Detailed information on CNT0002008 (Glycine max)


BLAST search results

BLAST vs PNRD: nothing found

BLAST vs Swiss-Prot:
sp|P00865|RBS1_SOYBN, E-value = 1e-51

BLAST vs NONCODE (A. thaliana): nothing found

Potentially orthologous lncRNAs:
CNT0045027 in A. thaliana

CNT0025516 in O. sativa

Most similar lncRNAs:
CNT0045027, E-value = 5e-17 (A. thaliana)
CNT0033559, E-value = 8e-16 (P. patens)
CNT0025516, E-value = 3e-21 (O. sativa)

Expression of CNT0002008

Created with Highcharts 4.1.6Chart context menuExpression (RPKM)6 564.5825 618.1698 070.67245.73511 190.7266 730.9976 997.0466 080.244149.2398.17676.41790.50889.885127.46194.137leaves (SRR924099)leaves (SRR924144)leaves (SRR926169)seed (SRR639168)shoot apical meristem (SRR824155)shoot apical meristem (SRR824156)shoot apical meristem (SRR824157)shoot apical meristem (SRR824158)shoot apical meristem (SRR824159)shoot apical meristem (SRR824160)shoot apical meristem (SRR824161)shoot apical meristem (SRR824162)shoot apical meristem (SRR824163)whole seed (SRR639162)whole seed (SRR639164)0k1k2k3k4k5k6k7k8k9k10k11k12k

Peptides detected in this lncRNA

>peptide 1 (65 aa)
EVWGLVGDEADALHLANVVESDDTDEAVGVCSLSLLKLLQHLRSISATKHRQLPHGPVASIVVSW*

Sequence

>CNT0002008
GAAGTCTGGGGGCTTGTAGGCGATGAAGCTGATGCACTGCACTTGGCGAACGTTGTCGAATCCGATGATACGGATGAAGCCGTTGGGGTATGCAGTCTTA
GCCTCTTGAAGCTCCTTCAACACCTGAGAAGCATCAGTGCAACCAAACATAGGCAGCTTCCACATGGTCCAGTAGCGTCCATCGTAGTATCCTGGTGACC
TGTTGTGCTCACGGTACACGAAACCGTGCTGCAAACAAACAGATCAACCATCAAAACTCAAAACCAAGTGCTTGT

lncRNA-RNA interactions

Number of interactions: 7

Potential function Interacting transcript Gene description Transcript biotype lncRNA id Alignment score (LAST) Alignment length Transcript region involved in interaction Genomic orientation of interacting RNAs
GLYMA13G07610.1 Ribulose bisphosphate carboxylase small chain 1, chloroplastic protein coding CNT0002008 682 284 CDS Trans
GLYMA19G06340.1 Ribulose bisphosphate carboxylase small chain 4, chloroplastic protein coding CNT0002008 825 275 CDS Cis
GLYMA19G06340.3 Ribulose bisphosphate carboxylase small chain 4, chloroplastic protein coding CNT0002008 825 275 CDS_UTR Cis
GLYMA19G06340.5 Ribulose bisphosphate carboxylase small chain 4, chloroplastic protein coding CNT0002008 825 275 CDS Cis
GLYMA19G06370.1 Ribulose bisphosphate carboxylase small chain 4, chloroplastic protein coding CNT0002008 817 275 CDS Cis
GLYMA19G06390.2 Ribulose bisphosphate carboxylase small chain protein coding CNT0002008 596 241 CDS Cis
GLYMA19G06420.1 Ribulose bisphosphate carboxylase small chain protein coding CNT0002008 621 239 CDS_UTR Trans