Sequence
atgc intronic sequence ATGC exonic sequence...aaccttgcatgaaacttagcatcctcgctaggtattaatttgctttttctcgtgctttactatttttcaagcattgtttcaatgttgtatcaggactgagAAGGATATCACTCCAATGGGTGGGTTTCCTCACTGTGGTGTGGTTAAGGATGATTATGTTTTGATCAAGGGGTGCTGTGTTGGGCCAAAGAAGAGGGTCG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0031g02050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 5
-----------------------------aaccttgcatga----aacttagcatcctcgctaggtattaatttgctttttctcgtgctttactatttttcaagcattgt-ttcaatgttgta-tcaggactgagAAGGATATCACTCCAATGGGTGGGTTTCCTCACTGTGGTGTGGTTAAGGATGATTATGTTTTGATCAAGGGGTGCTGTGTTGGGCCAAAGAAGAGGGTCG
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gtaccaattcgtctaccagatattacaccagcactccatgattgcaaatctgtcttct-gtttgatatgctattgcatctgtttgcgagcgaaacttaaacga-tattgtgcttgctcttgcgctcagGACTGAGAAGGACATCACTCCCATGGGTGGCTTCCCTCACTACGGTGTTGTGAAGGGCGACTACCTCATGATCAAGGGTTGCTGTGTTGGCCCCAAGAAG-------
upper sequence: Vv07s0031g02050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 6
-aaccttgcatgaaacttagcatcctcgctaggtattaatttgctttttctcgtgctttactatttttcaagcattgtttcaatgttgtatcaggactgagAAGGATATCACTCCAATGGGTGGGTTTCCTCACTGTGGTGTGGTTAAGGATGATTATGTTTTGATCAAGGGGTGCTGTGTTGGGCCAAAGAAGAGGGTCG
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gtactatttctgag-cttcttgtactaacttgca--caatctgtttacctttgttgctc-ttgttggtaacgaattgctgccat-ttg---cagGACTGAGAAGGACATCACTCCCATGGGTGGCTTCCCCCATTATGGTATCGTGAAGGGTGACTACCTGATGATCAAGGGCTGCTGTGTGGGTCCAAAGAAG-------
upper sequence: Vv07s0031g02050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G324314_T05 (Zea mays), 3'ss of exon 5
-aaccttgcatgaaacttagcatcctcgctaggtattaatttgctttttctcgtgctttactatttttcaagcattgtttcaatgttgtatcaggactgagAAGGATATCACTCCAATGGGTGGGTTTCCTCACTGTGGTGTGGTTAAGGATGATTATGTTTTGATCAAGGGGTGCTGTGTTGGGCCAAAGAAGAGGGTCG
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gtactatttctgagcttgtactaacttgca------caatctgtttacctttgttgctc-ttgttggtaacgaattgctgccat-ttg---cagGACTGAGAAGGACATCACTCCCATGGGTGGCTTCCCCCATTATGGTATCGTGAAGGGTGACTACCTGATGATCAAGGGCTGCTGTGTGGGACCAAAGAAG-------
upper sequence: Vv07s0031g02050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G801409_T04 (Zea mays), 3'ss of exon 4
aaccttgcatgaaa-cttagcatcctcgctaggtattaatttgctttttctcgtg--ctttactattttt-caagcattgtttcaatgttgtat-caggactgagAAGGATATCACTCCAATGGGTGGGTTTCCTCACTGTGGTGTGGTTAAGGATGATTATGTTTTGATCAAGGGGTGCTGTGTTGGGCCAAAGAAGAGGGTCG
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------gtactatttctgagcttcttgtacatgtactaacttgcacaatctgtttacctttgttgctcttgtttgtaacgaattgctgccatttgcagGACTGAGAAGGACATCACTCCCATGGGTGGCTTCCCCCATTATGGTATCGTGAAGGGTGACTACCTGATGATCAAGGGCTGCTGTGTGGGTCCAAAGAAG-------
upper sequence: Vv07s0031g02050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G135727_T04 (Zea mays), 3'ss of exon 4
aaccttgcatgaaacttagcatcctcgctaggtattaatttgctttttctcgtgctttactatttttcaagcattgtttcaatgttgtatcaggactgagAAGGATATCACTCCAATGGGTGGGTTTCCTCACTGTGGTGTGGTTAAGGATGATTATGTTTT-GATCAAGGGGTGCTGTGTTGGGCCAAAGAAGAGGGTCG
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-------------------------------ccactatggtatcgtgaagggtgactacctgatgatcaagggatgct---gtgtgggtccaaagaagagggtggtgaccctccgccag------tccctcctgaagcagACTTCCCGGCTGGCGCTGGAGGAGATCAAGCTC----------------------------
upper sequence: Vv07s0031g02050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G43170.7 (Arabidopsis thaliana), 3'ss of exon 5
----------aaccttgcatgaaacttagcatc-ctcgctaggtattaatttgctttttctcgtgctttactatttttcaagcattgtttcaatgttgtatcaggactgagAAGGATATCACTCCAATGGGTGGGTTTCCTCACTGTGGTGTGGTTAAGGATGATTATGTTTTGATCAAGGGGTGCTGTGTTGGGCCAAAGAAGAGGGTCG
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gtcagtagaaatttctctgtttcgtttcttttctcctgtctggtcatgattacttctgtggtttatctgagtctgatgataatgttttgtgtatgatgatatagGACTGAGAAGGATGTGACTCCAATGGGAGGCTTCCCACACTACGGTATTGTGAAGGATGACTACTTGATGATTAAGGGGTGCTGTGTTGGTCCCAAGAAG------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctcgtgctttactatttttcaagcattgtttcaatgttgtatcaggactgagAAGGATATCACTCCAATGGGTGGGTTTCCTCACTGTGGTGTGGTTAAGGATGATTATGTTTTGATCAAGGGGTGCTGTGTTGGGCCAAAGAAGAGGGTCG
tttactatttttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaccttgcatgaaacttagcatcctcgctaggtattaatttgctttttctcgtgctttactatttttcaagcattgtttcaatgttgtatcaggactgagAAGGATATCACTCCAATGGGTGGGTTTCCTCACTGTGGTGTGGTTAAGGATGATTATGTTTTGATCAAGGGGTGCTGTGTTGGGCCAAAGAAGAGGGTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- ccttgca
- - - - - - - - - -catcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgtt