2	2.99
3K_dl_TN_kon3	2.60
3K_dl_TN_rh1	4.60
3K_dl_TN_rh2	4.97
3K_dl_TN_rh3	3.70
3KB_dl_NN_kon1	0.54
3KB_dl_NN_kon2	0.39
3KB_dl_NN_kon3	0.00

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

Download

Name	TPM
K_dl_NN_kon1	1.40
K_dl_NN_kon2	1.92
K_dl_NN_kon3	1.60
K_dl_NN_krh1	0.59
K_dl_NN_krh2	1.21
K_dl_NN_krh3	2.62
K_dl_NN_rh1	2.11
K_dl_NN_rh2	1.27
K_dl_NN_rh3	1.41
K_dl_NT_kon1	0.47
K_dl_NT_kon2	1.21
K_dl_NT_kon3	1.34
K_dl_NT_krh1	1.51
K_dl_NT_krh2	0.00
K_dl_NT_krh3	0.15
K_kr_NN_kon1	0.54
K_kr_NN_kon2	1.58
K_kr_NN_kon3	0.62
K_kr_NN_krh1	3.73
K_kr_NN_krh2	2.06
K_kr_NN_krh3	1.55
K_kr_NN_rh1	1.90
K_kr_NN_rh2	1.35
K_kr_NN_rh3	2.88
K_sr_NN_kon1	3.50
K_sr_NN_kon2	2.58
K_sr_NN_kon3	1.98
K_sr_NN_krh1	0.16
K_sr_NN_krh2	0.55
K_sr_NN_krh3	0.26
K_sr_NN_rh1	2.55
K_sr_NN_rh2	1.86
K_sr_NN_rh3	2.93
K_sr_TT_krh1	1.55
K_sr_TT_krh2	1.13
K_sr_TT_krh3	1.14
K_sr_TT_rh1	4.85
K_sr_TT_rh2	2.15
K_sr_TT_rh3	4.28
KB_dl_NN_kon1	1.19
KB_dl_NN_kon2	1.42
KB_dl_NN_kon3	1.02
KB_dl_NN_krh1	0.57
KB_dl_NN_krh2	0.60
KB_dl_NN_krh3	1.46
KB_dl_NN_rh1	2.17
KB_dl_NN_rh2	1.79
KB_dl_NN_rh3	1.61
KB_dl_NT_kon1	0.64
KB_dl_NT_kon2	0.00
KB_dl_NT_kon3	0.46
KB_sr_NN_kon1	1.20
KB_sr_NN_kon2	1.55
KB_sr_NN_kon3	1.56
KB_sr_NN_rh1	1.69
KB_sr_NN_rh2	1.85
KB_sr_NN_rh3	2.41
KB_sr_TT_krh1	1.59
KB_sr_TT_krh2	1.56
KB_sr_TT_krh3	1.64
SW_dl_NN_kon1	1.48
SW_dl_NN_kon2	1.03
SW_dl_NN_kon3	0.89
SW_dl_NN_krh1	0.66
SW_dl_NN_krh2	2.03
SW_dl_NN_krh3	2.19
SW_dl_NN_rh1	0.47
SW_dl_NN_rh2	1.33
SW_dl_NN_rh3	1.26
SW_dl_NT_kon1	2.09
SW_dl_NT_kon2	1.07
SW_dl_NT_kon3	2.22
SW_dl_NT_krh1	0.93
SW_dl_NT_krh2	0.80
SW_dl_NT_krh3	0.48
SW_sr_NN_kon1	2.02
SW_sr_NN_kon2	4.23
SW_sr_NN_kon3	1.38
SW_sr_NN_rh1	2.24
SW_sr_NN_rh2	2.81
SW_sr_NN_rh3	1.78
SW_sr_NT_rh1	1.37
SW_sr_NT_rh2	1.58
SW_sr_NT_rh3	1.28
SW_sr_TN_krh1	0.31
SW_sr_TN_krh2	0.00
SW_sr_TN_krh3	0.15
SW_sr_TT_krh1	0.31
SW_sr_TT_krh2	0.73
SW_sr_TT_krh3	0.44

Annotations in other databases

BlastX Best Hit

Gene symbol	Organism	Query coordinates	Subject coordinates	Percent ident	E-value	Gene description
GXM2	ARATH	27-161	183-227	75.556	6.52e-17	Glucuronoxylan 4-O-methyltransferase 2

Blast GO

GO ID	Ontology	Description
GO:0005794	cellular component	Golgi apparatus
GO:0000139	cellular component	Golgi membrane
GO:0016021	cellular component	integral component of membrane
GO:0030775	molecular function	glucuronoxylan 4-O-methyltransferase activity
GO:0032259	biological process	methylation
GO:0009834	biological process	plant-type secondary cell wall biogenesis
GO:0045492	biological process	xylan biosynthetic process
GO:0045491	biological process	xylan metabolic process

Kegg

Kegg ID
ath:AT4G09990

miRNA

miRBase ID	E-value	Species	Clade
Unknown

Download

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