Sequence
atgc intronic sequence ATGC exonic sequence...ctttgttcacttcatatattctaaagaaaattgcacaatgaagcatttgcctgttttatacattgtgcactactaaacataactatggctaattgctcagGTGAATACTGGTGCAAAAGACAATATGATGCAGAGCTACTTCCTTTCAGAAACACTCAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
Basic information
species | Glycine max |
transcript | GLYMA13G00470.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G00470.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 13
ctttgttcacttcatatattctaaagaaaat-tgcacaatgaag----catttgcctgttttatacattgtgcactactaaacataactatggctaattgctcagGTGAATACTGGTGCAAAAGACAATATGATGCAGAGCTACTTCCTTTCAGAAACACTCAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
| | | || | | || | | || | | || | | || || | | | | || | ||| | | | | || | | |||||||||||||| | || || || |||||||| |||| |||||| |||| || ||||||||||| || ||| |||| ||||||||||||||||| ||
gtaagctttttttaattgtttttatgatagcatccatacttaaattcccactgagcgctagtgtaagacttacacaaattcttgtcaa-atattttggtctccagGTGAATACTGGCGAGAAGGATAACATGATGCAAAGCTTCTTCCTAGCAGAGACTCTCAAGTACCTATACCTCCTGTTCTCTCCTCCATCAGTCATATCCT
upper sequence: GLYMA13G00470.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G128914_T01 (Zea mays), 3'ss of exon 13
ctttgttcacttcatatattctaaaga--aaattgcacaatgaagcatttgcctgttttatacattgtgcactactaaacataactatggctaattgctcagGTGAATACTGGTGCAAAAGACAATATGATGCAGAGCTACTTCCTTTCAGAAACACTCAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
| | | | |||| | | | || || || | | |||||| ||| | ||||| ||||| || || ||||||||| ||||||| ||| || || ||||||||||||| |||||| |||| || |||||||||||||| || | || || |||||||||||||| ||
-gtaggtttcctcatgactcccattgatgaatttctgcggaataacatttgtctgacacaactattgt------tggaacatt----tgtct------tcagGTGAACACTGGTGAAAAGGATAACATGATGCAGAGCTTCTTCCTGGCAGAGACGCTCAAGTACCTCTACCTACTTTTCTCCCCTCCATCAGTCATATCCT
upper sequence: GLYMA13G00470.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G130889_T03 (Zea mays), 3'ss of exon 9
ctttgttcacttcatatattctaaag--aaaattgcacaatgaagcatttgcctgttttatacattgtgcactactaaacataactatggctaattgctcagGTGAATACTGGTGCAAAAGACAATATGATGCAGAGCTACTTCCTTTCAGAAACACTCAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
| | | |||| ||||| | || || | | | |||||| ||| | | | ||| | ||||| || || | ||||||| ||||||| ||||||||| ||||||||||| | |||||| |||| || || |||||||| || || | || || |||||||||||||| ||
-gtaggattcctcatgacttctattgttgaatttctgctgagtaacatttgtctg----aca-actgttcttgg---aacatt----tgcct------ttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAGACGCTGAAGTACCTGTACCTACTTTTCTCCCCTCCATCAGTCATATCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcctgttttatacattgtgcactactaaacataactatggctaattgctcagGTGAATACTGGTGCAAAAGACAATATGATGCAGAGCTACTTCCTTTCAGAAACACTCAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
ttttatacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttgttcacttcatatattctaaagaaaattgcacaatgaagcatttgcctgttttatacattgtgcactactaaacataactatggctaattgctcagGTGAATACTGGTGCAAAAGACAATATGATGCAGAGCTACTTCCTTTCAGAAACACTCAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - -cacttca
- - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - -tgcacaa
- - - - - - - - - - - - - - - - - - - - - gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaaca