Sequence
atgc intronic sequence ATGC exonic sequence...atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g41910.1 (Oryza sativa), 3'ss of exon 4
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctattt-atgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
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----gtatatacaagt---aatttttgtctaagtgcttgactagttttccataagctaattctttgaaactgttaactttctttttat-----atatgtagGAAGCTAACAAACCTCCAGATAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACGTTACTGGTTTGCCTGATGATGTCACAGCTGAGGAG
upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G084716_T01 (Zea mays), 3'ss of exon 4
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
|| || | || | || |||| | |||| | | | ||| | ||| || | | | | ||||| | ||||||||||||||||||| || |||||||| ||| | ||||| || |||||||| ||||| || || ||||| |||||||| || || || |||
------gt-tccatgtccagttttatagtcaattgactattttatgataaagctgctgg--agtta-gtagtaacctattgaacttttg-----tggtagGAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTGATGATGTCACGGTGGAGGAG
upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G411893_T01 (Zea mays), 3'ss of exon 3
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
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--------------------------------gtcaattgactat--tttatgataaagctgctggagttagtagtaacct-attgaacttttgtggtagGAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTGATGATGTCACGGTGGAGGAG
upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G171660_T02 (Zea mays), 3'ss of exon 4
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
| || || |||| | || |||||| || | || | ||| | || | || | || | | || | ||||||||||||||||||| || |||||||| ||| | ||||| || |||||||| ||||| || || ||||| |||||||| || || || |||
-gtatagtttccaagtc-attcttggagttatttgtaagt-ttgcgcattttaattctagtcttcaataaactagtaacct-attgaacttctgtggtagGAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTGATGATGTCACAGTGGAGGAG
upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G074351_T01 (Zea mays), 3'ss of exon 4
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
|| || || |||| | | | || |||||| | || || ||| || || || | | | | || | ||||||||||||||||||| || |||||||| ||| | |||||||| |||||||| || | || || || || ||||||||||| || || |||
--------gtatagtttccaagtcattcatggagttct---ttataagtttgcacatgttaattctagtcttcatgtaacctattgaacttctgtggtagGAAGCTAACAAACCTCCAGACAGTTGGTTTGATCTCAAAGTTAACACACATGTCTACATAACTGGTTTACCTGATGATGTTACAGTGGAGGAG
upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G353114_T01 (Zea mays), 3'ss of exon 7
-atttgggtgtctaagttgaaagttttagttatacttaggaatta-taactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
||||| | ||| | || |||| || | | | || | || ||| | ||| || | || | | | | ||||||||||||||||||| || |||||||| ||| | ||||| || |||||||| ||||| || || ||||| ||||||| || || || |||
tatttgaaccaaaaggttccatgtcc-agttttatagtcaattgactattttatgataaagctgctggagttagtagtaacct-attgaacttttgtggtagGAAGCTAACAAACCTCCGGACAGTTGGTTTGATCTCAAAGTAAACACACATGTCTATGTAACTGGTTTGCCTAATGATGTCACGGTGGAGGAG
upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 5
---------------------------------atttgggt---gtctaagttgaaagtt-ttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
||| || | || | || || ||| |||| | ||| | || | | || | ||| || | | | | | | || || ||||||||||| ||||| |||||||||||||| || ||||| ||||||| ||||||||||| || |||||||| || |||||||| ||| ||
gtgcgccttttctttccatcttatctatcaatggtttcaccctgatccattttcttatttcttggtttgacttggaaatgagtacct-cttctgggagacgaatggc---atctctattgatctcattctgtttcagGAAGCTAATAAACCCCCTGATAGTTGGTTTGAATTAAAGATTAATACGCATGTTTATGTCACTGGGTTGCCTGAGGATGTTACCACTGATGAA
upper sequence: Vv00s0499g00010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G31450.1 (Glycine max), 3'ss of exon 6
---------------------------------atttgggt---gtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
||| || | || | || | | | | | |||| || | || | ||| | | | | | | | | | | || || ||||||||||| ||||| |||||||||||||| || ||||| | ||||||||||||||||| || |||||||| || || ||||| ||| ||
gtgccccttttctttccatcttgtctatcaatggtttcaccctgatccattttcttatttcttgctttgacttggaa--atgagtacctcttttgggagacaaatggc-gcatatattgatctcattctgtttcagGAAGCTAATAAACCCCCTGATAGTTGGTTTGAATTAAAGATCAATACACATGTTTATGTCACTGGGTTGCCTGAGGACGTTACCACTGATGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
ctcattt CT-rich tract
tatttatgtttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgggtgtctaagttgaaagttttagttatacttaggaattataactagccatttggctatttatgtttttatttttctcactttgactcatttacagGAAGCTAACAAACCTCCTGATAGTTGGTTCGATTTAAAAGTTAATACACATGTTTATGTGACCGGGTTGCCAGATGATGTTACTGTTGACGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- ttgggtg
- - - - - - - - - - - - - - - - - - - - - - - -ctagcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctat