Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgatcttttggtctttgtctagttttgtgtctcgtttcttgtttacatgatctagaagatcctttggtttcagaacactctaggtcagcaatggagttttttgtagatagttatgtggaattttaatttctgatattctttttaaatgctcatttgatcatacagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
----gtgagtgatcttttggtctttgtct--agttttgtgtctcgtttcttgtttacatgatctagaagatcctttggtttcagaacactctaggtcagcaatggagttttttgtagatagttatg-tggaattttaatttctgatattctttttaaatgctcatttgatcatacagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT
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gttagtaattcatcttatgccttttacctgcaacattttatc-cgtgtgtactggaggtagtcgtggacttcttttgacggttggg-act-tggggctgcataagattctctattctatactagtaatagaatgtcacaatatcagcatgagataacaagaacctttaa----acagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT
upper sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
gtgagtgatcttttggtctttgtctagttttgtgtctcgtttcttgtttacatgatctagaagatcctttggtttcagaacactctaggtcagcaatggagttttttgtagatagttatgtggaattttaatttctgatattctttttaaatgctcatttgatcat--acagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT
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-------------------------------------------------------------------cctagacaactaaggctgtagcctatgtataacatatgctaataat--ttatattgcag---aagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
upper sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
gtgagtgatcttttggtctttgtctagttttgtgtctcgtttcttgtttacatgatctagaagatcctttggtttcagaacactctaggtcagcaatggagttttttgtagatagttatgtggaattttaatttctgatattctttttaaatgctcatttgatcatacagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT
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gttagtaacccc-----ccttga--acttcagtaacattattgttgattaga------aggcaatgcttagattttatcatttctaatggctacaa----acattttaagtttatttat-tgg--tcatggtct----tatctggtttaactggggcatc--ttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
upper sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 8
gtgagtgatcttttggtctttgtctagttttgtgtctcgtttcttgtttacatgatctagaagatcctttggtttcagaacactctaggtcagcaatggagttttttgtagatagttatgtggaattttaatttctgatattctttttaaatgctcatttgatcatacagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT
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-------------------------------------gatatattactaggatgatttagaat-ttttctgtatccagaatgatcttaccaag-----------tttgcaagtacttaagggacagtcgtattgttaat---------------------gagaattcagGTTTGAGGAGACTGAGCCTCCTGGAGCTAGGTCGTTTTTCACAGAGATTATTGCTTCAATTTCTGATATCAAGTTTGCAAGAGGTGGCCGGTACATTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgtggaattttaatttctgatattctttttaaatgctcatttgatcatacagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT
aattttaatttctgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgatcttttggtctttgtctagttttgtgtctcgtttcttgtttacatgatctagaagatcctttggtttcagaacactctaggtcagcaatggagttttttgtagatagttatgtggaattttaatttctgatattctttttaaatgctcatttgatcatacagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA