Sequence
atgc intronic sequence ATGC exonic sequence...ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 5
--ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcattt-ttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
|| | || ||| | || | | | | | || | | | || || ||||| | | | |||| ||| |||| ||||| ||||||||||||||||||||||||||||| || || |||||||| ||||| ||| | ||||| ||||| |||||||| ||||| || ||||
ttttatgggtcactgcatattgttttttattttttgatctct---cgaagtcaataatgagaaaatattacatatgtaatacatacctatttcttcttaacagGGGCATGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTTTGATAGCAGCCAATGAAAGCTGCCCACAACCCCAAA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 5
---------ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
||| | |||| || ||| | | | || | ||||| | | | | ||| | | || ||| | | | || |||| || ||||||||||||||||| |||||||||||||| || || |||||||| ||||| ||||| ||||| || || ||||| || ||||| || || |
tgtaaaatgctatcatttcaacttctt--ttatgggccactaagactaggtat-tggtttaca-tttgttgaagcctgagaaattacctatttcc---tcttaac--agGGACACGATATTCTCATGGCTACGATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTCTGATAGCAGCAAATGAAAGTTGCCCACAACCCCAGA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttt--tctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
||| | | |||| | | || | | |||| | | | | || ||| || ||||||| | || | ||||| || || ||||||||||||||||||||||||||||| || || |||||||| || | ||| | || || || || ||||| ||||||||||| || |
--aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 5
ctaaagacttg---actttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
|| | ||| || || || ||| | || | ||| | || ||| || ||||||| | | | || ||||| || || ||||||||||||||||||||||||||||| || || |||||||| || | ||| | || || || || ||||| ||||||||||| || |
--gaataattgtatgtttcaacaacacctatctccttgaatagagatgaatttgtctaac-aggaaataattgtatgtttaacaatacctattccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCCCAGA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
-ctaaagacttgactttaaggttctggatgtccaggc--ttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
| || | | | | || |||| ||| | | || | | | | ||| || |||| ||||| || ||| ||||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| || || || || |||||||| || |||||||| ||||| || ||||
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttctg---tagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
ctaaagacttgactttaa---ggttctggatgtccaggcttatatgcctg--gttgagagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
||| || | ||| || | || || | ||||| | ||| || | || | ||| |||||| ||||| |||| | |||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| || || || || || |||||||| |||||||| ||||| || ||||
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatattt---gtttttacttttccaatttc--tgcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 5
-ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaatct--agGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
|| |||| | || | || | | || || | | | | | | || |||| | ||| | || | ||| ||||||| |||||||||||||| |||||||||||||||||||| || |||||||| ||| ||||| | || ||||| || |||| |||||||| || ||||
gagtgagggttgatggagaagtattcattg---atgtttccatcttttgcttttcttatctctacttcattcttgttgaatgtattcttgttctattcttcagGGTCACGATATTCTCATGGCAACAATGCTTAATGGAGCAGCCATCATGGATGGTGCACTACTTTTAATCGCTGCAAATGAAACTTGTCCACAACCACAAA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G18330.1 (Arabidopsis thaliana), 3'ss of exon 4
ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaatc--tagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
|| | ||| | | | | || | || ||| | | || | ||||| | || |||| ||||||||||| ||||| |||||||| |||||||||||||| ||||||| || |||||||| || ||||| ||||| || |||||||| || ||||
-------------------gtattaatgagtttaatttacactttgtctctcaaaactagaaccattggctatatgtaactgagttgttttttattcatcagGGACATGATATTCTTATGGCGACAATGCTCAATGGAGCAGCAATCGTGGATGGTGCTTTACTTCTAATTGCTGCTAACGAGAGTTGTCCACAACCACAAA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttg--agagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
|| | | | ||||| | | | | ||| | | | || | | | | | || |||| ||| || || |||| || ||||| || ||||| |||||||| ||||||||||| ||||||||||| || ||||| | || ||||| || || | |||||||| || ||||
gtataaaatgagttttaacactat---ttctaaatcttttgtaaccattttctatatgttaatgaggtgttttgtgtgttgatt----------------agGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S207_94V6.1 (Physcomitrella patens), 3'ss of exon 4
ctaaagacttgactttaaggttc--tggatgtccaggcttatatgcctggttgagagtccagtaaagttttttat---gtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
| | |||| | || | || | ||||||| | | | | |||||| || | || | || | ||| | |||| || ||||||||||||||||| |||||||||||||| || ||||||||||| || |||||| | || || ||| || || || || ||||| ||||
-----aattcgactacacacatcacttaatctgagggcttatgggaagcggtactttcgtgttcttgtttttaatccggattgaaatgtttgtgtttgtttgcagGGACACGATATTCTCATGGCTACTATGCTTAATGGAGCTGCTATTATGGATGGTGCTTTACTTTTGATTGCCAGCAATGAGAGTTGCCCCCAGCCCCAAA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaa-----tctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
| ||| | |||||| | || |||| | | || | | | |||| |||||||||||||||||||| ||||||||||| || || || ||||| || || || ||| | || || |||||||||||| || ||||||||||
--------------------------------------------------gtaagttcgtcgtagttttc-gttttcttctagctgttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA
upper sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ26525 (Selaginella moellendorffii), 3'ss of exon 3
ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaa-----tctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
| ||| | |||||| | || |||| | | || | | | |||| |||||||||||||||||||| ||||||||||| || || || ||||| || || || ||| | || || ||||||||||||||| ||||||||||
--------------------------------------------------gtaagttcttcgtagttttc-gttttcttctagcttttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGTCCGCAGCCGCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttgagagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
ttttttatgtttttct CT-rich tract
taaagttttttatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttttctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - ctggatg
- - - - - - - - - - - - - - - ccaggct
- - - - - - - - - - - - - - - - - - - - -tgcctgg