Sequence
atgc intronic sequence ATGC exonic sequence...tatattactttgcagttgtattacttagtgtcaagtaatagtaaaataattctgtcaaattgtgcatcagcctgattaacaaatgcatgttttattttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0011g02950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g49900.1 (Oryza sativa), 3'ss of exon 4
tatattactttgcagttgtattacttagtgtca-agtaatagtaaaataattctgtcaaattgtgcatcagcctgattaacaaatgcatgttttat--tttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT
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-aaaatatctagagatattagttgttaatacaatagtagcgctaaagttaatttg--gatgttaacctttattttttttccttgcattggtttgactattcagAATGTGTAGAGCTTTAATGCCAGGAGATGAAGAAAGTATGAGCGATGAAGCTATTTGGGAGACACTTCCT
upper sequence: Vv01s0011g02950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G704032_T01 (Zea mays), 3'ss of exon 4
--tatattactttgcagttgtattacttagtgtcaagtaatagtaaaataattctgtcaaattgtgcatcagc-ctgattaacaaatgcatgttttattttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT
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gaaaaataaactattatttgttatttttggagacttactgtattag--tcactctggacattgacgtgtatgcatttcttggcatgttttttcattattc-agAATGTGTAGAGCTTTAATGCCTGGAGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACGCTTCCT
upper sequence: Vv01s0011g02950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G024690_T02 (Zea mays), 3'ss of exon 4
tatattactttgcagttgtattacttagtgtcaagtaatagtaa-aataattctgtcaaattgtgcatcagc-ctgattaacaaatgcatgttttattttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT
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--tactattatttgttatttttggtgggctgctgcctactgtattagtcactatggacattgacgtctatgcatttcttggcatggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT
upper sequence: Vv01s0011g02950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G32670.1 (Glycine max), 3'ss of exon 4
------tatattactttgcagttgtattacttagtgtcaagtaatagtaaaataattctgtcaaattgtgcatcagcctgattaacaa--atgcatgttttattttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT
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gctaggcatgcttctgctcaatgttaataaattata-caagctgcaataca----ttctcttataacaaatggatgctttattgacaacaatgcctatttcat---agGATGTGTAGGGCTTTGATGCCTGGAGATGATGAAAATTTGACCGACGAAGCAGTATGGGAAACTCTTCCG
upper sequence: Vv01s0011g02950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G34710.1 (Glycine max), 3'ss of exon 4
-----tatattactttgcagt-tgtattacttagtgtcaagtaatagtaaaataa-ttctgtcaaattgtgcatcagcctgattaacaaatgcatgttttattttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT
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tgctcaatgttaataaattatacaagctgcttagctgcaagctgcaatacattctcttctgacaaatgg---at--gttttattgacaaaa--atgccttttcatagGATGTGTAGGGCTTTGATGCCTGGAGATGATGAAAATCTGACCGACGAAGCAGTATGGGAAACTCTTCCG
upper sequence: Vv01s0011g02950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G68820.1 (Arabidopsis thaliana), 3'ss of exon 4
tatattac-tttgcagttgtattacttagtgtcaagtaatagtaaaataattctgtcaaattgtgcatcagcctgattaacaaatgcatgttttattttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT
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-gtattccattcaaagcttttttgattt-tgttcacccttcttacta-----ctcttagagtacggaacaattaaatcttttt-tgcaactattcctgcagAATGTGCAGGACGCTCATGCCTGGAGATGAAGAAACTATGAGTGATGAAGCCATATGGGAAACACTTCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataattctgtcaaattgtgcatcagcctgattaacaaatgcatgttttattttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT
gattaac putative branch site (score: 2)
ttttatttt putative PPT
atgttttatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatattactttgcagttgtattacttagtgtcaagtaatagtaaaataattctgtcaaattgtgcatcagcctgattaacaaatgcatgttttattttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - tgcagtt
- - - - - - - - - - - - - - - tcaagta
- - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaat