Sequence
atgc intronic sequence ATGC exonic sequencegtatttgatttgtcttccctcattcagtgacaaagatgagctctgttttacaatccaaggggttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
Basic information
species | Glycine max |
transcript | GLYMA02G03800.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g56110.2 (Oryza sativa), 3'ss of exon 7
-------gtatttgatttgtcttccctcatt----cagtgacaaagatgagctctgttttacaatccaaggggttgatcatttgactcttaac--ttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
| | || ||| || | || | | | | | |||| | | | | | || | | || |||||||| |||||||||| ||||| || || |||||||||||||||| | | || || || || || ||||| ||||| ||| | ||||||||| | || ||
gaagcttaagtcagcttggtcatctattgtttttgccttcctagaatctaatcatgttattttggcttttaacattttaaattacttgtggacctttcagGATGCAGATGCTTCTATTCGCAAGAGGGCCCTTGAACTTGTTTTTTTGTTAGTCAACGATACAAATGTAAAGCCTTTGACTAAAGAGCTTGTCGACTACT
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G054210_T01 (Zea mays), 3'ss of exon 7
-------------gtatttgatttgtcttccctcattcagtgacaaagatgagctctgttttacaatccaaggggttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
||| | | | | || | | | | | || | | | || | || | ||| | | |||||||| | ||||| || ||||| ||||| || ||||||||||||||| | || || ||||| || ||||| ||||| ||| | |||||||| || |||||
tgtcttaccccccgtaggtcaagtttttttttttactgtttcaagcagtctattttgttattctggtttttattatttctaattgctgtgtacctttcagGATGCCGATGCCTCCATTCGCAAAAGGGCTCTTGAACTTGTTTATTTGTTAGTCAATGATACAAATGTAAAGCCTTTGACTAAAGAGCTCATCGATTACT
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G017421_T02 (Zea mays), 3'ss of exon 7
--------gtatttgatttgtcttccctc--attcagtgac---aaagatgagctctgttttacaatccaaggggttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
| || |||| ||| || | |||| || | || || | | | | || || | || ||||||| |||||| || ||||| ||||||||||| |||||||||||| | | || ||||| || ||||| ||||| ||| | || || ||| | ||||| |
ttcaacacattttctatttatctgccttatggaccagtcactttgtactggattcctaatctgcttctttacttattttcaatcacatatgtatgctcagGATGCAGATGTCTCTATTCGTAAAAGAGCCCTAGAACTTGTTTATCTACTTGTCAATGATACAAATGTAAAGCCATTGACTAAGGAACTTGTTGATTACC
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 7
-----------------gtatt-tgatttgtcttccctcattcag--tgacaaagatgagctctgttttacaatccaaggggttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
|||| | | ||| | || ||| |||| | ||| | ||| ||| || | ||| | || | ||| |||||||||||||||| |||| |||||| || ||||| ||| |||| || | |||||||||| ||| |||||||| | ||||| ||||||||||| |||
tccgactttgtgtcttagtatagtaaaccatctaattctgtgtaggtcgactgagatca-ttctttatta-aatggaaagtgtttaatatcttgt-----gctttagGATTCAGATGCTTCAATTCAGAAAAGGGCACTTGAGCTTATTTACCTTCTAGTGAATGAGAATAACGTGAAGCCACTAGCAAAGGAGCTTATAGAATATT
upper sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 7
-------gtatttgatttgtcttccctcattcagtgacaaagatg--------agctctgttttacaatccaaggggttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
|| ||| | |||| || | ||| ||| |||| || | ||| | |||| | | ||| ||| | | ||||||||||||||||||| ||||||||||| |||||||||||| |||||||| | |||||||| | ||||||||||| |||||||||||||| || |||||||
tcgtgtagttttttagttgtgttatcggatt--gtgtcaaaattgccacagccacttctaatatacatatagaaagcttgtaactttaatattctctttcagGATTCAGATGCTTCAATTCGGAAAAGGGCCCTTGAACTTATTTATGTTCTAGTGAATGACAGCAATGTGAAGCCTTTGGCAAAAGAGCTAATTGATTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagatgagctctgttttacaatccaaggggttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
tcttaac putative branch site (score: 2)
ctctt CT-rich tract
ttttacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgatttgtcttccctcattcagtgacaaagatgagctctgttttacaatccaaggggttgatcatttgactcttaacttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT