Sequence
atgc intronic sequence ATGC exonic sequencegtatggtacttcattgttgtttttctgtttctacttgatacctgtattaatatatcatgttaaatttgagtcttttttcttgttgcatatagttcctttatacattttcttcttaaaggtatcccctaggtggggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC
Basic information
species | Glycine max |
transcript | GLYMA12G37100.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 11
gtatggtacttcattgttgtttttctgtttctacttgatacctgtattaatatatcatgttaaatttgagtcttttttcttgttgcatatagttcctttatacattttcttcttaaaggtatcccctaggtggggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC
| ||| | | || || | || | | | | | |||| | || ||| | ||| || || | || | || ||| | ||||| || | ||||||||| || | || | || || | ||| |||| || ||||| |||||||| ||||||||||||||||| ||||||||||| |
------------------------------------------------------------------gtaccactttgttctatttcaccaacttacaatgcat-tctacttccc-----tttcacctgcttcctgagcacaacatccc----atcatctctttt--------ctgaagGTCGTTGAAATTGCAACCAATGCATTGGATGTCTTCAAAAGTGATGCAAAAAAGATGGTAGTTGCACTTGTTGATATGGAGCGTGCCTTTGTCCCACCAC
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatggtacttcattgttgtttttctgtttctacttgatacctgtattaatatatcatgttaaatttgagtcttttttcttgttgcatatagttcctttatacattttcttcttaaaggtatcccctaggtggggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC
| | || | | |||| | || || | | || || | || || |||| |||| | | || | ||||||| ||||| |||| ||||| || || || || ||||||||| | ||||| ||||| |||||| ||||||||||||||||||| ||||| |||||||
------------------------------------------------------------------------------------gta-attatgcttttactgctctttcagttgcatttttcgtcttactaatagctgtttcttttcttaaataatcgtc------aacc-----agGTTGTAGCTATAGCAAGTGCCGCACTTGATGGATTCAAGAATGAAGCTAAGAAGATGGTAGTTGCATTAGTTGATATGGAGCGTGCATTTGTACCACCTC
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatggtacttcattgttgtttttctgtttctacttgatacctgtattaatatatcatgttaaatttgagtcttttttcttgttgcatatagttcctttatacattttcttcttaaaggtatcccctaggtggggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC
| | ||| | ||| | | | | | | ||| | | || || || || || | || ||| ||| || |||||| ||||| |||| || || || || || || ||||||||| | |||||||||||||||||||||||||||||||| || |||||||| |||||||
------------------------------------------------------------------------------------gta-ataatgattttttg-gtgctttattcagtaatattttatcatttcggta-acagttattcctttctgac------taatcatcaacca-gGTTGTAGCTATAGCAAGTGCAGCACTTGATGGTTTCAAGAATGAAGCCAAGAAAATGGTGGTTGCACTAGTTGATATGGAACGCGCTTTTGTACCACCTC
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 11
gtatggtacttcattgttgtttttctgtttctacttgatacctgtattaatatatcatgttaaatttgagtcttttttcttg-ttgcatatagttcctttatacattttcttcttaaaggtatcccctaggtggggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC
|| | | | || | | |||||| | | | | |||| | | | ||| | ||| || || ||| | || || ||| | | | | | | | ||| | ||| || ||| | | || |||||||||| |||||||| || || ||||| | ||| ||||||||| | ||||||||||||||||| ||||| ||||||||||| |||||||| || ||||
------------------gtatattttctttgattgcgcacctgttcttgtg---ctggcagtatttatttatatattcaggattgtgcgtaatt---ttaatccttcatacctaaaaaatctattcgattt------tttattttatttttttattttttattttttatttttattagGTTGTGGCAATTGCAACTGCTGCACTAGATGTGTTCAAGAATGAAGCTAAGAAAATGGTGGTTGCCCTAGTGGATATGGAGCGAGCTTTTGTGCCCCCTC
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S33_163V6.1 (Physcomitrella patens), 3'ss of exon 11
gtatggtacttcattgttgtttttctgtttctacttgatacctgtattaatatatcatgttaaatttgagtcttttttcttgttgcatatagttcctttatacattttcttcttaaaggtatcccctaggtggggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC
||| ||||| || || || | || | ||| ||| || | | | | | || | || | | || || | || | ||| | ||| || |||| || ||||| | | ||||| || | | | | |||||||||||||||||| ||||| || ||||| ||||||||||| ||| |||||||||
------------------------------------------------------gtttgtacaatttcggttccttc----gtagtatctgcttcg---ataaatgtggtacattatagtgtgtt--------gggctaaaattattcaatgatt-ctttgaggctatgcgtttgcagATTGTTGCCATTGCCAGTTCAGCGCTGGACGAATACAGGGTTGAATCAAAGAAAATGGTTGTTGCTCTTGTTGACATGGAGCGTGCATTTATCCCACCTC
upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S109_214V6.1 (Physcomitrella patens), 3'ss of exon 11
gtatggtacttcattgttgtttttctgtttctacttgatacctgtattaatatatcatgttaaat-ttgagtcttttttcttgttgcatatagttcctttatacattttcttcttaaaggtatcccctaggtg---gggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC
| ||| ||| | ||| | | | | | |||| || | | || | | |||| | | | ||| ||| || ||| | | | | | | ||| ||| | || | | || | | || || | | |||| | || | |||| || ||||| || || ||||| || | || || ||| ||||||||||||| ||||| || ||||||||||||||||| ||| | || ||||
------------------------------gtgctt-atagatttatctctttctactatcaaatgttcactaaattctgtgactgcaaaaattatagttacccatctttttcattgaatttcacacaatgtgcttgggcttacagtat-tcaatggttactcggtgttataatcctgca-gATTGTTGCCATTGCTACTGCTGCGCTGGATGAGTATAGAGCAGAAGCAAAGAAAATGGTTGTTGCGCTTGTTGATATGGAGCGTGCATTTATTCCCCCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctaggtggggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC
tcataac putative branch site (score: 2)
tctttc putative PPT
ttgtttaaaaatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggtacttcattgttgtttttctgtttctacttgatacctgtattaatatatcatgttaaatttgagtcttttttcttgttgcatatagttcctttatacattttcttcttaaaggtatcccctaggtggggagtgcactttctctttcataaccttgtttaaaaatctttcaagGTTGTGGCTATTGCAACCGCCGCGCTAGAAGGGTTTAAGAATGAATCAAAGAAAATGGTGGTTGCACTAGTTGATATGGAGCGTGCTTTTGTCCCACCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG