Sequence
atgc intronic sequence ATGC exonic sequence...tgatgagtcagcttttgtagcatcactctttgttattgtacctctttcaaagtggatgatagctaaatttgctattactttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 2
tgatgagtcagcttttgtagcatcactctttgttattgtacctctttcaaagtggatgatagctaaatttgctattactttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
| |||||| | | | | | ||| || | | || | | ||||| | | ||| ||| || | || || | | || |||| || ||||| ||||| ||||| |||||||| ||||||||||| ||||||| |||||||| || | || || ||| | || |||| ||| ||||
--gtaagtcaggatcttcatga-cgctcattctc-tagttcaccattcaatatt--ttccagcaaaa------ataagttctctatcatgtat-ctacagGTTATTTTAACCCCAACTCATCTTGCTATTGTCATGGAATATGCCTCTGGTGGTGAGCTTTTCGAGAGAATTTGTAAGAATGTACGGTTCAGTGAAGATG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 3
tgatgagtcagcttttgtagcatcactctttgttattgtacctctttcaaagtggatgatagctaaatttgctattactttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
|| | | || | ||| ||| || | || | |||| | | ||| | | || || | ||||| || |||||||| |||||||| |||||||| ||||||||||| |||| || ||||||||||| | ||||| ||| | ||| |||| ||| ||||
----------------gtgagttgggattgtgatgctgtttctccccagaatt---ccattgttaaacatttttttattcttctttgtatg----tctagGTTATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGGATATGTAAGAACGTGCGATTCAGTGAAGATG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G171435_T01 (Zea mays), 3'ss of exon 2
tgatgagtcagcttttgtagcatcactctttgttattgtacctctttcaaagtggatgatagctaaatttgctattactttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
|| | | || | ||| ||| || | | || | | |||| | | |||| | | | | | ||||| || |||||||| |||||||| |||||||| ||||||||||| |||| || ||||||||||| | ||||| ||| | ||| |||| ||| ||||
----------------gtgagttgggattgtgatgctgtttctcccccagaattcat--ttgttaaacacttttgaaatttctttg----tata-tctagGTTATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 2
tgatgagtcagcttttgtagcatcactctttgttattgtacctctttcaaagtggatgatagctaaattt-gctattactttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
| | | || | | || |||| | | || | ||||| ||| ||| | | | ||| | ||||| |||| ||||||| |||||||| || ||||| || ||||| ||||||||||| ||||||||||||| ||||| || ||||| ||||||| || | ||||||||
----------gttggtatatttttatatttatatatttt-tatgttcagaggtgga--ataatcgtattcagggaaaatgttctttgaaatttcactc-agGTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 2
tgatgagtcagcttttgtagcatcactctttgttattgtacctctttcaaagtggatgatagctaaatttgct-attactttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
||| | | || | | | | | || | ||| | | | | | | ||| | | || ||| ||| ||| |||| || |||||||| || ||||| |||||||| ||||||||||| |||| |||||||| ||||| || ||||| || || || || | ||||||||
tgaaaaacttaatatttttataattgtatattctacgatgtttctatacagaggaggggcaatcgagtttatttgtaacgttctatataatttcacgc-agGTAATTTTAACACCTACTCATCTTGCTATTGTAATGGAATATGCATCTGGGGGAGAGCTCTTTGAGAAAATCTGCAATGCTGGACGTTTTACTGAGGATG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G20610.2 (Glycine max), 3'ss of exon 2
---tgatgagtcagcttttgtagcatcactctttgttattgtacctctttcaaagtggatgatagctaaatttgctattactttcctgga-aatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
|||| | || || || | | | | ||| || | | | | || | | | |||| | | | | || | ||| |||| |||| || |||||||| || ||||| |||||||| ||||||||||| |||| |||||||| ||||| || ||||| || ||||| || | |||||||
ccttgatatttttataatttta-tattatattctacgaatgtgtctgtatagaggagg--ggcaatcacatttatttgtgatgttctatataattacacgc-agGTAATTTTAACACCTACTCATCTTGCTATTGTAATGGAATATGCATCTGGGGGAGAGCTCTTTGAGAAAATCTGCAATGCTGGGCGTTTTACCGAGGATG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 2
---tgatg-agtcagcttttgtagcatcactctttgttattgtacctctt-tcaaagtggatgatagctaaatttgctattactttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
| || | | | || | || | ||| |||| | ||| |||| | | || | |||| | ||| | | ||||||| || || || || ||||| | |||||||| ||||||||||||||||||||||| |||| ||| || || || || || || || || | ||| ||||
gtataatataatacaccttgatgtttcttctgtgtgtgtttgtgtattaagtcagtgtggtttagagtttgttttgtgtgtgtttttgta------atggtttagGTGATTTTGACGCCTTCCCATTTGGCTATTGTTATGGAATATGCTGCTGGTGGAGAACTTTATGAGCGGATTTGTAATGCCGGACGGTTTAGTGAAGATG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------tgatgagtcagcttttgtagcatcact--ctttgttattgtacctctttcaa---agtggatgatagctaaatttgct-attacttt------------cctggaaatca--cactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
| || | ||||| | | ||||| | | | | || | | | | ||| ||||| | | | ||| | || | ||| || | |||| | || |||||||| ||| |||| || |||||||| ||||||||||||||||| || || || || || || || ||||| || |||| ||| ||||
gtgatttttctaggcggttgtttttgctttcacgggtttgagaactttggatatatgaatgtatcgattggattggtaatactggaattttttgaacattttggagtactaaatcttgtacttcaactacctcagGTTCTGTTGACACCAACTCATTTAGCCATCGTGATGGAGTATGCTGCTGGTGGAGAACTGTTCGAGCGAATTTGTAATGCAGGTCGGTTCAGTGAAGATG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------tgatgagtcagcttttgtagcatcactctttgttattgtacctctttcaaagtggatgatagctaaatttgctattactt-tcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
|| || | | | ||| | ||| | || |||| | | || | || | || | ||| ||| | || ||| | | || || |||| || || |||||||| | || |||||||||||||||||||||||||||||||| ||||| || || || || |||| || |||| ||| ||||
gtgatcattctagactttttgattttttattattattaatttttttttccctgaacttgtagaccctgggtgtgtggatgaactttctgg-attgacattactggaagatattggacatttaggagtactaaagcttgtacttgaact---atttcagATCATGTTGACTCCAACCCACTTGGCCATTGTGATGGAATATGCTGCTGGTGGAGAGCTGTTTGAGCGAATTTGTAAAGCAGTCCGGTTCAGTGAAGATG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------tgatgagtcagcttttgtagc--atcactctttgttattgtacctctttcaaagtggatga--tagc-taaatttgctattact----ttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
| ||| ||||| || || | | || | | || || || || || || |||| || | | || | | || || ||||||| | || ||||||||| | |||||||| ||||||||||||||||||||||| |||||||| || || || || ||||| ||||||| ||| ||||
gtgagaaacctacacatatttcttattattccaagggtctcaagatttgtggccggtcgcacaatgatgtacctactggactaacatgattgtcttattgtacattttgtagcattgaaactcgtacttgtttcatttcagGTCATGCTGACTCCAACCCATTTGGCTATTGTTATGGAATATGCTGCTGGTGGAGAACTTTTTGAGCGAATCTGTAACGCAGGCCGCTTCAGTGAAGATG
upper sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 3'ss of exon 2
----tgatgagtcagctttt--gta----gcatcactctttg---ttattgtacctctttcaaagt----ggatgata-gctaaatttgctattactt-tcctgga------aatcacac----------tttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
| || ||||| || ||| ||| | || | |||| | | | | || | | |||| | | | | | || |||| | ||||| |||| || ||||||| || || || |||||| | || ||||||||||||||||| || ||||||||||| ||||| || || || || || || || |||| || ||||
gtgtgaaagaagcagctctttcgtattttgcagaggttttggaatctattttgcatggataaatattctggcatgacatggttagctccctgttacaaattctggagtgctaaatcttgtgctcgtttcattcagGTCATGTTGACCCCGACCCATTTGGCCATTGTGATGGAATATGCGGCGGGTGGAGAGCTGTTTGAGCGAATTTGTAATGCTGGTCGGTTCAGCGAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaaagtggatgatagctaaatttgctattactttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
agctaaa putative branch site (score: 3)
taaatttgctatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatgagtcagcttttgtagcatcactctttgttattgtacctctttcaaagtggatgatagctaaatttgctattactttcctggaaatcacactttagGTCATATTAACACCAACCCATCTAGCTATTGTGATGGAATATGCTGCTGGTGGAGAGCTTTTTGAACGTATATGCAAGGCAGGGCGCTTCATTGAGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - catcact
- - - - - - - - - - - - - - - - - - - - - - - - - -gtggatg