Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgtttttcctccgccatcatttgtttaatcatcttaagattcagtccattttatttttaaattttccttctctgcctacttgtgttggatgtggcaatggattttgatcgactttttacttcatgaaccagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
gtgagtgtttttcctccgccatcatttgtttaatcatcttaagattcagtccattttat--ttttaaattttccttctctgcctacttgtgttggatgtggcaatggattttgatcgactttttacttcatgaac-cagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAG
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--------------------------------gtaag--tgaaattca-tccattttgtagccttacatttatcttttctat-tacatctgct---ttcgtgagtgcatacttaa-----ttctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
upper sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 15
gtgagtgtttttcctccgccatcatttgtttaatcatcttaagattcagtccattttatttttaaattttccttctctgcctacttgtg-ttggatgtggcaatggattttgatcgactttttacttcatgaaccagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAG
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--------------------------------------------gtaagtaaaatgaaaatttacctttt--ttaaatatctgtttgtggttgtaaaaagtagtgagccatgctt-actttttgaacgattg--cagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG
upper sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 16
gtgagtgtttttcctccgccatcatttgtttaatcatcttaagattcagtccattttatttttaaattttccttctctgcctact--tgtgttggatgtggcaatggattttgatcgactttttacttcatgaaccagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAG
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-----------------------gtaagtctctaaatattgaactccg--cctttttagtcatccgttttaccattaggattactaatgaatgtactttgatgctgagttttg---gaatccttatcctctttaccagAAAATCGGGTATGACAATGCTGCAGCAGTTGCCAAGAAAGCTCACAAAGAAGGATGTACATTGAAG
upper sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 15
gtgagtgtttttcctccgccatcatttgtttaatcatcttaagattcagtccattttatttttaaattttccttctctgcctacttgtgttggatgtggcaatggattttgatcgac-tttttacttcatgaaccagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAG
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-----------------------------gtaagtctctaaatattaa----acttctttgtcaagtcatccatatt---ctcattatgat-----tacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG
upper sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT5G50950.1 (Arabidopsis thaliana), 3'ss of exon 15
gtgagtgtttttcctccgccatcatttgtttaatcatcttaagattcagtccattttatttttaaattttccttctctgcctacttgtgttggatgtggcaatggattttgatcgactttt-tacttcatgaaccagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAG----------------------------------
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-----------------------------gtaagtctctaaatattaa----acttctttgtcaagtcatccatatt---ctcattatgat-----tacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacttgtgttggatgtggcaatggattttgatcgactttttacttcatgaaccagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAG
ttttgat putative branch site (score: 4)
ctttttacttc putative PPT
tttttactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgtttttcctccgccatcatttgtttaatcatcttaagattcagtccattttatttttaaattttccttctctgcctacttgtgttggatgtggcaatggattttgatcgactttttacttcatgaaccagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG