Sequence
atgc intronic sequence ATGC exonic sequence...ttttgtcggtttcttggaaattaactttaattcagcttttatctttacaatttatatggagacaagaacaactgatgatgcgcgagcttttctttgttagGAGGAGACTCCAAGACGCTCATGTTTGTACAGATCAGTCCTAATGAGAATGACTTGAGTGAGACTCTTTGCTCCCTCAATTTTGCAAGTAGAGTGAAAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0027g00080.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os12g42160.1 (Oryza sativa), 3'ss of exon 12
ttttgtcggtttcttggaaattaactttaatt--cagcttttatctttacaatttatatggagacaagaacaactgatgatgcgcgagcttttctttgttagGAGGAGACTCCAAGACGCTCATGTTTGTACAGATCAGTCCTAATGAGAATGACTTGAGTGAGACTCTTTGCTCCCTCAATTTTGCAAGTAGAGTGAAAGG
|| | | | | || | || | | || |||| | || ||||| | || || || | | | ||| |||||||||||||| | |||||||| |||||||| || |||||||| || || |||| ||||||||||| || || ||||| || |||||| ||
--------gtatgtagaactttttccttgagtggtaggatttacatctattctttatttttt--tggtaataa-tgtttgcaaacaaaac----------agGTGGAGACTCCAAGACTTTGATGTTTGTTCAGATCAGCCCAAATGAGAACGATGTGGGTGAAACTCTTTGCTCGCTAAACTTTGCGAGCAGAGTGCGGGG
upper sequence: Vv19s0027g00080.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G400223_T01 (Zea mays), 3'ss of exon 11
ttttgtcggtttcttggaaattaactttaattcagcttttatctttacaatttatatggagacaagaacaactgatgatgcgcgagcttttctttgttagGAGGAGACTCCAAGACGCTCATGTTTGTACAGATCAGTCCTAATGAGAATGACTTGAGTGAGACTCTTTGCTCCCTCAATTTTGCAAGTAGAGTGAAAGG
|| | | | || || | | | || ||||| |||| | | | ||| | | | | ||| ||||| ||||| || | |||||||| || ||||||||||||||||| ||| || |||| |||||||| || | || || || || ||||| |||
--------gtatgtagtttttttgtttcatagaattgtgtaatcttacactttagtttagttttatgatt-----caatgtttaaacaatac------agGTGGAGATTCCAAAACTTTGATGTTTGTTCAAATCAGTCCTAATGAGAACGACGTGGGTGAAACTCTTTGTTCATTGAACTTCGCGAGCAGAGTACGAGG
upper sequence: Vv19s0027g00080.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA15G40350.1 (Glycine max), 3'ss of exon 14
--------------------------ttttgtcggttt--cttggaaattaactttaattcagcttttatctttacaatttatatggagacaagaacaactgatgatgcgcgagcttttctttgttagGAGGAGACTCCAAGACGCTCATGTTTGTACAGATCAGTCCTAATGAGAATGACTTGAGTGAGACTCTTTGCTCCCTCAATTTTGCAAGTAGAGTGAAAGG
|| | | || || | | | ||| |||| | || ||| | | || | || ||||| | | ||| | ||| ||||||||||||| ||| | ||||||||||||||||||||||||||||| ||||| ||||||||||| ||||||| || || ||||| |||||||| | |||
gtacttatttctccatgcaaagaaacttatctagggttgcttcttttgctcgtgtatgcctgacttctatcctccacatgtatgcaaatataactagaaaatttgatggacaatcttgttttt-ctagGAGGAGACTCAAAGGCACTCATGTTTGTACAGATCAGTCCTAATGAAAATGATTTGAGTGAGACAATTTGCTCTCTGAACTTTGCTAGTAGAGTAAGAGG
upper sequence: Vv19s0027g00080.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G18590.1 (Glycine max), 3'ss of exon 14
--------------------------ttttgtcggtttcttggaaattaactttaattcagcttttatctttacaatttatatggagacaagaacaactgatgatgcgcgagcttttctttgttagGAGGAGACTCCAAGACGCTCATGTTTGTACAGATCAGTCCTAATGAGAATGACTTGAGTGAGACTCTTTGCTCCCTCAATTTTGCAAGTAGAGTGAAAGG
|| | | || || || | || | || | || ||| | | ||| | | | || || || || | | ||| | ||| ||||||||| || ||| | ||||||||||||||||||||||||||||| || || ||||||||||| ||||||| || || ||||| |||||||| | |||
gtacttatttctccatgcaaagaaacttatctaggcttgtttcttttgcacgtgtatgc--ctgacttctatctatcctatgcaaatatgaaaataaaatttgttgaacaatcttgttttt-ccagGAGGAGATTCAAAGGCACTCATGTTTGTACAGATCAGTCCTAATGAAAACGATTTGAGTGAGACAATTTGCTCTCTGAACTTTGCTAGTAGAGTAAGAGG
upper sequence: Vv19s0027g00080.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G72250.1 (Arabidopsis thaliana), 3'ss of exon 15
-----------ttttgtcggtttcttggaaattaactttaatt-cagcttttatctttacaatttatatggagacaaga-acaactgatgatgc--gcgagcttttctttgttagGAGGAGACTCCAAGACGCTCATGTTTGTACAGATCAGTCCTAATGAGAATGACTTGAGTGAGACTCTTTGCTCCCTCAATTTTGCAAGTAGAGTGAAAGG
| || | | | | |||| || || | || | |||| || | | | | | | || | |||| || | | || ||||||||| || || || |||||||||||||| ||||||||||| |||||||| |||||||| || ||||| || |||||||| || ||||||| |||
gtattgaattttcttcttgaagctgcaaccactttctttgtttacatatgtttcactgacaaattctgtttatctgttataaagcttacgatgaaaatttactggtatatgacagGAGGAGATTCAAAAACCCTCATGTTTGTACAAATCAGTCCTAACGAGAATGATCAAAGTGAGACACTATGCTCACTGAATTTTGCTAGCAGAGTGAGAGG
upper sequence: Vv19s0027g00080.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: PP1S403_54V6.1 (Physcomitrella patens), 3'ss of exon 11
------ttttgtcggtttcttggaaattaactttaattca---gcttttatctttacaatttatatggagacaagaacaactgatgatgcgcgagcttttctttgtt----agGAGGAGACTCCAAGACGCTCATGTTTGTACAGATCAGTCCTAATGAGAATGACTTGAGTGAGACTCTTTGCTCCCTCAATTTTGCAAGTAGAGTGAAAGG
| | || | || | | | | || ||| ||| || | || | || |||| || ||||||| ||| |||||| ||||| ||||| || ||||||||||| || ||||||||||| ||| || |||||||||||||| || | ||||| |||||| ||||| |||
gtatcttactttctactcctcgctggcggatctcagaccatatgctgctatattcaaggctt-ttcattaccattgtttgtgctcgatgtaacagtttttcttggttttacagGAGGGGACTCTAAGACACTGATGTTTGTACAAATTAGTCCTAATGAAGCTGATTTAAGTGAGACTCTTTGTTCATTGAATTTCGCAAGTCGAGTGCGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaatttatatggagacaagaacaactgatgatgcgcgagcttttctttgttagGAGGAGACTCCAAGACGCTCATGTTTGTACAGATCAGTCCTAATGAGAATGACTTGAGTGAGACTCTTTGCTCCCTCAATTTTGCAAGTAGAGTGAAAGG
aactgat putative branch site (score: 3)
cttttctttgtt putative PPT
tttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgtcggtttcttggaaattaactttaattcagcttttatctttacaatttatatggagacaagaacaactgatgatgcgcgagcttttctttgttagGAGGAGACTCCAAGACGCTCATGTTTGTACAGATCAGTCCTAATGAGAATGACTTGAGTGAGACTCTTTGCTCCCTCAATTTTGCAAGTAGAGTGAAAGG
- - - - - ttcttgg
- - - - - - - - -aaattaa
- - - - - - - - - - - - - - - ttcagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgcgc