Sequence
atgc intronic sequence ATGC exonic sequencegtttttatgtcattctgtatcttggttttctatgagcgattgtttgctttatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 3'ss of exon 6
gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctttatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
| || || || |||| || | | ||| | || || | | || | || || ||| |||||| ||| || || || ||||| || |||||| |||||||||||||||||||||| || ||||| |||||||||||||||||||| |||||||
----gtttgccaccttgaatctcacttgttctgcttttactgtgtcaattggtaccttacagtcttggtgtttgtat--cagGGTTTGGGTAAGCATGACATCATCTGCATTGAGGATCTTGTTCATGAGATCATGACTGTTGGCCCACATTTCAAGGAGGCCAACAACTTCCTCTGGCCAT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 6
----gttt--ttatgtcattctgtatcttggttttctatgagcgattgtttgct--ttatcttgttgct-aacctgcttttg--tgatgat-agGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
|||| | ||| | || || || | ||| || ||| ||| | | || || | ||| | ||| | || ||| ||||||||| || || || ||||| || |||||| | || |||||||||||||| || || || || |||||||||||||||||||| ||||| |
gtatgtttgctcttgtaggctttcattgtg-ttgtatatatgccatttacagctaatcaaattcttatttggcctattgttggtcaaccattagGGCTTGGGGAAGCATGACATCATCTGCATTGAGGATCTTGTCCACGAGATCATGACTGTCGGTCCACACTTCAAGGAGGCCAACAACTTCCTGTGGCCCT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G094051_T05 (Zea mays), 3'ss of exon 5
gttttta----tgtcattctgtatcttg-----gttttctatgagcgattgtttgctt-tatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
|||| || || | ||| |||| | || |||| | || || || || | |||| | ||| | ||| ||||| ||| || || ||||| || |||||| |||| ||||||||||||||||| || || || |||||||||||||||||||| |||||||
gtttgtaaacttggaactctacatctggttcctgtgttctgtttatatatgacaatttacatgatgatctccaccttttggtgttctatcagGGCTTGGGCAAGCACAACATCATCTGCATTGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCCAACAACTTCCTGTGGCCAT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 6
gttttta---tgtcattctgtatcttggttttctatgagc-gattgtttgctttatcttgt-tgctaacctgc----ttttgtga--tgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
|||| | | |||| | || | | | | ||| | | |||| | | || || | | || | ||| ||| | ||| ||||| ||| || |||||||| || |||||| ||||||||||||||||||| || || || || |||||||| ||||||||||| |||||||
gtttgcaatcttgagctctgcacctggatcctttgtgatctgcttgtatttgacaatttacatgatgatctccaccatttggtgttctatcagGGCTTGGGCAAGCACAACATCATTTGCATTGAGGATCTTGTTCATGAGATCATGACTGTCGGCCCACACTTCAAGGAGGCGAACAACTTCCTTTGGCCAT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
----------------gtttttatgtcattc-tgtatcttggtttt--ctatgagcgattgtttgctt-tatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
| | || | ||| ||| | || || | | | ||| || || || | |||| | |||| | ||| |||| ||| || || ||| | || |||||| |||| ||||||||||||||||| || || || |||||||| ||||||||||| |||||||
gtttgtaaacttggaactgtacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G178807_T01 (Zea mays), 3'ss of exon 5
--------gttttta--tgtcattctgtatcttggt-tttctatgagcgattgtttgctttatct---tgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
| | | | | ||| |||| | || | | | | | || |||| | | ||||| |||| || || || ||||| | |||||| | ||| || ||||| || || ||| |||| ||||||||||| ||||| || || || || ||||||||||||||||| |||||||
gtttttccatccacaactaccgtgctgaatctgattacatccacattccaatttccgccttatgtatattttgcttaccttctgttc--attatagGGCCTTGGGAAGCATAATATCATCTGCATCGAGGACCTTGTTCACGAGATCATGACGGTTGGCCCACACTTCAAAGAGGCCAACAACTTCCTCTGGCCAT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G100225_T01 (Zea mays), 3'ss of exon 5
-----------------gtttttatg-tcattctg-tatcttggttt--tctatgagcgattgtttgctttatctt-------gttgctaacctgcttt-tgtg-atgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
| || | |||| | || | || || | | | || ||| | || | | |||| |||| || |||| | |||||| ||| || ||||| || || ||| | || ||||||||||| || || || || || |||||||||||||||||||| ||||| |
gtttgtcacctgcaacaactaccgtgctgattccgataatccgattaggtccacatttcagttccagccttagataaaaaagagtctttgttttactttctgtgcgtgttagGGCCTCGGGAAGCACAATATCATCTGCATTGAGGACCTTGTCCACGAGATCATGACGGTCGGCCCGCACTTCAAGGAGGCCAACAACTTCCTCTGGCCGT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G02270.1 (Glycine max), 3'ss of exon 6
gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctttat-cttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
| || | | ||| | | | || || | || | | | || | || || ||||| ||||| ||||| |||| |||| ||| || || | || |||||||| || ||||||||||| |||||||||||||| ||||||||||| ||||||||||| |||||||
-gtattgt-ttattttacaattc--ttccttacagattttaattaattcgctacatgcttcttacttgcttg---gatgacagGCTCTGGGCAAGTATGGAATCATATCCACTGAAGATCTGATCCATGAGATCATCACTGTTGGACCTCACTTTAAGGAGGCTAACAACTTCCTTTGGCCAT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G18170.1 (Glycine max), 3'ss of exon 6
---------gttt-ttatgtcattctgtatcttggttttctatgagcgattgtt----tgctttatcttgttgc-taacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
|| | || ||| | || | | || | || | ||||| | ||| | || || | | || | || ||| || ||||||||||| ||| || |||||| | |||||||| || |||||||||||||||||||||||||| || |||||||||||||| || || ||||| |
gtccgtgtggtctattctgtagtcctctgtaaacacttccattgcttgtttgttctattacttagtttttttccctgacataacatt-caatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATCATGACTGTTGGACCTCACTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G23750.2 (Glycine max), 3'ss of exon 6
gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctttatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
| ||| | | | | | || || | || | | | || | || | || || ||||| ||||| |||| |||| || | ||| || |||| || |||||||| || ||||||||||| |||||||| ||||| ||||||||||| ||||||||||| |||||||
---gtattgttaatttacaattctgtattacaaatttgaattaattcacta-catgcttctgacttgcttg---gatgacagGCGCTGGGCAAATATGGAATCATTTCCACTGAAGATCTGATCCATGAGATCATCACTGTTGGGCCTCACTTTAAGGAGGCTAACAACTTCCTTTGGCCAT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
----------------gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctttatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
| | || || ||||| || | | | | || || | || | ||| || | || ||| || ||||||||||| ||| || |||||| | |||||||| || |||||||| ||||||||||||||||||| |||||||||||||| || || ||||| |
gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgt--tctattactcagttttttcgctgacataacatt-caatgccagACTTTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G01250.2 (Arabidopsis thaliana), 3'ss of exon 6
-----------gtttttatgtcattct--gtatcttggtttt---ctatgagcgattgtttgctttatct-tgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT-------------------------------------------------------------------------------
|| | | ||| ||| | || ||||| || | | | | | | | | | | || | | | | ||||| | || ||| |||||| ||||||| || ||| | || || ||||| | || || ||||||||||| ||||| |||||||||||||| |||||||
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatcaggctcttggaaagcatggtatcatttgcactgaggatttgatccacgagattctaacagtaggacctcatttcaaggaagCCAACAACTTCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAAATCACTACGTGGAAGGTGGTGATGCCGGAAACCGTGA
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------gtttttatgtcattctg--tatcttggtttt---ctatgagcgattgtttgctttatct-tgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
|| | | ||| ||| | || ||||| || | | | | | | | | | | || | | | | ||||| | || ||| |||||| ||||||| || ||| | || || ||||| | || || ||||||||||| ||||| |||||||||||||| |||||||
gtttgagatctgtctctctgtggctcttgcttctttagttttgttctgatatcaagtttaagactcacgaattcttcttccatacaaaaccaaaatcagGCTCTTGGAAAGCATGGTATCATTTGCACTGAGGATTTGATCCACGAGATTCTAACAGTAGGACCTCATTTCAAGGAAGCCAACAACTTCCTTTGGCCAT
upper sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
----------------gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctttatcttg--ttgctaacctgcttttgtgatg-atagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
|| | ||| | | | | | | || ||||| | || || | | | || | || ||||| | || ||||| ||||| || || || || ||||| |||||||||||| | |||||||||||||| || ||||| ||||||||||| ||||| | |
tcgtataaatagctgcattgcgacacaattaaaattagtaggacctgacgtgt-atcctttgcagtgatttcacctgatgaattctgttgattttgtgtagGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctatgagcgattgtttgctttatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
tgctaac putative branch site (score: 1)
cttttgt putative PPT
tttatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttatgtcattctgtatcttggttttctatgagcgattgtttgctttatcttgttgctaacctgcttttgtgatgatagGCTTTGGGGAAGTTTGGTATTATTTGCATGGAAGATCTTATTCATGAGATCATGACTGTTGGACCTCATTTTAAGGAGGCCAACAACTTCCTATGGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG