Sequence
atgc intronic sequence ATGC exonic sequence...gacattcaaatccctttcttatattgttgaacttgtcagtgttacaaaaaaaccttcatctgattgacctcaactaagtcatttcatgtaaattttctagTGGCTATCTAGCACCAGAGTATGCAATGCGCGGGCACCTGACAGAAAAGGCTGATGTCTTCAGTTTTGGAGTCGTTGCTCTAGAGATCCTGAGTGGAAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0092g00570.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os08g10300.1 (Oryza sativa), 3'ss of exon 23
gacattcaaatccctttcttatattgttgaacttgtcagtgttacaaaaaaaccttcatctgattgacctcaactaagtc-atttcatgtaaattttcta-gTGGCTATCTAGCACCAGAGTATGCAATGCGCGGGCACCTGACAGAAAAGGCTGATGTCTTCAGTTTTGGAGTCGTTGCTCTAGAGATCCTGAGTGGAAGA
| | || | | | || || | | | | | | ||| || | |||| | || || | | | ||| | | |||||||| ||||| |||||||||||| | || || ||||| |||||||||||||| ||| |||||||| ||||||||||| | | ||| ||
----------------gtatgcacatttcaccctttct---tttcttatgagtttacctttga--agtctaagctaattttatctcgtctgaccttttgaagCGGCTATCTGGCACCCGAGTATGCAATGAGAGGCCATCTGACTGAAAAGGCTGATGTTTTCGCATTTGGAGTTGTTGCTCTAGAAACAGTTGCTGGCCGA
upper sequence: Vv10s0092g00570.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os04g22470.1 (Oryza sativa), 3'ss of exon 19
gacattcaaatccctttcttatattgttgaacttgtcagtgttacaaaaaaaccttcatctgattgacctcaactaagtcatttcatgtaaattttctagTGGCTATCTAGCACCAGAGTATGCAATGCGCGGGCACCTGACAGAAAAGGCTGATGTCTTCAGTTTTGGAGTCGTTGCTCTAGAGATCCTGAGTGGAAGA
|| | ||| || ||| ||| | | || || | | || ||| | | | | ||| | | | || ||||| || ||||||||||| ||||||||||||||| | || || || |||||||||||||||| || |||||||| ||| || |||| | ||| ||
-----gtaagaacattt----taccactgatcttcttatgattgtaaca-----tcaatatgaatc-ctactattaacttgtcttat----atttttaagGGGCTATCTAGCTCCAGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATGTTTTTGCATTTGGAGTGGTTATGCTGGAGACTGTCGCTGGGCGA
upper sequence: Vv10s0092g00570.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os08g10290.1 (Oryza sativa), 3'ss of exon 22
-----gacattcaaatccctttcttatattgttgaacttgtcagtgttacaaaaaaaccttcatctgattgacctcaactaagtcatttcatgtaaattttctagTGGCTATCTAGCACCAGAGTATGCAATGCGCGGGCACCTGACAGAAAAGGCTGATGTCTTCAGTTTTGGAGTCGTTGCTCTAGAGATCCTGAGTGGAAGA
||||| | | || | || |||| || || | ||| ||| | | | | || | || ||||| || | ||||| ||||||||||| ||||| |||||||||||| | || || ||||| |||||||| || || || ||||| || || || | |||| | ||| ||
gtatgaacatttta-taccatgctcttatt-ccgagtttat----gttcaaaacataacctaatatttttatcctcacctgacc-------------ttttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGCCATCTGACTGAAAAGGCCGACGTTTTTGCATTTGGGGTAGTCGCCTTGGAGACTGTTGCTGGTCGA
upper sequence: Vv10s0092g00570.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os05g16824.1 (Oryza sativa), 3'ss of exon 22
gacattcaaatccctttcttatattgttgaacttgtcagtgttacaaaaaaaccttcatctgattgacctcaactaagtcatttcatgtaaattttctagTGGCTATCTAGCACCAGAGTATGCAATGCGCGGGCACCTGACAGAAAAGGCTGATGTCTTCAGTTTTGGAGTCGTTGCTCTAGAGATCCTGAGTGGAAGA
|| | ||| | || || ||||| ||| || ||||| | || |||| |||| | |||||| ||||||||||| ||||| |||||||||||| | || | |||| |||||||||||||| || || || || || || || |||| | ||| |
-----gtaagaacatttttatcatctctgttcttgtggctgtaacttcaaaacaaa-agctaattg----taacttgtctgtc--------attttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGCTGATGTTTTTGCATTCGGGGTGGTCGCGCTCGAGACTGTTGCTGGTCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaaccttcatctgattgacctcaactaagtcatttcatgtaaattttctagTGGCTATCTAGCACCAGAGTATGCAATGCGCGGGCACCTGACAGAAAAGGCTGATGTCTTCAGTTTTGGAGTCGTTGCTCTAGAGATCCTGAGTGGAAGA
gattgac putative branch site (score: 3)
ttttct putative PPT
atttcatgtaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gacattcaaatccctttcttatattgttgaacttgtcagtgttacaaaaaaaccttcatctgattgacctcaactaagtcatttcatgtaaattttctagTGGCTATCTAGCACCAGAGTATGCAATGCGCGGGCACCTGACAGAAAAGGCTGATGTCTTCAGTTTTGGAGTCGTTGCTCTAGAGATCCTGAGTGGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- cattcaa
- - - - - -ccctttc
- - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgta