Sequence
atgc intronic sequence ATGC exonic sequence...ttattttgttaggtgacttgggacttagctcacaacaaagtatatgggttttgttacttttctctctgtgtatatataaataaaatattttaaatttcagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTG
Basic information
species | Glycine max |
transcript | GLYMA12G06690.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 5
ttattttgttaggtgacttgggacttagctcacaacaaagtatatgggttttgttacttttctctctgtgtatatataaataaaatattttaaatttcagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTG
|| || | ||| | || | | || | | | | ||| || | | || ||| ||| |||||| |||||| || ||||||||||||||| ||| ||| || ||||||||| |||||||| || ||| | || || |||||||| || |||||||||||||| || |
---gttggtgatatgaatgtcattgcagatatcttgaatggagacagctttgtcaacaaattttgctaattatgcataccct---tattttg----tcagGTAAGCCATCATCCCCCAATGGGTGTTGCTCACTGCGAGAATGAACATTTTACTTACGATATCACGTCTAAGTTGAAGACCAAGTTTTTGGGAAATTCAG
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 5
ttattttgttaggtgacttgggacttagctcacaacaaagtatatggg-----ttttgttactt--ttctctctgtgtatatataaataaaatattttaaatttcagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTG
| ||||| | | | | || | || | | || ||||| | || | ||| ||| ||| | | | | | | |||||| || ||||||||||||||| ||||||| || ||||||||||||||||| |||||| | || || ||| |||| || ||||| |||||||| ||
--------gtcggtgatacgaatgtcatcgcagattaacttgaacggagacaactttgtcaacaaattttttctaattatgtattt-tgtactctcatttttatcagGTAAGCCATCATCCCCCAATGGGTGCTGCTCACTGTGAGAATGAGCATTTTACTTATGATATCACGTCTAAGGTGAAGACAAAGTTCTTGGGAAATTCAT
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 5
ttattttgttaggtgacttgggacttagctcacaacaaagtatatgggttttgttac---ttttctctctgtgt-atatataaataaaatattttaaattt-cagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTG
| | || || | | || | | || || | | | | | | ||| | || ||||| ||| || | ||| ||| ||||| || |||||||| ||||||||||||| ||||||||||| ||||| || | || || | || ||||||||||||||||| ||||||| |||||||
--gtgcggctatacatctcattgttactcacatagtggataatgactaattcgcaataagtcatatatttgtttcatttataa-taagttactgtaatttttcagGTTAGCCATCATCCACCAATGAGTGCTGGTCATGCCGAGAACGAGCACTTCATTTACGACATCACATCAAAGTTGAAAACTAAACTTTTGGGTAACTCTG
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 5
ttattttgttagg-tgacttgggacttagctcacaacaaagtat-atgggttttgttacttttctctctgtgtatatataaataaaatattttaaatttcagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTG
|| | | | | | ||| | ||| | | ||| | | |||| || || || | | | | ||| ||||||||| || |||||||| || |||||||||| |||||| || ||||||||||| || ||||| || || ||||| || ||||| || ||||| || ||||
--atctggatgttctctcatggaaggatgcttcctcatgattattgttttctctgttctaaagttcataatggtaatgtgtctgcattcattttgatttcagGTCAGCCATCATCCTCCGATGAGTGCTGGGCATGCTGAAAATGAGCATTTCACTTATGAAGTTACATCAAAATTAAAAACCAAATTTTTAGGGAACTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggttttgttacttttctctctgtgtatatataaataaaatattttaaatttcagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTG
ttttctctctgtgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattttgttaggtgacttgggacttagctcacaacaaagtatatgggttttgttacttttctctctgtgtatatataaataaaatattttaaatttcagGTGAGTCATCATCCCCCAATGAGTGCTGCGCATGCCGAGAATGAGCATTTTACATATGATGTGACTTCAAAGTTGAAAACTAAGTTTTTGGGAAACTCTG
- - - - - - -tgacttg
- - - - - - - - - - - - - - - cacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa