Sequence
atgc intronic sequence ATGC exonic sequence...attttacatattgaaataaaacgttttcatcaatttttacatactttttattttcactatttttagtgttttctcatgttaattttttcatgacaaacagAAAGATGTAGAATTGGATCTACTCCACAAAACGAGTGGTATTTCTTCAGTCACAAGGATAGAAAGTACCCCACAGGTTCAAGGACTAATAGAGCAACGAA
Basic information
species | Glycine max |
transcript | GLYMA12G00540.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G00540.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G33280.1 (Arabidopsis thaliana), 3'ss of exon 1
attttacatattgaaataaaacgttttcatcaatttttacatactttt-tattttcactatttttagtgttttctcatgttaattttttcatgacaa-acagAAAGATGTAGAATTGGATCTACTCCACAAAACGAGTGGTATTTCTTCAGTCACAAGGATAGAAAGTACCCCACAGGTTCAAGGACTAATAGAGCAACGAA
| || | | ||| || | | | | | ||| || | | | | | |||||| || ||| ||||| | ||| ||||| || |||||||| ||||||||||||||||| ||||||||||| || || || ||||| |||||||| || | ||||| |
-------------gtacgttcttttattaataatacatatacgatccaatcctctagttatattagatactatacaaaagcattttttttttgtttttgtagATAGATGCAAAATAGGATCAACGCCACAAAATGAGTGGTATTTCTTCAGCCACAAGGATAGGAAATATCCGACAGGGTCAAGGACAAACCGTGCAACCCA
upper sequence: GLYMA12G00540.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 1
attttacatattgaaataaaacgttttcatcaatttttacatactttttattttca-ctatt--tttagtgttttctcat-gttaatttttt-catg-acaaacagAAAGATGTAGAATTGGATCTACTCCACAAAACGAGTGGTATTTCTTCAGTCACAAGGATAGAAAGTACCCCACAGGTTCAAGGACTAATAGAGCAACGAA
| | ||| | | | | || ||| |||||||| | | | |||| ||| |||| | | | ||| ||||| | || | |||| |||||||| ||||| || || |||||||| |||||||| |||||||| ||||||||||| ||||| || ||||| ||||||||||||||||| || ||
-----caacagccaaacatatccctaatatttattggc-tatacttttgttgatgaattattattttgatgttgtaacttagttgattttgtgtatatgtatgcagAGAGATGTAGGATTGGGTCCACACCACAAAATGAGTGGTACTTCTTCAGCCACAAGGATAGGAAGTATCCAACAGGGTCAAGGACTAATAGAGCCACAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttattttcactatttttagtgttttctcatgttaattttttcatgacaaacagAAAGATGTAGAATTGGATCTACTCCACAAAACGAGTGGTATTTCTTCAGTCACAAGGATAGAAAGTACCCCACAGGTTCAAGGACTAATAGAGCAACGAA
tgttaat putative branch site (score: 3)
ttttttcat CT-rich tract
atgttaattttttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttacatattgaaataaaacgttttcatcaatttttacatactttttattttcactatttttagtgttttctcatgttaattttttcatgacaaacagAAAGATGTAGAATTGGATCTACTCCACAAAACGAGTGGTATTTCTTCAGTCACAAGGATAGAAAGTACCCCACAGGTTCAAGGACTAATAGAGCAACGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt