Sequence
atgc intronic sequence ATGC exonic sequence...tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatttttatgtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 2
---tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttattt--ttatgtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
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taaattttttttgtgtatatcc-ttgaaattgcaaaaatatgtttgtatcttagttgctcgatttagaggttgctcacttaacaaatgacacatat----tgcagTGTCATTGTGGAAGCTCTTAAGGTGGATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
tttgcccttgcctgttt-ctat--taaacctctatgaacgtctcaatttaacacttatttt-tatgtcagttctaatatagtaaagaatatatatatca-tgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
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-----ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
tttgcc--cttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatttttatgtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
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cttgcttgcttggcgttttattttaacttattaataacagaataatcggtgacctatcac-attctatttgttgta-aacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
-tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatt-tttatgtcagttctaatatag-taaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
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tggctctcttgcttgtttggcgt---tttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 2
-tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatttttatgtcagttctaatatagtaaagaatat-atatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
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aagtaaatttggtagagtttattggtaggttctggt--ttttgatctaccgctcttcaaactacaaatatgtttgttgcttagctaacgaaacatttttcagTGTCATTGTGGAAGCTCTCAAGATGGACAGTTTGCAGAAACTCTGTTCATCGCTTGAGCCTATTCTCCGAAGAGTT
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 2
--tttgcccttgcctgtttcta--ttaaacctctatgaacgtctcaatttaacacttatttttatgtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
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attttcttagagtttagtgataagttacagtttttaatccaccacccttcaattcaaactacaaatatatttgttgcttagttaacgaaacatttttca----gTGTCATTGTGGAAGCTCTCAAGATGGACAGTTTGCAGAAACTCTGTTCATCGCTCGAGCCCATTCTCCGAAGAGTT
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatttttat-gtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
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-aaagaagattttatttcttattaatcataatccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
-tttgcccttgcctgtt-tctatta-aacctctatgaacgtctcaatttaacacttatttttatgtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
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atagggttttatttcttattaattataattcatctagttgtttctaatttatatttattgtta-gtttcatataattgattgatgcacatacttttc--gcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 2
tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatttttatgtcagt-tctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
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---------gtaattcactagttcttcttactgaaaatat--atacaac---tgtttctacaaaaatctctgactttggttatcttttggtttgcac-cagTGTGATTGTTGAGGCTCTGAAAGTAGATAGTTTGCAGAAGCTTTGCTCCTCTTTGGAACCTATTCTCCGCCGAGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacacttatttttatgtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
ttctaat putative branch site (score: 2)
ttctaatatagtaaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatttttatgtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - -ccttgcc
- - - - - - - - - - - - - - -tatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaagaa