Sequence
atgc intronic sequence ATGC exonic sequence...gtgattttcttgtatcttccaagtctaagagtactctgcatttcttttatttataatttacacacaatttgattgaaaggtctcatgatggttgttgcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 6
gtgattttcttgtatcttccaagtctaagagtactctgcatttcttttatttataatttacacacaatttgattgaaaggtctcatgatggttgtt-gcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG
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-tggtatctattgagcttcttgatctccacacagtacgaacccgctccaatgcccgaatccctttcatttatctctcccttctttttaattttgtccacagAGTGCTCCGATCTCGATCCTGGAGCAGCACGAGCTCGCGAGCATGACGCTGGACTACAGGAAGGAGTGTGGCCGCGACAGCGTGCTGCAGTCGCTCACCA
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G007489_T01 (Zea mays), 3'ss of exon 6
gtgattttcttgtatcttccaagtctaagagtactctgcatttcttttatttataatttacacacaatttgattgaaaggtctcatgatggttgttgcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG
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acgttgctagtacggttgatcagctgagctgcttcttgatctttgcctagtacgaagcaaagccccttagtgcctgaaccctttttcttcttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G08060.3 (Glycine max), 3'ss of exon 5
gtgattttcttgtatcttccaagtctaagagtactctgcatttcttttatttataatttacacacaatttgattgaaaggtctcatgatggttgttgcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG
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-----------gtatttttctgttctt---gtattctaatcaactgcaatccatg-ttagttc----tttaaccaaaggactgtcttttgattgttgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCATGACTTTAGAGTATAGGAGAGAGTGTGGTAGGGACAGTGTGCTGGATTCCCTGACTG
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G12940.2 (Glycine max), 3'ss of exon 6
gtgattttcttgtatcttccaagtctaagagtactctgcatttcttttatttataatttacacacaatttgattgaaaggtctcatgatggttgttgcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG
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---gtatttttctgttcttgtattctaa---tccactgcagtccttgt-tttgttgttaac-caaa--------ggactgtcctttgattgtt--tgcagAGTGCTCCACAGCCAATCTTGGAGAGTCATGAGCTTTCTTCCGTGACTTTAGAGTATAGGAGGGAGTGTGGTAGGGACAGTGTGCTGGATTCCCTGACTG
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G21910.1 (Glycine max), 3'ss of exon 6
----gtgattttcttgtatcttccaagtctaagagtactctgc-atttcttttatttataatttacacacaatttgattgaaaggtctcatgatggttg-ttgcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG
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cactagcattccattttatgttttatttgtt----tagtttgttatttgcttggattttgattagaatgc--tttaccaaaagaattttgctttggacaactgcagAGTGCTCCACAGCCACTTTTGGAGAGCCATGAGCTGTGTGCCATGACATTGGAGTACAGGAGGGAGTGTGGCAGGAACAGTGTGCTGGATTCCCTCTCTG
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 6
gtgattttcttgtatcttccaagtctaagagtactctgcatttcttttatttataatttacacacaa--tttgattgaaaggtctcatgat-ggttgttgcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG
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--aaacatattttaccctttatgttttatt-tgtttagtttgttatgcatttggattttgatcagaacgtttaaccaaagaattatgctattgactcctgcagAGTGCTCCGCAGCCACTTTTGGAGAGCCATGAGCTATGTGCCATGACATTGGAGTACAGGAGGGAGTGTGGCAGGAACAGTGTGCTAGATTCCCTCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttataatttacacacaatttgattgaaaggtctcatgatggttgttgcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG
atttgat putative branch site (score: 5)
ttataatttacaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattttcttgtatcttccaagtctaagagtactctgcatttcttttatttataatttacacacaatttgattgaaaggtctcatgatggttgttgcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - ccaagtc
- - - - - - - - - - - - - - - - actctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcatga