Sequence
atgc intronic sequence ATGC exonic sequencegtctcgctccatttgtattctgatttagtggttttgtatcaaagcatcagtagttgaattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g60790.1 (Oryza sativa), 3'ss of exon 2
----------gtctcgctccatttgtattctgatttagtg-gttttgtatcaaa-gcatcagtagttgaattggtgcgtgtttggaattg-tgtgat-cagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
| | || |||| ||| | | | | | | | | | ||| | | ||| | | | |||| | | || | ||||||||||| |||||||||||| ||||||||||||||||||||| || || | ||||| || |||||||| ||||| | ||
gtaaggcgaagcgaatccccttttgccctctctcgttgcgcgcgaggcacccactggatctctgtgttgatttgggaatctttgctttgggtgcgggacagGACAAGGCGATCAAGAGGTTTCAGGTGAGGAACATCGTGGAGCAGGCCGCCATCAGGGACGTCCAGGAGGCGTGCGTGCACGATG
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g39960.2 (Oryza sativa), 3'ss of exon 2
-----------------gtctcgctccatttgtattctgatttagtggttt-----tgtatcaaagcatcagtagttg----------aattggtgcgtgtttgga--attgtgtgat--cagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
||| || || |||| | ||| || | || ||| | ||| | ||| ||| || || |||| | | | | ||||||||||| ||||||||||| ||||||||||||||| ||||| || || | |||||||| |||||||| |||||| |||||
gttcgcggattcagattctcttgcagatttgttattatcattcagcgtgttattactgttacgcgaaatctgcggtttcggcttggctgattcgttggttcttgggtcgtcgccttgtcgcaggacaagGCCATCAAGAGGTTCCAGGTGAGGAACATCGTCGAGCAGGCGGCCATCAGGGATGTCCAGGAGGCGTGCGTCCATGACG
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G899149_T01 (Zea mays), 3'ss of exon 2
--------gtctcgctccatttgtattctgat-ttag----tggttttgtatcaaagcatcagtagttgaattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
| | | | | ||| ||| | |||| | ||||| || | | | | | | || | ||| ||||| ||||| |||||| |||| |||||||||||||| || ||||| ||||| ||||| ||||| ||||||||||| || ||||
tgtgctcagacatgtttgacttgcattgcaacattagaacttaattttgctctgaactgtgtatgttgtagaagatatatgatgtttgctgtacttgcagGATAAGGCTATCAAGCGGTTCTTGGTGAGGAACATTGTTGAGCAGGCTGCCGTGAGAGATGTGCAGGAGGCCTGTGTACATGATG
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G129015_T02 (Zea mays), 3'ss of exon 2
------gtctcgctccatttgtattctgat-ttagtggttttgtatc-aaagcatcagtagttgaattggtgcgtgtttggaattgtgtgat-----cagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
| | | | || || || || | | | |||| | | | || || ||| || | |||| | | | | | ||||| ||||| |||||| |||| |||||||||||||| || ||||| ||||| |||||||| || ||||||||||| || ||||
gttcttggatattttgacctgcgttgcaatatttgggctcaattatctgtcgaaactgttgtggaaaatgtatgacgttggcactattttttactcgcagGATAAGGCTATCAAGCGGTTCTTGGTGAGGAACATTGTTGAGCAGGCTGCTGTGAGGGACGTGCAGGAGGCCTGTGTGCATGATG
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G827266_T02 (Zea mays), 3'ss of exon 2
--gtctcgctccatttgtattctgatttagtggttttgt-atcaaagcatcagtagttgaattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
| | | | | | || ||| | | | | || | | | || || || | || | | || || | ||||||||||| |||||||||||| |||||||||||||||||| || || || | ||||| || ||||| || |||||||||||
gtgaggagatgcctccacagtcgcctttctttttctcttcatttacccgt--gtggtggagtccttg---atcttgatgctcgtta-cagGACAAGGCGATCAAGAGGTTTCAGGTGAGGAACATCGTGGAACAGGCGGCCATCAGGGACGTCCAGGAAGCATGCGTCTATGATG
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G827266_T03 (Zea mays), 3'ss of exon 2
--gtctcgctccatttgtattctgatttagtggt-tttgtatcaaagcatcagtagttgaattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA-----
| | | | | | || ||| | | | | || | | | || || || | || | | || || | ||||||||||| |||||||||||| |||||||||||||||||| || || || | ||||| || ||||| || |||||||||||
gtgaggagatgcctccacagtcgcctttctttttctcttcatttacccgt--gtggtggagtccttg---atcttgatgctcgtta-cagGACAAGGCGATCAAGAGGTTTCAGGTGAGGAACATCGTGGAACAGGCGGCCATCAGGGACGTCCAGGAAGCATGCGTCTATGATGGTAAA
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G14950.1 (Glycine max), 3'ss of exon 2
----------gtctcgctccatttgtattctgatttagtggttttgtatcaaagca-tcagtagttg-----aattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
| || || || | | || | || || ||| || | | | || ||| || | ||| | | ||||||||||| |||||||||||| ||||||||||||| || || || |||||||| || |||||||||||||| || ||||||||
gttcgttcttatttcactttcttaaacgttcaaatttttttttctgcggcaattcaattaatttttttttgcgatttgtaaaaaaataaaataataataacagGACAAGGCTATCAAGAGGTTTCTGGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTTCAGGAGGCTTGTGTCTATGAAC
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G39940.1 (Glycine max), 3'ss of exon 2
-gtctcgctccatttgtatt--ctgatttagtggttttgtatcaaagcatcagt--agttgaa----ttggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
||| | || || | | | | |||| | | | || || | | || || ||| ||| || | | ||||||||||| |||||||||||| ||||||||||||| || || || |||||||| || ||||| |||||||| || ||||| ||
gttcttatttcactttcttcaaccttccttttttttttatttttatgcggcaattcaattaaagattttgagatttgtgaaaaaaattaataacagGACAAGGCTATCAAGAGGTTTCTGGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAGGCTTGTGTCTACGAAC
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 2
--------------------------------gtctcgctccatttgtattctgatttagtggttttgtatcaaagcatcagtagttgaattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
| | | | | ||| ||||| | | |||| ||| | | | | || | | | |||| | ||||||||||| |||||||||||| | ||||||||||| || || || |||||||| || ||||| ||||| ||||| ||||||||
gtttttttttattttattattatcattatttcgctttctttcttccaccttcagatttgtgcgaggcatttcaattt-tcaacaactaaccttttgtgc---tcgctctgtgaaa-cagGACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G21370.1 (Glycine max), 3'ss of exon 2
------gtctcgctccatttgtattctgatttagtggttttgtatcaaagca--tcagtagttgaattggtgcgtgtttggaattgtgtgat-cagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
||| || ||| | | | ||||| | | ||| ||| || |||| | | |||| ||||||||||| |||||||||||| | ||||||||||| || || || |||||||| || ||||| ||||| ||||| ||||||||
gttattatctatttcgctttcttccttccaccttcagatttgtg-cgaggcatttcaaattttcaattaaccttttgtgctcgccccgtgaaacagGACAAGGCCATCAAGAGGTTTCTTGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCCTGTGTCTATGAAC
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G40660.1 (Glycine max), 3'ss of exon 2
------gtctcgctccatttgtattct--gatttagtggttttgtatcaaagcatcagtagttgaatt------ggtgcgtgtttggaattgtgtgat-------cagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
| || || | | | || |||| | |||| | | || | |||| | | | ||| | || | | || ||||||||||| |||||||||||| ||||||||||||| || || || |||||||| || ||||| ||||| || || ||||||||
gtttttatttcactttctcttaaaccttcaattttttttttttttgttttaggcgtttcaattgacctttttacgctttgtgaataaaaaaatattattaaaaaacagGACAAGGCCATCAAGAGGTTTCTGGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAAC
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G38950.1 (Glycine max), 3'ss of exon 2
--------------gtctcgctccatttgtattctgatttagtggttttgtatcaaagcatcagtagttgaattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
| | || || | | || | |||||| | |||||| | | ||||| | ||| | | ||||||||||| ||||||||||||||||| |||||||| || || || |||||||| || ||||| ||||| || || ||||||||
gttgtttttattattatttatttcactttcttccaccttcaaattttttgtg-cgaagcatt--tcaattaattgaaaaaaat--aaaataat---aacagGACAAGGCCATCAAGAGGTTTTTGGTTAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAAC
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G06000.1 (Glycine max), 3'ss of exon 1
----------------gtctcgctccatttgtattctgatttagtggttttgtatcaaagcatcagtagtt---gaattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
||| || || || || || ||| | |||| | | || | ||| | | || |||| | | ||||||||||| || ||||||||| ||||||||||||| || || || |||||||| || ||||| ||| |||||
gtttttttattttactttcttatacctttaaagttttgtgcaaggcatttca-gttaaagtttttgcgctttgtggattttttttttcttcaaatta-ataa-cagGACAAGGCTATTAAGAGGTTTCTGGTGAGGAACATTGTTGAACAGGCTGCAGTCAGAGATGTGTTGGAAGCCTGT----------
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G16600.1 (Glycine max), 3'ss of exon 1
-----gtctcgctccatttgtattctgatttagtggtttt---gtatcaaagcatcagtagttg-----aattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
||| | || || | || | | |||| ||| || |||| ||| || ||| | | ||||||||||| | ||||||||||||||||||||||| || || || ||| ||| || |||
gttcgttcttatttcactttcttaaacgttcaattttttttctacggcaattcaattaaagttttttgtgatttgtaaaaaaaaataataataataacagGACAAGGCTAGGAAGAGGTTTTTGGTGAGGAACATTGTTGAACAGGCTTTAGTCAGAGAT-------------------------
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G40590.1 (Arabidopsis thaliana), 3'ss of exon 2
-----gtctcgctccatttgtattctgatttagtggttttgtatcaaagc-atcagtagttgaattggtgcgtgtt-tggaattgtg----tgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
||| |||| | | | || || | | | | | | || | | || ||| | | ||| ||| | | | || |||||||||| || |||||||| | ||||||||||| |||||||| ||||| | || ||||||||||| || ||||||||||
gtactctcttcctccttctcttctccaatcaatcaatctccagtaactcctatgtggattttgattagatcttgtggtggtaatataaatttggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCTATTAGAGATGTTCAGGAAGCTAGCGTCTATGAGG
upper sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G40510.1 (Arabidopsis thaliana), 3'ss of exon 2
---gtctcgctccatttgtattctgatttagtggttttgtatcaaagcatcagtag---ttgaattggt------gcgtgtttggaattgtgtgat-cagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
|||| || || | |||| | | | | | | | || | | || |||| ||| | | | | | ||| | || |||||||||| || |||||||| | ||||||||||| |||||||| ||||| | || ||||||||||| || ||||||||||
gtactctctttcaccttctcttctcaatcaatcaatctccagtaattcttatgtgtattttgatttgatcttgtggtggttctataataatttgggatagGACAAGGCCATTAAGAGGTTCATTGTGAGGAACATTGTGGAGCAGGCTGCTATTAGAGATGTTCAGGAAGCTAGCGTCTATGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtatcaaagcatcagtagttgaattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
ttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctcgctccatttgtattctgatttagtggttttgtatcaaagcatcagtagttgaattggtgcgtgtttggaattgtgtgatcagGACAAGGCAATCAAGAGGTTTTTGGTGAGGAACATCGTGGAGCAAGCTGCAGTGAGGGATGTTCAGGAGGCCTGCGTCTATGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG