Sequence
atgc intronic sequence ATGC exonic sequencegtactactgttcactaatattaattattaaaagcccatggaacccagtgtctttgttacatttattaaggcattagtttcccataataccccaacaacaaatcacagagttttcaatgttttggtacctaccagaatagtttctaaaagaatttctcaccctattcttacaactattcattttcttcaaatgggttccagGTAAGAAGAGAGAAAATCAGTGAGAGGATGAAGCTCTTGCAAGCACTTGTTCCTGGTTGTGACAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g01256.2 (Oryza sativa), 3'ss of exon 2
gtactactgttcactaatattaattattaaaagcccatggaacccagtgtctttgttacatttattaaggcattagtttcccataataccccaacaacaaatcacagagttttcaatgttttggtacctaccagaatagtttctaaaagaatttctcaccctattcttacaactattcattttcttcaaatg--ggttccagGTAAGAAGAGAGAAAATCAGTGAGAGGATGAAGCTCTTGCAAGCACTTGTTCCTGGTTGTGACAAG----------------------------------
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------------------------------------------------------------gtcactcactcaccagtcttttgt--tctcttatc--tgaatcgttgttatcttaat----tagtagtaac---agctgtttgttagtg--cccttcacttaactacaggagtagtaacatctgttgatttgttacttatagGTGAGAAGGGAGAAGATCAGTGAGAGGATGAAGATGCTGCAAAGCCTGGTTCCTGGTTGTGACAAGGTCACAGGGAAAGCCCTCATGCTAGATGAGATCA
upper sequence: Vv17s0000g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g42470.1 (Oryza sativa), 3'ss of exon 2
gtactactgttcactaatattaattattaaaagcccatggaacccagtgtctttgttaca-tttattaaggcattagtttcccataataccccaacaacaaatcacagagttttcaatgttttggtacctaccagaatagtttctaaaagaatttctcaccctattcttacaactattcattttcttcaaatgggttccagGTAAGAAGAGAGAAAATCAGTGAGAGGATGAAGCTCTTGCAAGCACTTGTTCCTGGTTGTGACAAG
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----------------------------------------------gtactactactgcacttcactttggttttggttt----tgatttttctgctgcttttgcatgagtggtttttggcttgcagctt--ctgcatcttttct-------cctggtctctgattcttggtgacatt--ttctctcta---------cagGTGAGGAGGGAGAGGATCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTCCCTGGTTGTGACAAG
upper sequence: Vv17s0000g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G882527_T04 (Zea mays), 3'ss of exon 2
gtactactgttcactaatattaattattaaaagcccatggaacccagtgtctttgttacatttattaaggcattagtttcccataataccccaacaaca--aatcacagagttttcaatgttttggtacctaccagaatagtttctaaaagaatttctcaccctattcttacaactattcattttcttcaaatgggtt-ccagGTAAGAAGAGAGAAAATCAGTGAGAGGATGAAGCTCTTGCAAGCACTTGTTCCTGGTTGTGACAAG
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-------------------------gtacagtacacctctcactcta-atccttgtagcattaatttgacagttagtcgtgtgtaatagtttggtctcagtacttcctgcctcccctctttttcgttatcttc---------tcttgcatgaactgatgaacacctcccgatggcaattttttttgttggttggccttattagGTGAGGAGAGAGAGGATCAGTGAGAGGATGAGGATGCTGCAAGCACTGGTCCCTGGTTGTGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagaatttctcaccctattcttacaactattcattttcttcaaatgggttccagGTAAGAAGAGAGAAAATCAGTGAGAGGATGAAGCTCTTGCAAGCACTTGTTCCTGGTTGTGACAAG
ttcttac putative branch site (score: 2)
tattcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactactgttcactaatattaattattaaaagcccatggaacccagtgtctttgttacatttattaaggcattagtttcccataataccccaacaacaaatcacagagttttcaatgttttggtacctaccagaatagtttctaaaagaatttctcaccctattcttacaactattcattttcttcaaatgggttccagGTAAGAAGAGAGAAAATCAGTGAGAGGATGAAGCTCTTGCAAGCACTTGTTCCTGGTTGTGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC