Sequence
atgc intronic sequence ATGC exonic sequence...attttttgctatgctgtaaagtatgatttcttgactgtttctatgttctccctttttttaacctttatagtccttcttaaactaagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGGAGGTATCATGTTACTGAGTATTTGGGATCTGCTGCATTTAGC
Basic information
species | Glycine max |
transcript | GLYMA08G06160.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------attttttgctat--gctgtaaa-gtatgatt-tcttgactgtttc-tatgttctccctttttttaac---ctttatagtccttcttaaactaagtttttgttgct--cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGGAGGTATCATGTTACTGAGTATTTGGGATCTGCTGCATTTAGC
|||| | ||| ||| || || | | || || || | | | | || | ||||||| || || ||||| | || | | | | ||||||||||||||| || ||||| ||||||||||||||| | |||||||| || |||||| | |||||||| | ||||||||||| || ||||| || |||
gtattttctttaaatgattgttccatctgttaatcttgttaaagcataaaaaaatgatatggtaatttccagttatctattgtccttgtgtgcctgtgttcacagtgtggcacctacgccgtatttttaaaagatattttatatcttctaacaccgtctcctgttaattaacagAACTGGCTTTGAAGAAGACAAAAATTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGGTCAGCTGCTTTCAGC
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------attttttgctat--gctgtaaa-gtatgatt-tcttgactgtttctatgttctccctttttttaacctttatagtccttcttaaactaagtttttgttgct---cagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGGAGGTATCATGTTACTGAGTATTTGGGATCTGCTGCATTTAGC
||||| | ||| ||| || || | | || || || | || ||||||| ||| | | | || | ||| | | | | || | ||||||||||||||| || ||||| || |||||||||||| | |||||||| || |||||| | |||||||| | ||||||||||| || |||||||| |||
gtaatgcatttaaatgtttgtcccatattttaatcttactaaagcataaaaaatgatgtggtgattttcagttatctattgtccttgtgtgcctgtgttcacagtgtggcacttaaacctttttataaagtattttgtgtattctaacattatctcctattaattatcagAACTGGCTTTGAAGAAGACAAAAACTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGTTCAGCTGCATTCAGC
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------attttttgctatgctgtaaagtatgatttcttgactgtttctatg---------------ttctccc---tttttttaacctttatag--------tccttcttaaactaagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGGAGGTATCATGTTACTGAGTATTTGGGATCTGCTGCATTTAGC
| ||| |||| |||| ||| || | || ||| | | | |||| | || | |||| | | | ||||| | | || |||||| ||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||| || ||||| | || ||||| |||||| || | ||||| || || ||||||
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
upper sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
attttttgctatgctgtaaagtatgatttcttgactgtttctatgttc-------tccctttttttaacctttatagtccttcttaaactaagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGGAGGTATCATGTTACTGAGTATTTGGGATCTGCTGCATTTAGC
|| | | | | | || | || || | | | ||| || |||| | || | | || | |||||| | ||||||||| |||||||||||||| || |||||||||||||||||||| || ||||||||| | ||||||||||| |||||| | || || |||||||| |||
-------gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctccctttttttaacctttatagtccttcttaaactaagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGGAGGTATCATGTTACTGAGTATTTGGGATCTGCTGCATTTAGC
ttttaac putative branch site (score: 2)
tttttgtt putative PPT
tttttttaacctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttttgctatgctgtaaagtatgatttcttgactgtttctatgttctccctttttttaacctttatagtccttcttaaactaagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGGAGGTATCATGTTACTGAGTATTTGGGATCTGCTGCATTTAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - ctatgct
- - - - - - - - - - - - - - - - - ctgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctt