Sequence
atgc intronic sequence ATGC exonic sequence...gtttctaatatttgaggatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttctttgctattgtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
---gtttctaatatttgaggatctctccttgtttgtggtattat-tactttgccttcttatgtgctagggacagtaacctcctcatttctttgctattgtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG
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tgagtttcttccccctcaattcttagttatgttca-gatataatgctcttggtactctcatcctcccatggc--ttagttgttcaacttcttgatggt-tgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG
upper sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
gtttctaatatttgaggatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttctttgc-tattgt--gcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG
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--atctgcaaatgaatgacattttcccataaattct-tagtaacattcagatatgatgctctagatactcctatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG
upper sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 6
gtttctaatatttgaggatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttctttgc-tattgt--gcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG-------
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--atctgcaaatgaatgacattttcccataaattct-tagtaacattcagatatgatgctctagatactcctatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGGTCATTT
upper sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 6
---gtttctaatatttgaggatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttctttgctattgtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG
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acaagctctatcagttgtattttaattcatgtaacaagctctctcaattcactta---gcatcttcattatctgcatctaatattgctgctactactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG
upper sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------gtttctaa-tatttgaggatc----tctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaac-------------ctcctcatttctttgctat---tgtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG
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gtacttttgaagtttgaacttccaccattcatttcatcttataatcaaatctatagtgtgtatatggctatttaataattattgtcttttttattttgatatcttttcaaagattgagtagaccttggggtcattaatgaaaaattatactcgtttaatattgctgctataactacgcagACTGATACCAAAAAGATATCTGCTGTCTCAATATTTTTTGAGACAATGCCATATAGATTGAACGAAAGTACGGGATACATTGACTATGACCAG
upper sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 6
gtttctaatatttgaggatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttctttgctatt------gtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG
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-tctttgtttattcttgttctctcttcatt----attttattgtcttccatttcactatcctgatgatgaaaaattaat-atatagttactattttcacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCATATAGACTGAACGAAAACACGGGACACATTGACTATGATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgccttcttatgtgctagggacagtaacctcctcatttctttgctattgtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG
cagtaac putative branch site (score: 2)
cctcctcatttctttg CT-rich tract
atttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttctaatatttgaggatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttctttgctattgtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - -ctctcct
- - - - - - - - - - - - - - -ttgtggt
- - - - - - - - - - - - - - - - - - - - - - - tgccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtgc
