Sequence
atgc intronic sequence ATGC exonic sequence...aaaaatatatataaacattattgttgtagttatgttgatgacttgtctgagcacatcttgttttaattcatggttcatcttgttttttcttgtattgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
Basic information
species | Glycine max |
transcript | GLYMA07G18310.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g39090.1 (Oryza sativa), 3'ss of exon 3
aaaaatatatataaacattattgttgtagttatgttgat--gacttgtctgagcacatcttgttttaattcatggttcatct-tgttttttcttgtattgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
| || | | | || | | | || ||||| |||| | || | || | | | || | | |||| | | ||||||||| ||||||| |||||||||||||| ||||| |||||||||||||||||| |||| ||||||||||| || || ||||| | |||||| ||||||||
---atcatgttttaccacgtatttccttttttctttgatcagactcagacagtgatatacaggcttggtactcaagatagctgtttcacttctgttgtcgcagAGCATACCTGGCTTCAAAATGCTAAGAAAGCTCCAAATGTTCCACTTGGAGATATTGTAAAGTCAAGGCTGAAACAGTTTTCAAGGATGAATAGATTCAA
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 3
aaaaatatatataaacatta-ttgttgtagttatgttgatgacttgtctgagcacatcttgttttaattcatggttcatcttg-----ttttttcttgtattgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
|| | || |||||| || | || || ||| | |||| | | || || ||| ||| ||| |||||| ||| | || || |||| ||||| ||||| |||||||||||||| ||||| |||||||| ||||||||| |||| ||||||||||| || |||||||| | ||||| ||||||||
-aaggtcactacttacattaattagtataaataacttgttaacttttgt-----tattttcctttttttcttggggaatcttgatatcctttcttttttaccacagAACATCCATGGCTTCAAAATGCTAAGAAAGCTCCAAATGTTCCTCTTGGAGATATTGTGAAGTCAAGGCTCAAACAATTTTCTAGAATGAATAGATTCAA
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G030673_T01 (Zea mays), 3'ss of exon 3
aaaaatatatataaacattattgttgtagttatgttgatgacttgtctgagcacatcttgt-tttaattcatggttcat-----cttgttttttcttgtattgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
| | | ||| |||||| ||||| | | || | || | | ||| | || |||| || || ||||| ||| |||||||||||||||| |||||||||||||| ||||| |||||||| |||||||| |||| ||||||||||| || || ||||| | |||||||||||||||
------gttttcatgatgtatagttgtatacatgttcaaagtccatatggaattacctggcatcccatttagggctcatgcctcttttttgtttctgttatcacagAGCATCCCTGGCTTCAAAATGCTAAGAAAGCTCCAAATGTTCCTCTTGGAGACATTGTAAAGTCAAGGCTGAAACAGTTTTCAAGGATGAACAGATTCAA
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G088361_T01 (Zea mays), 3'ss of exon 3
-aaaaatatatataaacattattgttg--tagttatgttgatgacttgtctgagcacatcttgttttaattcatggttcatcttgttttttcttgtattgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
|| || || | | |||| | ||| | | | | || | || |||| | ||||| ||| |||||||||||||||| |||||||||||||| ||||| || ||||| |||||||| |||| ||||||||||| || || ||||| | |||||||||||||||
tcgaattacctagcatc-ccattgccccctcccctctttgggggttcaggtaggtactctaaagtcccccctccccctcttctt--tgtttctgttatctcagAGCATCCCTGGCTTCAAAATGCTAAGAAAGCTCCAAACGTTCCTCTTGGAGACATTGTAAAGTCAAGGCTGAAACAGTTTTCAAGGATGAACAGATTCAA
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G311220_T03 (Zea mays), 3'ss of exon 3
--------aaaaatatatataaacattattgttgtagttatgttgatgacttgtctgagcacatcttgttttaattcatggttcatcttgttttttcttgtat--tgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
|||| ||| || | |||| |||| ||| | | | || | |||| ||| | | | | ||| | | | |||| |||| ||||| |||||||| ||||||||||||||||| || ||||||||| |||| ||||||||||| || |||||||| | |||||| ||||||||
ttttcccccaaaagtcatacaactcccacctctgta-ttat--------cttttttcactttgtcct-ttttgattgaggaatgctgacatttccccgcaaaaaatacagAACATCATTGGCTTCAAAATGCAAAGAAGGCTCCTAATGTCCCTCTTGGAGATATTGTAAAGTCAAGGCTCAAACAATTTTCTAGGATGAATAGATTCAA
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G51850.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------aaaaatatatataaacattattgttgtagttatgttgatg-acttgtctgagcacatcttgttttaattcatggttcatcttgttttttcttgtattgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
| ||| | | | ||| | | | || | || ||| | || | | |||| || || | || || ||||| | | |||||| || ||| | || || || ||||| ||||| |||||||| |||||||||||||| ||||| ||| | ||||||||||| |||||||| |||||||
gtacatagaagctacctttgccttatgctctttctctctgcatctgttattatctcttttcccaattacttcactgatctggagatactccaaaagattttttttatgcttattcctgcttt-tgttattgtttctcatttgctagAGCACCCATGGATTCAGAACGCAAAGAAAGCTCCCAATGTTCCTCTTGGAGATGTTGTGAAGTCGAGGTTGAAGCAATTTTCAGTGATGAACCGATTCAA
upper sequence: GLYMA07G18310.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 3
aaaaatatatataaacattattgttgtagttatgttgatgacttgtctga-gcacatcttgttttaattcat--ggttcatcttgttttttcttgtattgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
| ||| || | ||| | | | ||| || | | ||| ||| | | | || | || | || || | ||| | || ||||||||||| | |||||||| |||||||| || ||||| |||||||| |||||||||||||||||| ||||||||||||| ||||| |||||||||||||||||
gattttatgcatgatgtttagtagttgaaatatattaa--aattgcatgatggatgccaaattatgttttgttcaatttatactttttctctctgc-ttgcagAGCATTCTTGGCTCCAGAATGCTAAAAAAGCTCCAAATGTTCCTCTTGGAGATGTTGTCAAGGCAAGGCTTAAGCAGTTTTCAATGATGAACAGATTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgagcacatcttgttttaattcatggttcatcttgttttttcttgtattgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
ttttaat putative branch site (score: 3)
ttcatcttgttttttc putative PPT
atcttgttttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaatatatataaacattattgttgtagttatgttgatgacttgtctgagcacatcttgttttaattcatggttcatcttgttttttcttgtattgcagAGCATCCCTGGCTCCAAAATGCTAAGAAGGCTCCTAATGTTCCACTTGGAGATGTTGTCAAGTCAAGGCTTAAGCAATTTTCGATGATGAACAGATTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
aaaaata
- - - - - - - - - - -tgttgta
- - - - - - - - - - - - - - - - - -tgatgac
- - - - - - - - - - - - - - - - - - - - - ttgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - gcacatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcatgg