Sequence
atgc intronic sequence ATGC exonic sequence...ctcatttttgaactacctctagtttgatgtaaactggatgattaatgattaatgaagctggtttcttaatgtggaagtgtacatgtatgtttctttgtagGTTATGATGATTACATGTCATTTCTATGTGGTATTAATGGCTCAGCTCCTGTGGTGCTAAACTACACCGGTCAAAATTGCGGGCTTTATAATTCGACTGT
Basic information
species | Glycine max |
transcript | GLYMA15G21920.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G21920.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G20430.1 (Arabidopsis thaliana), 3'ss of exon 9
ctcatttttgaactacctctagtttgatgtaaactggatgattaatgattaatgaagctggtttcttaatgtggaagtg--tacatgtatgtttctttgtagGTTATGATGATTACATGTCATTTCTATGTGGTATTAATGGCTCAGCTCCTGTGGTGCTAAACTACACCGGTCAAAATTGCGGGCTTTATAATTCGACTGT
||| || || | ||| || | || | | | || | ||||| || | | | ||||| || ||||| ||| || || ||||||||||| ||||| || ||||| |||||||| ||||| | ||||||||||| ||||||| || | ||| | || |
-------gtgagttaaac---acttaacataaccttggcagttttctacattttca---aattaccaaatgtagacaccattttaacggtctttctatgcagGTTTTGAAGACTATATGTCATTTCTTTGTGGCATCAATGGATCAGCTCCAGTGGTATTCAACTACACCGGCACAAATTGCTTGCGGAACAATGCAACAAT
upper sequence: GLYMA15G21920.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 9
ctcatttttgaactacctctagtttgatgtaaactggatgattaat----gattaatgaagctggtttcttaatgtggaagtgtacatgtatgtttctttgtagGTTATGATGATTACATGTCATTTCTATGTGGTATTAATGGCTCAGCTCCTGTGGTGCTAAACTACACCGGTCAAAATTGCGGGCTTTATAATTCGACTGT
| | || || | || | ||| | | || || || | | | || | | || || || ||||| ||| | | |||||||||||||||||| |||||||| || ||||| || ||||| ||||||||| |||| || |||||||| ||| | | || || ||| | || ||
tttaacttggatatttctatgttttacaatcagctttttgcttctccttgaactgaataaatcagaattccaagttgaaa---tacat-tatttgttgatgtagGTTATGATGATTATATGTCATTCCTTTGTGGCATCAATGGGTCAGCTCCTATGGTTCTGAACTACACTGGTGAGATGTGTGGAGTTTCCACCATGAATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattaatgaagctggtttcttaatgtggaagtgtacatgtatgtttctttgtagGTTATGATGATTACATGTCATTTCTATGTGGTATTAATGGCTCAGCTCCTGTGGTGCTAAACTACACCGGTCAAAATTGCGGGCTTTATAATTCGACTGT
tcttaat putative branch site (score: 3)
tgtttcttt putative PPT
tttcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcatttttgaactacctctagtttgatgtaaactggatgattaatgattaatgaagctggtttcttaatgtggaagtgtacatgtatgtttctttgtagGTTATGATGATTACATGTCATTTCTATGTGGTATTAATGGCTCAGCTCCTGTGGTGCTAAACTACACCGGTCAAAATTGCGGGCTTTATAATTCGACTGT
- - - - - - ctacctc
- - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - tggatga
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtat