Sequence
atgc intronic sequence ATGC exonic sequence...tatattttgcctgtggacggtagtttctttttctcgttgttttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
tatattttgcctgtggacggtagtttctttttctcgttgttttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
|| | | | || | | | || | || || | | |||| | | || |||| ||| || || | ||||| ||||| ||||||||||| |||||||| || || |||||||| ||||| |||||||| ||||| |||||||| || || ||||| ||
------------gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcctcaccttaaaaagattatgaactc-----tttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
upper sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
-tatattttgcctgtggacggtagtttctttttctc---gttgttttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
||| | ||| || || || || |||| || | | | | || | || ||| ||| || || |||| | || || | ||||| |||||||||||||||||||||||||| || || |||||||||||||| || ||||| || ||||||||||| || ||||| || ||
gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactc--atattacaaaattctggtc-----aatttctctt-----agGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
upper sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
tatattttgcctgtggacggtagtttctttttctcgttgttttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
|| || | || || || | ||||| | || || || || | ||| | || | || | || || | || | || || ||| | || || |||||||||||||||||||||||||| || || |||||||||||||| || || ||||| || ||||||||||| ||||| | ||
-gtacgctgaatctgaacc-tactatcttta---catttttatagatgattcaacatcaccaacttatgttccaaattttatggtcaatttttctt--agGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
upper sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
---------------------------------------------------------------------------------------------tatattttgcctgtggacggtagtttctttttctcgt---tgtt-ttattgctttgtgcttcaaa-atctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
| | || | |||| || | || | | | || ||| || || ||| | | || || | | | ||||||||| ||||||| ||||||| |||||||||||||| ||||||||||| |||||||||||||||||||| ||||| || || || |||||||||||||| |||||||||
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagctt-cttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
upper sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G20590.1 (Glycine max), 3'ss of exon 9
tatattttgcctgtggacggtagtttctttttctcgttgttttattgctttgtgcttcaaaatctcaagtct-cttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
|| ||| | || | | || | | || | | || | |||| || || | | ||| || || | ||||||| ||||||||||||||| |||||||||||||||||||||||||| || || ||||||||||| |||||||| || || || |||||||||||||| |||||||||
-ttaagttgttaggtgatgtcatttaaaaggttttatttcatctcttaacagttcctcaagatgaaaactaaattcatctcattgacatgttgttttgcagCTACTTAGCTCCTGAATATGCAATGACTGGCCATCTTCTGGTCAAGAGTGATGTTTATAGTTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
upper sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G01210.1 (Glycine max), 3'ss of exon 10
tatattttgcctgtggacggtagtttctttttctcgttgttttattgctttgtgcttcaaaatctcaagt-ctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
|| | | | || || | | | || || | | | | ||||| || | | | ||| || || | ||||||| ||||||||||||||| |||||||||||||||||||||||||| || || ||||| ||||| |||||||| || || || |||||||||||||| |||||||||
-ttaagtggttaggtgatggcatgtaaaaggtttcatttcagctcttaacaattccttaaaatgaaaactgcattcatctcattgacatgttgttttgcagCTACTTAGCTCCTGAATATGCAATGACTGGCCATCTTCTGGTCAAGAGTGACGTTTATAGTTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
upper sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G42600.1 (Glycine max), 3'ss of exon 4
tatattttgcctgtggacggtagttt---ctttttctcgttgtt-ttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
| || ||| || | ||| | | | || || || | | || | || | | || | | || || ||||||||| |||||| ||||||| ||||||||||||||||| ||||| || |||||||||||||||||||| ||||| || || || ||||||||||||| |||||||||
----agatcccggtgaacttttttttacacagatatacattaccatttctgtgcatttcctctagatgaaactgattttttgccattaaaatcttgttttgcagCTATGTAGCTCCTGAATATGCAATGACTGGTCATCTCCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAAGTGGAAGAAAG
upper sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
tatattttgcctgtggacggtagtttctttttctcgttg--ttttattgctttgtgcttcaaaat-----ctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
| | || | | ||||||| | | || | | ||| | | | | | || | || | | | | || | | ||| || | || || ||||| |||||||| || ||||| || ||||| ||||||||||||||||| || ||||| ||||| |||||||| | ||| | ||
-------ttctcttgtattctcgtttcttctattttttagatatctttggctggaccgctagcgttgttacttgattcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA
upper sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S95_115V6.1 (Physcomitrella patens), 3'ss of exon 7
tatattttgcctgtggacggtagtttctttttctcgttgttttattgctttgtgcttcaaaatc--tcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
| |||| | | ||||| | | | | | | | | | | | | | | || | | | | | | ||| ||| | || || || || |||||||| || |||||||| || || || || |||||||||||||| || || |||||||||||||| | ||| | ||
-ttcttttacat-tggaccacatctagaactaccacattaatcagaatgtcaggacttagccttggtttctgcactgacctattggttgattcaaactgcagGTACGTTGCCCCTGAGTACGCAATGACAGGACATCTTCTTGTTAAGAGCGACGTTTACAGTTATGGAGTGGTACTTCTTGAGCTCCTCTCGGGACGGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
cttcttgttttcc CT-rich tract
aataaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatattttgcctgtggacggtagtttctttttctcgttgttttattgctttgtgcttcaaaatctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - -tgcctgt
- - - - - - - - - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaac