Sequence
atgc intronic sequence ATGC exonic sequencegttgcattgcttgtttcttaattaacatctctctctttctcccccccccccaccccccccacacacacacatatatatatatatatatgatgccttgactaaaatattctgtgatgatatatttataatattcttttctgcaagCAGGCTGTCGAATCGTGGTTAGTGGATAAAGCTGTTCTACCAATCGAAAATTCTGTTGGTGGAAGCATCCACCGTAATTATGATTTACTTCTTGGACACA
Basic information
species | Glycine max |
transcript | GLYMA09G00650.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G00650.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G11790.2 (Arabidopsis thaliana), 3'ss of exon 3
gttgcattgcttgtttcttaattaacatctctctctttctcccccccccccaccccccccacacacacacatatatatatatatatatgatgccttgactaaaatattctgtg----atgatatatttataatattcttttctgcaagCAGGCTGTCGAATCGTGGTTAGTGGATAAAGCTGTTCTACCAATCGAAAATTCTGTTGGTGGAAGCATCCACCGTAATTATGATTTACTTCTTGGACACA---
| | | | | || |||||| || ||| || |||| | | ||| | || | |||||| ||| || | |||||||| || ||||| ||||||||||| || |||| ||||| ||||| || ||||| || |||||||||||||||||||| |||||| | || |
------------------------------------------------------gttttgatttat-cggtcacttcta-atatattctatccctacacaaaaaggtacggtgctttactatgtctttatatgattgattctt-----cagGCTGTTGAGCTCTGGTTGGTGGATAAAGCAGTATTACCGATCGAGAATTCAGTAGGTGGTAGTATCCACCGTAATTATGATTTGCTTCTTCGTCATAGGC
upper sequence: GLYMA09G00650.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0116g01670.t01 (Vitis vinifera), 3'ss of exon 3
gttgcattgcttgtttcttaattaacatctctctctttctcccccccccccaccccccccacacacacacatatatata-tatatatatgatgccttgactaaaatattctgtgatgatatatttataatattcttttctgcaagCAGGCTGTCGAATCGTGGTTAGTGGATAAAGCTGTTCTACCAATCGAAAATTCTGTTGGTGGAAGCATCCACCGTAATTATGATTTACTTCTTGGACACA---
|| || | || |||||| | ||| | || || | | | | ||| | | || | ||| ||| || |||| |||| | |||| |||||| ||||| ||||| ||||| ||||| || |||||||| |||||||||||||| |||||||||||| | || ||||| ||||
--------------------------------------------------------gttcagccaaatactaatatatgctttatggttattgaattaatttacacattttaaactcttaattaactaaatttccattttgcagGCAG----TTGAATTGTGGTTGGTGGAGAAAGCAGTTCTCCCAATTGAGAATTCTGTAGGTGGAAGCATCCATCGTAATTATGATCTTCTCCTTGGCCACAGGC
upper sequence: GLYMA09G00650.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S84_76V6.1 (Physcomitrella patens), 3'ss of exon 3
gttgcattgcttgtttcttaattaacatctctctctttctcccccccccccaccccccccacacacacacatatatatatatatatatgatgccttgactaaaatattctgtgatgatatattta-----taatattctt--ttctgcaagC-AGGCTGTCGAATCGTGGTTAGTGGATAAAGCTGTTCTACCAATCGAAAATTCTGTTGGTGGAAGCATCCACCGTAATTATGATTTACTTCTTGGACACA---
| || | | || | ||| | | || | || | | || | | ||| | || ||||| || || | ||||| |||| || || ||| | || || | ||| || | || || || |||||| ||||||||||||| || || ||||||||||||||||| | ||
-------------------------------------------------------gcttgtgacctaaatattgaaataggaaagtttggctgttagaagagagcatgtttttctgaacttcttggtcattaatacgtttacttttccaagccagGCAGTAGAGCTTTGGCTGGTTGACAGAGCAGTGTTGCCGATAGAGAATTCTCTTGGTGGAAGCATTCATCGCAATTATGATTTACTTCTGCGTCATCGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgccttgactaaaatattctgtgatgatatatttataatattcttttctgcaagCAGGCTGTCGAATCGTGGTTAGTGGATAAAGCTGTTCTACCAATCGAAAATTCTGTTGGTGGAAGCATCCACCGTAATTATGATTTACTTCTTGGACACA
gactaaa putative branch site (score: 2)
tattcttttct putative PPT
taaaatattctgtgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgcattgcttgtttcttaattaacatctctctctttctcccccccccccaccccccccacacacacacatatatatatatatatatgatgccttgactaaaatattctgtgatgatatatttataatattcttttctgcaagCAGGCTGTCGAATCGTGGTTAGTGGATAAAGCTGTTCTACCAATCGAAAATTCTGTTGGTGGAAGCATCCACCGTAATTATGATTTACTTCTTGGACACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG