Sequence
atgc intronic sequence ATGC exonic sequence...ttcttacttgaaactttatttgcaacagttctatttgaaatatgaaaccaatttcaattaaacggaatgtgacgtttatatgtaaaaaattctactacagGGCAAGCAAAGCATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATC
Basic information
species | Glycine max |
transcript | GLYMA01G42900.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G42900.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------------------------------ttcttacttgaaactttatttgcaacagttctatttgaaatatgaaaccaatttcaattaaacggaatgtgacgtttatatgtaaaaaattctac-----tacagGGCAAGCAAAGCATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATC
| || || |||| || | | || | | | ||| || | | ||| || | | || ||| | | | || || | ||||| ||||||||||| ||| |||||||||||||||| ||||| ||||||||| ||| | ||||||| ||||||||||||| |||| | ||||||||||
gtagtattctgctcttatttcccctataataccaccttacatgacttagaccaacaattaacgtggagaaaatttccatgtgcttcactggagtgccgtaatt--aactctaatggaaaaa---caaacaaaaacattacagtttgttctgacaattttagtttgttccttaattcgaggtacttgtatatggttgcagGGAAAGCAAAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
upper sequence: GLYMA01G42900.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------------------ttcttacttgaaactttatttgcaacagtt---ctatttgaaatatgaaaccaatttcaattaaacggaatgtgacgttta---tatgtaaaaaattctactacagGGCAAGCAAAGCATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATC
| ||| ||| || || | | | ||| |||| | ||| || | | | | ||| | | | || | ||||| || |||||||| ||| |||||||||| ||||| ||||| ||||||||| ||| | ||||||| ||||||||||||| |||| | ||||||||||
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatcccttaactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
upper sequence: GLYMA01G42900.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 2
------ttcttacttgaaactttatttgcaacagttctatttgaaatatga-aaccaatttcaattaaacggaatgtgacgtttatatgtaaaaaattctactacagGGCAAGCAAAGCATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATC
| || |||| | || ||||| | ||| | ||| | |||| || | | || || ||| ||| | | | |||| ||||||||||| ||| |||||||||| || |||||||| |||||||| ||| | ||||||| ||||||||||||| |||| | ||||| ||||
ttgagatgctacagccaaacacaagttatg-cagttttttttttcttctgatggctggcttcagtttatctt--tgcaac-cttacttgtttcta---cggatgtagGGAAAGCAAAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACATTACATCAAACTTGTGCTGAGGTCAATTCGCATC
upper sequence: GLYMA01G42900.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 2
ttcttacttgaaactttatttgcaacagttctatttgaaatatgaaaccaatttcaattaaacggaatgtgacgtttatatgtaaaaaattctac---tacagGGCAAGCAAAGCATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATC
||| || || | | ||| | | | | | | | || | | | | | | || || || || | |||| ||||||||||| ||| |||||||||| || |||||||| |||||||| ||| | |||| || ||||||||||||| |||| | || |||||||
-ctttaaatgccacatccaaatagaaggttatgca-gttttttaatgatggctctagtttctcagtttatctttgtaacctg-aattgtttgtatggatgtagGGAAAGCAAAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACGTTACATCAAACTTGTGCTGAGGTCAACTCACATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccaatttcaattaaacggaatgtgacgtttatatgtaaaaaattctactacagGGCAAGCAAAGCATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATC
ttctact CT-rich tract
tttatatgtaaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcttacttgaaactttatttgcaacagttctatttgaaatatgaaaccaatttcaattaaacggaatgtgacgtttatatgtaaaaaattctactacagGGCAAGCAAAGCATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATC
- - - - - - - - - - tgcaaca
- - - - - - - - - - - - - - - - - - - - - tgaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat