Sequence
atgc intronic sequence ATGC exonic sequencegttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctgttttgttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g21160.1 (Oryza sativa), 3'ss of exon 2
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttgg--tttctaaatcgctgtttt--gttttgt----tgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
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gtatataatgcgatgttgcaatgatgcttcttccttctttcatggcgggct-cggtaggacgcgatct---gattggcatttttgcattgctgttcttggcaacgcgccgcgctgcagCATCTACGGGCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTTTACCCGGAGACGGTGAAGCTGATCTTG
upper sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g21140.1 (Oryza sativa), 3'ss of exon 2
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctt-tcggttggtttctaaatcgctgttttgttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
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gtataatgcgatgttgcaatga--tgtttctt---ctttcatggcggactcggtagaa--cgcgatctgattggcatgtttgctgttcttggcaatgcgcccgcgctgcagCATCTACGGTCCGGTGCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCTGAGACGGTGAAGCTGATCTTG
upper sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G819035_T01 (Zea mays), 3'ss of exon 3
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctgttttgttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
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-gtatgcatgcacacacggtaatgtgatgctccaatctttgcgtccg-----tagaaacccgtttggttgcgtgacttgaccctcgcgcttcttagcaatgcggt-gtagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTATCCAGAGACCGTGAAGCTCATCCTG
upper sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G003424_T01 (Zea mays), 3'ss of exon 2
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctgttttgttttgttgt----tgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
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-----gtatgca---tgcacacacggtaatgtgatgctccaatctttgcttccgtagaaccccgtttggttggctgacttgaccatcgcgcttcttgttggcaatgcggtgcagCATCTACGGTCCAGTTCACGACGTGCGCATCCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTCTACCCAGAGACGGTGAAGCTCATCCTG
upper sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G086614_T01 (Zea mays), 3'ss of exon 2
----gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttggttt-ctaaatcgctgttttgttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
| | || || | | | || || || | | ||| | | |||| | | || |||||||| | |||| || | || | | ||||| | |||||||||||| || ||| | || || || ||||||||| | ||||||||||| || |||||||| || |||||||| ||||||||||| ||
gtatgctatgcatgcacacatgttaatgtgattgatgctgcaatct--ttgcttcggtagaag--aaccccgtttggttggttgaccctcgcgcttcttggcaatgcggc-gcagCATCTACGGTCCAGTTCACGACGTGCGCATTCCCTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCAGAGACGGTGAAGCTCATCCTG
upper sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G311665_T01 (Zea mays), 3'ss of exon 2
gttttgaccacaattttcatgaattgtttct-tggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctg--ttttgttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
|| |||| || | || | | | | || | | | ||| | | ||| | | | | || ||||| | ||| || || || || ||| | ||||| || ||||||||| | ||||||||||| || |||||||| || || ||||| |||||||| || ||
-------------------gtaactgttcctctagtctgccgtgctccacttccactaccagccgccgctccggcctctgacgcgtgcgccgggctccggcgaggcactgcagCATCTACGGCCCCGTCCACGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGGTTCGTCACCTTCGTGTACCCGGAGACGGTGAAGCTGATCCTG
upper sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G01340.1 (Glycine max), 3'ss of exon 3
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaat---tgtgggaagttgagagctttcggttggtttctaaatcgctgttttg--ttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
|| | || || | || ||||| | | | | |||| ||||| | | | | ||| | ||||| || |||||||||||||| | |||||||| ||||| |||||||||||||| ||||||||| | ||||| || ||||| ||||| |||||||||||||| |||||||| ||| |
------------gttattattgtttaggt-ttaactttgttaactggggtcagtgtgcatagttggtcaatggcag--aaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCAGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
upper sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G35980.1 (Glycine max), 3'ss of exon 3
gttttgaccacaattttcatgaattgtttctt-ggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctgtttt--gttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
||| | | | || | | ||| ||| | || | |||||| ||||| | ||| | | | || ||||| || |||||||||||||||| || ||||| ||||| |||||||||||||| ||||||||| | ||||| || ||||| ||||| |||||||||||||| |||||||| ||| |
gttattattgc--ttaggtttagctgtaactttagcttcgactgggatcattgtgcatagttg---gtcagcggcagaaatattaacttgagtttttaattctgttgttgaagCATTTATGGCCCAGTGCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGCTTTGTTACCTTTGTTTATCCAGAGACTGTGAAGCTTATTCTA
upper sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G01350.1 (Glycine max), 3'ss of exon 2
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaat---tgtgggaagttgagagctttcggttggtttctaaatcgctgttttg--ttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
|| | || || | || ||||| | | | | |||| ||||| | | | | | ||| | ||||| || |||||||||||||| | ||||| || ||||| |||||||||||||| ||||||||| | ||||| || ||||| ||||| |||||||||||||| |||||||| ||| |
------------gttattattgtttaggt-ttaactttgttaactggggtcagtgtgcatagttggtcgatggcag--aaatattaacttatagtttttatttctgttgttgaagCATATATGGTCCTGTCCAAGACGTGAGGATCCCATACCAGCAGAAGCGAATGTTTGGTTTTGTTACCTTTGTTTATCCAGAGACCGTGAAGCTTATTCTA
upper sequence: Vv13s0158g00370.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S31_251V6.1 (Physcomitrella patens), 3'ss of exon 2
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctgttttgttttg--ttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
||| | | | | | ||||| | | ||| | ||| | ||| | | || | || ||||| | | || || || ||||||||| |||||||| ||||||| |||||||||||| ||||||| || ||||| || || || ||| |||| || || || ||||||
--------gtcaacggtgacagccttactgtactttttgcatattgaaatacttggagatcc---tcttatgaccaat---caattttctcatttgtgcgggatgaatgcagGGCTTACGGTCCAGTCCAAGATGTTCGGATCCCCTATCAGCAGAAGCGGATGTTTGGTTTTGTGACTTTTGTATATTCAGAAACTGTTAAAGCAATTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagttgagagctttcggttggtttctaaatcgctgttttgttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
ttctaaa putative branch site (score: 2)
ttttgtt putative PPT
tttctaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgaccacaattttcatgaattgtttcttggttttgtgcaattgaattgtgggaagttgagagctttcggttggtttctaaatcgctgttttgttttgttgttgaagCATTTTCGGTCCAGTTCAAGATGTGAGGATCCCATATCAGCAGAAGAGGATGTTCGGGTTTGTAACCTTCGTTTATCCAGAGACAGTGAAGCTCATTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA