Sequence
atgc intronic sequence ATGC exonic sequence...agtgtatggtgtggcactcttttatcttttcgagaaatatatcaaatgtttaatattttgaagcatctctttttcattttcattattcacaaataaatagGATTATGATCCATATGAGGAGAATCCTGGAATTGCTCCATTCAGTGAGCCTGAAAGTCAAATTATGCGGAAACTTGCCATATCTTTTGAACCACATCTAT
Basic information
species | Glycine max |
transcript | GLYMA06G02070.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G02070.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G42320.1 (Arabidopsis thaliana), 3'ss of exon 6
-----agtgtatggtgtggcactcttttatcttttcgagaaatatatcaaatgtttaatattttgaagcatctctttttcattttcattattcacaaataaatagGATTATGATCCATATGAGGAGAATCCTGGAATTGCTCCATTCAGTGAGCCTGAAAGTCAAATTATGCGGAAACTTGCCATATCTTTTGAACCACATCTAT
| | ||||| | | || ||| | |||| |||| ||| | | | | | || | | ||| || | | | ||||||||||||||| ||| |||||||| |||| |||||| || |||||||| |||| |||||| |||||||| || |||||||| ||||| || || |||
gtacttcttcacctcactgcactttcctttcccttcaa------tatcccttgtt-aatgtgtc-acgaacctttgtccttgttttgttctcggcg--tttccagGATTATGATCCATCTGAAGAGAATCCAGGAACTGCTCCGTTTAGTGAGCCCGAAACTCAAATAATGCGGAAGCTAGCCATATCATTTGATCCTCACATAT
upper sequence: GLYMA06G02070.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0122g01410.t01 (Vitis vinifera), 3'ss of exon 6
agtgtatggtgtgg-cactcttttatcttttcgagaaatatatcaaatgtttaatattttgaagcatctctttttcattttcattattcacaaataaatagGATTATGATCCATATGAGGAGAATCCTGGAATTGCTCCATTCAGTGAGCCTGAAAGTCAAATTATGCGGAAACTTGCCATATCTTTTGAACCACATCTAT
||||| | || | || | | ||| | | | ||| | | || | ||| | |||| | | | |||| ||| | |||||||||||||||||||| || |||||||||| |||||| || ||||||||||| | |||||| ||||||||||| ||||||| ||||| |||||| |||
gttgtattgcaaattcagtgttatgttgtttggtggtgggacttttccgttctttttcttttatcatttaatttttctatctctgattctttaatta-tagGATTATGATCCATATGAAGAAAATCCTGGAACTGCTCCTTTTAGTGAGCCTGAGACTCAAATAATGCGGAAACTCTCCATATCATTTGATCCACATATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtttaatattttgaagcatctctttttcattttcattattcacaaataaatagGATTATGATCCATATGAGGAGAATCCTGGAATTGCTCCATTCAGTGAGCCTGAAAGTCAAATTATGCGGAAACTTGCCATATCTTTTGAACCACATCTAT
gtttaat putative branch site (score: 4)
tttttcattttcatta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgtatggtgtggcactcttttatcttttcgagaaatatatcaaatgtttaatattttgaagcatctctttttcattttcattattcacaaataaatagGATTATGATCCATATGAGGAGAATCCTGGAATTGCTCCATTCAGTGAGCCTGAAAGTCAAATTATGCGGAAACTTGCCATATCTTTTGAACCACATCTAT
- - - tggtgtg
- - - - - - -gcactct