Sequence
atgc intronic sequence ATGC exonic sequence...ggaaaaataaaatagccatacacaatattttttatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g38900.1 (Oryza sativa), 3'ss of exon 3
ggaaaaataaaatagccat-acacaatattttttatgagttaacaattctgc-attgtat-atcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
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gatactcttctattttcttgatgtattctgtcgttcagcatgatgattaaactagagaatgatcaatgtcat--tgattatactt-ttactgctcactcacagGTGCGTGAGATGCCGAATGTATTAATTCTTCCTCGAAGTGCAGATTACAGTGAAGAAGTGTGGATTGAAATCAGAGAAAAGGCACTCGCAATATTGCAAT
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 2
-----------ggaaaaataaaat-agccatacacaatattttttatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
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ttttctgcattgctatggtggtgccacttgttcatcatccatcttataaaaaaagaactt---gttgttcagcaaaatgatg--gat-------actatttatttgacatagGTAAGGGAGATGCCAAATGTTTTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATCACGATATTGCAGT
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G418294_T01 (Zea mays), 3'ss of exon 3
ggaaaaataaaatagccatac--acaatattttttatgagttaacaattctgcattgtatatcaaggcgatg--ttaattagccccat-catgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
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---actttgcacttgtgatgcttgctgtacttataatacgctaatagaaaag--tcatgtttcaaacaaatgatttaatacttgttatgtgttcattgatcacagGTGCGTGAGATGCCAAATGTATTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAGATCAGAGAGAAAGCAATCGCAATATTGCAGT
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------------------ggaaaaataaaatagccatacacaatattttt----tatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
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gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaac-ctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtga--------ctgatcattgttgtg-tacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
ggaaaaataaaatagccat-acacaatattttttatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
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ctcataatcatatatatattagattacgtctgtcagtctacaacaatgatagttttaatagatagattatactaacatactttgt-gtgtgtctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
---ggaaaaataaaatagccatacacaatattttttatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccat-catgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA-
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ccactcacaatcatatatatatata---tgtctatcagtctacaacaatgatagttttaatacatagatgatgctaacatactttgtgcatg--tctgcatcaggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------ggaaaaataaaatagccatacaca---atattttttatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
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gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgt-tgtttatcctgcatccatta----tatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
upper sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
-----ggaaaaataaaatagccatacacaatatttt--ttatgagttaacaattctgcattgtatatcaaggcgat-----gttaattagccccatcatgactttgctt----cagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
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gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgcattgtatatcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
tgttaat putative branch site (score: 3)
ctttgcttc putative PPT
atgttaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaaaaataaaatagccatacacaatattttttatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- -aaaataa
- - - - - - - -ccataca
- - - - - - - - - - - - - - - - - - - - aacaatt
- - - - - - - - - - - - - - - - - - - - - - - - tgcattg