Sequence
atgc intronic sequence ATGC exonic sequence...gaaaatattggcagcttctctaatttattatgctttctcttaattctttttcaaaattgatgttgcttgttctgctgtggcttgtaatatcattgtttagGGTATGAGGATGCTGCTCTGAAAACCCAACGCAGTCTTGCTTTGTTGAACTTTGGTCAAAATGTTATATTTAGTACCGCTCTTTCATCAGCAATGGTGCT
Basic information
species | Glycine max |
transcript | GLYMA02G40490.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G40490.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g03770.1 (Oryza sativa), 3'ss of exon 9
----gaaaatattggcagcttctctaatttattatgctttctcttaattctttttcaaaattgatgttgcttgttctgctgtggcttgtaatatcattgtttagGGTATGAGGATGCTGCTCTGAAAACCCAACGCAGTCTTGCTTTGTTGAACTTTGGTCAAAATGTTATATTTAGTACCGCTCTTTCATCAGCAATGGTGCT
||| | || | | ||| || | | |||| ||| |||||| | | || | | || | || ||| | || ||||||||||||||| |||||||||||| | || ||||| | |||||||||| |||||| | |||||||| | ||| | || | || ||||| |
tctgatgaatcctagctgacatgttgctttggcatatatcgta--aattggtttataaaatttgatctattaattactatttctttttcacaat--ttggtcagAGTATGAGGATGCTGCACTGAAAACCCAAAGTAGCCTTGCCTACCTGAACTTTGGACAAAATATCATATTTAGCTCGGCTTTATCCACGGCTATGGTTTT
upper sequence: GLYMA02G40490.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G032936_T01 (Zea mays), 3'ss of exon 4
gaaaatattggcagcttctctaatttatta-tgctttctcttaattctttttcaaaattgatgttgcttgtt--ctgctgtggcttgtaatatcat---tgtttagGGTATGAGGATGCTGCTCTGAAAACCCAACGCAGTCTTGCTTTGTTGAACTTTGGTCAAAATGTTATATTTAGTACCGCTCTTTCATCAGCAATGGTGCT
| | || || | | | | | |||| | | ||| ||| | | || | | | | || || || || || | || |||||||||||||| |||| |||||| | |||||||| | |||||||||| ||||||||||| ||||| | ||| | || |||||||||| |
-----tcgtcccacctgtcttgtaacactggcacacagcataaattgatatgttaaagagatctaatctattaattatttttg-ttacaacatgatttgtgatcagATTATGAGGATGCTGCATTGAAGACCCAAAGTAGTCTTGCCTACCTGAACTTTGGCCAAAATGTTATCTTTAGCTCAGCTTTATCTACAGCAATGGTTTT
upper sequence: GLYMA02G40490.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G58270.1 (Arabidopsis thaliana), 3'ss of exon 7
----------gaaaatattggcagcttctctaatttattatgctttctcttaattctttttcaaaattgatgttgcttgttctgctgtggcttgtaatatcattgtttagGGTATGAGGATGCTGCTCTGAAAACCCAACGCAGTCTTGCTTTGTTGAACTTTGGTCAAAATGTTATATTTAGTACCGCTCTTTCATCAGCAATGGTGCT
| || | | | | | || || ||| | | || | | ||| | || || | ||||| | | ||| | || || | ||||| |||||||| ||| |||| ||| | ||||||||||| || |||||||| |||| | | ||||||||||| ||| | ||| ||||||||||| |
tttttctaggaagaaaaccgattgatattttaccataatatattattgctccgtccatttacc---ttaatttatcttgtgacgattctgctgcttatccca-------gAATATGAAGATGCTGCCCTGCAAACTCAAAGAAGTCTTGCTTTCTTAAACTTTGGACAAAGTATCATATTTAGTACAGCTTTATCAACAGCAATGGTGTT
upper sequence: GLYMA02G40490.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g08350.t01 (Vitis vinifera), 3'ss of exon 11
----gaaaatattggcagcttctctaatttattatgctttctcttaatt-ctttttcaaaattgatgttgcttgttctgctgtggcttgtaatatcattgtttagGGTATGAGGATGCTGCTCTGAAAACCCAACGCAGTCTTGCTTTGTTGAACTTTGGTCAAAATGTTATATTTAGTACCGCTCTTTCATCAGCAATGGTGCT
| | |||| || | | || || | | | | | | |||| | |||| |||| || |||| || | || || || ||||||||| |||||||| | ||||| ||||||||||||||||| ||||||||||| ||||| | |||||||| ||||| || ||| |||| |||||| |
atatcatgaaattgccatatcttataggttctagggatagaaatgactgactttgtttaaatatttgtt-----ttatgctactactaatgatgctatctttcagGGTATGAAGATGCTGCCTTAAAAACGCAACGCAGTCTTGCTTTTTTGAACTTTGGCCAAAACTTAATATTTAGCACCGCCCTATCAACAGCTATGGTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttcaaaattgatgttgcttgttctgctgtggcttgtaatatcattgtttagGGTATGAGGATGCTGCTCTGAAAACCCAACGCAGTCTTGCTTTGTTGAACTTTGGTCAAAATGTTATATTTAGTACCGCTCTTTCATCAGCAATGGTGCT
aattgat putative branch site (score: 4)
taatatcattgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaaatattggcagcttctctaatttattatgctttctcttaattctttttcaaaattgatgttgcttgttctgctgtggcttgtaatatcattgtttagGGTATGAGGATGCTGCTCTGAAAACCCAACGCAGTCTTGCTTTGTTGAACTTTGGTCAAAATGTTATATTTAGTACCGCTCTTTCATCAGCAATGGTGCT
- - - - - -cagcttc
- - - - - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgta