Sequence
atgc intronic sequence ATGC exonic sequence...gcaaaatgaattcaatttttcctgttgaggctctaaacttagatttgtggtttctccatcatattcttttaccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
gcaaaatgaattcaatttttc--ctgttgaggctctaaacttagatttgtggtttctc-catcatattcttttaccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG
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--gtacttactttgatccctcatttgcattgtctttctgtaatagttaataaaagctaatggcttatcctcttctaacttgttgtt-atgggctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 3
gcaaaatgaa-ttcaatttttcctgttgaggctctaaacttagatttgtggtt--tctccatcatattcttt--taccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG
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---gtatgtactttgatctctttcgcaatgcttctggtggagtatctgaagagaacatcggttatatccattactaactctttatgttttatgtccggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------gcaaaatgaattcaatttttcctgttgaggctctaaacttagatttgtggtttctc------catcatattcttttaccctttg--ctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG
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gtaaagttccatgatagaagagatctttatgttctagttctagacatgttctcagtttctggcactgaagcaatatgcgaagcatcctaccgttccctgttttggagttttttttttttttttttgtatgtcttcccaatcatttgcttgttgggctgatgcatgcgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAG
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------gcaaaatgaattcaatttttcctgttgaggctctaaacttagatttgtggtttctccatcatattcttttacccttt--gctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG
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gtaaagttccatgatggaagagatctttattttcttctagttctagaagacattttctcagtttttggcatagaagcaatatgagaagcaccctaccattccattttttggagtttgttttttgatgtct---tcccaatcatttgcttgttgggctgatgcatgtgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATCGATGACAG
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 3
gcaaaatgaattcaatttttcctgttgaggctctaaacttagatttg--tggtttctccatcatattcttttaccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG
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----------gtaagtttctggaacagaagc---aaatcaggattcaaccatttcctgctatgtagcttgtttctatttgctgatgaatatgtatcttatagGGGTTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCACAGTGGACAATGCGCAATGTCGATGACAG
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------------gcaaaatgaattcaatttttcctgttgaggctctaaacttagatttgtggtttctccatcatattcttttaccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG
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gtaagattttaatgaagcttacagtacctaagattttaagaagaaatgcatgcatctggtgtaagagactttgtaattgtaattgattgtgtaattgtaaaatactgttcaatattttctatgtatcctctactt-ttgctgatgcaaagtcttttagGGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAG
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 3
-----gcaaaatgaattcaatttttcctgttgaggctctaaacttagatttgtggtttctccatcatattcttttaccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG
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ctgatgcaaagtcttttaggggttttacttaaataatttgtaaaacactgttcaatattttc--catgttcccactgcttttgctgatgc---aaagtcttttagGGGTTTGATAATCTCAGGAGTCAAAGTGTTGCTCCTCCACAGTGGACCATGCGCAACACTGATGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtggtttctccatcatattcttttaccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG
tgttgat putative branch site (score: 4)
atcatattctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaaaatgaattcaatttttcctgttgaggctctaaacttagatttgtggtttctccatcatattcttttaccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- -aaatgaa
- - - - - - - - - - cctgttg
- - - - - - - - - - -ctgttga