Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatcaattcactttattattttggttcaggttcagctgattttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTACGGGCTTCAGCAATTATCACTAATGCACCCTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
Basic information
species | Glycine max |
transcript | GLYMA08G15380.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G15380.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G64740.1 (Arabidopsis thaliana), 3'ss of exon 8
---------gtaagcatcaattcactttattattttggtt-caggtt-cagctgattttccattgacct--taaataacttgtttttgtaatgatattaaatatgt-gaagGTACGGGCTTCAGCAATTATCACTAATGCACCCTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
|| | || | || | | || || | || | || | ||||| | | | ||| | || | | | | | ||| |||| |||| | || | || | | ||||| || || ||||||||||| ||||||||||||||||| ||||||||||| || ||||||||||| |||||||
gtaaatgatatactttttaaagctctaaaccttcttctttgtaaattacgtcttgccatttattgaaatggttcctgactcttgatttcatctacaaaacttttgttgaagATACGAGTCTCTGGGGTTCTATCAAATGCTCCTTACCTTCTGAATGTCGATTGTGATCACTACATCAACAATAGCAAAGCTCTTAGAGAAGCAATGTGTT
upper sequence: GLYMA08G15380.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G39350.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagcatcaattcactttattattt-tggttcaggttcagctgattttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTACGGGCTTCAGCAATTATCACTAATGCACCCTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
||||| || ||| || |||||| || || | | || | | | |||| | | | || | | | ||||| | || | || || || | | || || || || ||||| ||||| ||||||||||||||||| ||||| ||||| ||| |||||||| |||||||||
gtaagtat-aatgtgtttctttatttatgaatctctcttttcggagccctgacttctcataaactaaaactcatcttacttcttct-------tgaagATCCGAGTCTCTGCTGTTCTATCAAACGCTCCTTACCTTCTTAATGTCGATTGTGATCACTACATCAACAACAGCAAAGCAATTAGAGAATCTATGTGTT
upper sequence: GLYMA08G15380.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G09870.1 (Arabidopsis thaliana), 3'ss of exon 8
----------gtaagcatcaattcactttattattttggttcaggttcagctgattttccattgaccttaaataacttgtttttgtaatgatattaaatatg--tgaagGTACGGGCTTCAGCAATTATCACTAATGCACCCTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
| || | | || | |||| |||| | || | | || | | | || | | ||| || || | ||| || |||| ||||| |||| | || | | || | | ||||| || |||||||| ||||| ||||||||||||||||| || |||||||| || ||||||||||| |||||||
gtaaataattatgctcaactctccagtgtatt-ctttgaattgatttatgtttatctctcgctaacttc--ctgactctttcttctcatgttaccgtatataattgaagATACGAGTCTCTGGAGTTCTATCAAATGCTCCTTATCTTCTAAATGTCGATTGTGATCACTACATCAATAATAGCAAAGCTCTTAGAGAAGCAATGTGTT
upper sequence: GLYMA08G15380.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G21770.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagcatcaattcactttattattttggttcaggttcagctgattttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTACGGGCTTCAGCAATTATCACTAATGCACCCTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
|| || ||| ||| ||| ||||| | || |||||| ||| | | | |||| | ||| | ||||| | |||| || || || || | ||||| || || ||||| ||||| || |||||||| ||||| ||||| ||||||||| ||||||||||||||||||
gttaggatctgttcctttt--catttttctc-----tcttttgatttccca--aatttcgtaaaactaaactcattaacctctct-------tgaagATCCGGGTATCTGCTGTTCTCTCAAATGCTCCTTACCTTCTTAATGTGGACTGTGATCATTACATCAACAACAGCAAGGCAATTAGAGAAGCTATGTGTT
upper sequence: GLYMA08G15380.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0031g02060.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------------------gtaagcatcaattcactttattattttggt-tcaggttcagctgattttcca-ttgaccttaaataacttg--tttttgtaatgatattaaatatgtg-aagGTACGGGCTTCAGCAATTATCACTAATGCACCCTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
| | || || | ||| | | | | |||| | ||| | || ||| | ||| ||| ||| | || | ||| || | ||||| || | ||||||| | || | ||||| || ||||||||||| ||||| ||||| || || || ||||||||||||||||||||||||||||||||||
gtaaaccttaaatcaataacaccttcatagatcctttttctttggttgcctttccttgtcttctgtttttacttttagtataatacctggtttcgatgaataaacacttggcacagaatttattgagctttgttgctgtttttatgaatatccaagGTGCGAGTTTCAGCAGTCATTTCAAATGCCCCGTATCTTCTGAACGTTGACTGTGACCATTATATCAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTACGGGCTTCAGCAATTATCACTAATGCACCCTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
aaataac putative branch site (score: 2)
ttaaataacttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatcaattcactttattattttggttcaggttcagctgattttccattgaccttaaataacttgtttttgtaatgatattaaatatgtgaagGTACGGGCTTCAGCAATTATCACTAATGCACCCTATCTTCTGAATGTTGATTGTGATCACTACATTAACAATAGCAAGGCACTTAGAGAAGCTATGTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC