Sequence
atgc intronic sequence ATGC exonic sequence...ctttcttcatttcaaatattataaagaaaattgcacaatgaagcatttacccgttttatacattgtgcactactaaacataactatggctaaatgctcagGTGAATACTGGTGCAAAAGATAATATGATGCAGAGCTACTTCCTTTCAGAAACACTTAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
Basic information
species | Glycine max |
transcript | GLYMA17G06600.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 13
ctttcttcatttcaaatattataaagaaaat-tgcacaatgaag----catttacccgttttatacattgtgcactactaaacataactatggctaaatgctcagGTGAATACTGGTGCAAAAGATAATATGATGCAGAGCTACTTCCTTTCAGAAACACTTAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
| | ||| || | || | | || | | || | | || || | | | | | || | ||| | | | | || | | |||||||||||||| | || ||||| |||||||| |||| |||||| |||| || || |||||||| || ||| |||| ||||||||||||||||| ||
gtaagctttttttaattgtttttatgatagcatccatacttaaattcccactgagcgctagtgtaagacttacacaaattcttgtcaa-atattttggtctccagGTGAATACTGGCGAGAAGGATAACATGATGCAAAGCTTCTTCCTAGCAGAGACTCTCAAGTACCTATACCTCCTGTTCTCTCCTCCATCAGTCATATCCT
upper sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G128914_T01 (Zea mays), 3'ss of exon 13
-ctttcttcatttcaaatattataaagaaaattgcacaatgaagcatttacccgttttatacattgtgcactactaaacataactatggctaaatgctcagGTGAATACTGGTGCAAAAGATAATATGATGCAGAGCTACTTCCTTTCAGAAACACTTAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
||| | | | || | || || | | ||||| | | | ||||| ||||| || || ||||||||| ||||||| ||| ||||| ||||||||||||| |||||| |||| || || ||||||||||| || | || || |||||||||||||| ||
gtaggtttcctcatgactcccattgatgaatttctgcggaataacatttgtctgacacaactattgt------tggaacatt----tgtct------tcagGTGAACACTGGTGAAAAGGATAACATGATGCAGAGCTTCTTCCTGGCAGAGACGCTCAAGTACCTCTACCTACTTTTCTCCCCTCCATCAGTCATATCCT
upper sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G130889_T03 (Zea mays), 3'ss of exon 9
-ctttcttcatttcaaatattataaagaaaattgcacaatgaagcatttacccgttttatacattgtgcactactaaacataactatggctaaatgctcagGTGAATACTGGTGCAAAAGATAATATGATGCAGAGCTACTTCCTTTCAGAAACACTTAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
||| | | | ||| || || | | | ||||| | | | | | ||| | ||||| || || | ||||||| ||||||| |||||| || ||||||||||| | |||||| |||| || || |||||||| || || | || || |||||||||||||| ||
gtaggattcctcatgacttctattgttgaatttctgctgagtaacatttgtctg----aca-actgttcttgg---aacatt----tgcct------ttagGTGAACACTGGTGAAAAAGACAACATGATGCAGAGTTTCTTCCTGGCAGAGACGCTGAAGTACCTGTACCTACTTTTCTCCCCTCCATCAGTCATATCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttacccgttttatacattgtgcactactaaacataactatggctaaatgctcagGTGAATACTGGTGCAAAAGATAATATGATGCAGAGCTACTTCCTTTCAGAAACACTTAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttcttcatttcaaatattataaagaaaattgcacaatgaagcatttacccgttttatacattgtgcactactaaacataactatggctaaatgctcagGTGAATACTGGTGCAAAAGATAATATGATGCAGAGCTACTTCCTTTCAGAAACACTTAAGTACCTCTATCTCTTGTTTTCTCCTCCATCAGTCATTTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - cttcatt
- - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - -tgcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaaca