Sequence
atgc intronic sequence ATGC exonic sequence...aaattcaaccaaatgaagccttttaccatttacttggctagctttggcatttctagtgaagaaacaaaaacaattaaagggataacacgttttgttgcagAATGAAGATGGAGGTTGGGGGCTACACATTGAGGGCCCGAGCACCATGTTTGGTACTGTGCTAAGCTATGTTACTCTAAGATTGCTTGGTGAAGGAGGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os11g08569.1 (Oryza sativa), 3'ss of exon 3
aaattcaaccaaatgaagccttttaccatttacttggctagctttg-gcatttctagtgaagaaacaaaaac---aattaaagg-gataacacgttttgttgcagAATGAAGATGGAGGTTGGGGGCTACACATTGAGGGCCCGAGCACCATGTTTGGTACTGTGCTAAGCTATGTTACTCTAAGATTGCTTGGTGAAGGAGGTT
||| || ||| || | || | | || | ||| ||| | | || || |||| | || | | | |||||||||||||||||||| |||||| | ||||||||||||| ||||||||| |||| | || | ||||||| || | ||||||||||| || ||
-aat---acttaattaa-tcacccactaatcgctgctccgtttttacaagattcaaacatgcatgcataagtctagattattcctaacaatatatataattgcagAATGAAGATGGAGGGTGGGGGTTGCACATTGAGGGCCACAGCACCATGCTTGGCTCATCCCTGAACTATGTTGCTTTGAGATTGCTTGGGGAGGGTCCAA
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 3
aaattcaaccaaatgaagccttttaccatttacttggcta-gctttggcatttctagtgaagaaacaaaaacaat-taaagggataacacgttttgttgcagAATGAAGATGGAGGTTGGGGGCTACACATTGAGGGCCCGAGCACCATGTTTGGTACTGTGCTAAGCTATGTTACTCTAAGATTGCTTGGTGAAGGAGGTT
| | | || ||| || | | || || ||| |||| | | || | || |||||||||||||||| ||||| | ||||||||||||| |||||||||||||| | | | | | |||||| || | ||||||||||| || ||
------------------------gtaagaaatctaattacacttctacaatcttga--aataagtaaaggcaatgttttccttttctgtgtgtaagtgtagAATGAAGATGGAGGATGGGGTTTGCACATTGAGGGCCACAGCACCATGTTTGGCTCAGCGTTGACATATGTTTCTTTGAGATTGCTTGGGGAGGGGCCAG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 3
aaattcaaccaaatgaagccttttaccatttacttggctagctttggcatttctagtgaagaaacaaaaacaattaaagggataacacgttttgttgcagAATGAAGATGGAGGTTGGGGGCTACACATTGAGGGCCCGAGCACCATGTTTGGTACTGTGCTAAGCTATGTTACTCTAAGATTGCTTGGTGAAGGAGGTT
| ||| | || ||| |||| || ||| | ||| | ||| | | | || ||||||||||||| || ||||| | ||||||||||| || |||||||||||||| | | || | ||| |||||| | ||||||||||| || |||
---------------------gcaaggattcagtt--ctaaatttgtcaaccctacagtgctaacggtgat--ctaattttgtcgc---tgcaactgtagAATGAAGATGGTGGCTGGGGCTTGCACATTGAGGGTCCAAGCACCATGTTTGGCTCAGCACTGACCTACGTTACTTTGAGATTGCTTGGAGAGGGACCAG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G821318_T01 (Zea mays), 3'ss of exon 1
aaattcaaccaaatgaagccttttaccatttacttggctagctttggcatttctagtgaagaaacaaaaacaattaaagggataacacgttttgttgcagAATGAAGATGGAGGTTGGGGGCTACACATTGAGGGCCCGAGCACCATGTTTGGTACTGTGCTAAGCTATGTTACTCTAAGATTGCTTGGTGAAGGAGGTT
| | |||| ||| | ||| || | | || | | || | | | | | | || |||||||||||||||| ||||| | ||||||||||||| ||||||||| || | | | | | ||||||| || | || |||||||| || |
-------------------gtaaggctattttattgataaacttgaaagttgcgtgctgggagagagcaaacttcattactctccctgaatataatgtagAATGAAGATGGAGGGTGGGGATTGCACATTGAGGGCCACAGCACCATGCTTAGCTCAGCCTTGAACTATGTTGCTTTGAGGTTGCTTGGGGAGAGCCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcatttctagtgaagaaacaaaaacaattaaagggataacacgttttgttgcagAATGAAGATGGAGGTTGGGGGCTACACATTGAGGGCCCGAGCACCATGTTTGGTACTGTGCTAAGCTATGTTACTCTAAGATTGCTTGGTGAAGGAGGTT
ggataac putative branch site (score: 3)
ttttgtt putative PPT
aaacaaaaacaattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaattcaaccaaatgaagccttttaccatttacttggctagctttggcatttctagtgaagaaacaaaaacaattaaagggataacacgttttgttgcagAATGAAGATGGAGGTTGGGGGCTACACATTGAGGGCCCGAGCACCATGTTTGGTACTGTGCTAAGCTATGTTACTCTAAGATTGCTTGGTGAAGGAGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - tcaacca
- - - - - - -tgaagcc
- - - - - - - - - - - -taccatt
- - - - - - - - - - - - - - - tacttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataacac