Sequence
atgc intronic sequence ATGC exonic sequence...atgtttgaaagtgtcccatttttaaggctagttttcctgttcgtctcagtgacactgcaaattcttcatcattcacaatgttatgattttgatcttgcagCTATACCTGGGGATTGGGAAATATGGGACAACTTGGGCATTGTTCTCTGCAATACGGGGATAAGGAGCTGGTACCAAGGCGAGTAGTTGCTCTTGATGGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0083g01020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g40260.1 (Oryza sativa), 3'ss of exon 6
--atgtttgaaagtgtcccatttttaaggctagttttcctgttcgtctcagtgacactgcaaattcttcatcattcacaatgttatgattttgatcttgcagCTATACCTGGGGATTGGGAAATATGGGACAACTTGGGCATTGTTCTCTGCAATACGGGGATAAGGAGCTGGTACCAAGGCGAGTAGTTGCTCTTGATGGG
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agcttattttatgccttctattgtggaacatatgtctaatagac-taacaggaacatgattgtttctttttaatttttttaaatatcacct-aattttgcagATATACTTGGGGACTGGGAAGCATGGGACAGCTTGGGCATTGCTCTCTTCAGTCTGGAGATAAGGAGCTGATCCCAAGGCGTGTTGTTGCTCTTGACAGA
upper sequence: Vv14s0083g01020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G074024_T02 (Zea mays), 3'ss of exon 6
atgtttgaaagtgtcccatttttaaggct--agttttcctgttcgtctcagtgacactgcaaatt----cttcatcattcacaatgttatgatttt--gatcttgcagCTATACCTGGGGATTGGGAAATATGGGACAACTTGGGCATTGTTCTCTGCAATACGGGGATAAGGAGCTGGTACCAAGGCGAGTAGTTGCTCTTGATGGG
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--------aatcattccgatttcatacttttcgcttttttgatgattgaaaacctattccaagtagggacttgattatttgtaattataatatctttggtttttgcagGTATACTTGGGGACTGGGAAGCATGGGGCAGCTTGGGCATTGCTCCCTCCAATCTGGAGATAATGAGCTGATCCCTAGGCGAGTTGTGGCCCTTGATGGT
upper sequence: Vv14s0083g01020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G50920.1 (Glycine max), 3'ss of exon 5
atgtttgaaagtgtcc---catttttaaggctagttttcctgttcgtctcagtgacactgcaaattcttcatcattcacaatgttatgattttg-atcttgcagCTATACCTGGGGATTGGGAAATATGGGACAACTTGGGCATTGTTCTCTGCAATACGGGGATAAGGAGCTGGTACCAAGGCGAGTAGTTGCTCTTGATGGG
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----ttggggatccataagcagtattatcaataatttgttattaaatttgagtgcttgtgataatacttcatcacttgttatattttgtccttggatcttgcagCTACACATGGGGGCTAGGAAATATGGGCCAGCTTGGGCATTCTTCACTCCAGTATGGGGATAAAGAGTTACTGCCAAGGAGGGTGGTTACCCTTGATGGT
upper sequence: Vv14s0083g01020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G02300.1 (Arabidopsis thaliana), 3'ss of exon 6
--atgtttgaaagtgtcccatttttaaggctagttttcctgttcgtct-cagtgacactgcaaattcttcatcattcacaatgttatgattttgatcttgcagCTATACCTGGGGATTGGGAAATATGGGACAACTTGGGCATTGTTCTCTGCAATACGGGGATAAGGAGCTGGTACCAAGGCGAGTAGTTGCTCTTGATGGG
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ggaagcaaatgaattcctgacttgcaagtcttcttcccttttgcttatattttctcggtttatcttattcagtgtccactgc-ttatctctttcgtg--gcagTTACACTTGGGGATTAGGAAGCATGGGTCAACTTGGGCATGTTTCTCTTCAATCCGGGGATAAGGAGTTAATACCAAGGAGAGTCGTTGGTCTCGATGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagtgacactgcaaattcttcatcattcacaatgttatgattttgatcttgcagCTATACCTGGGGATTGGGAAATATGGGACAACTTGGGCATTGTTCTCTGCAATACGGGGATAAGGAGCTGGTACCAAGGCGAGTAGTTGCTCTTGATGGG
ttttgat putative branch site (score: 4)
aatgttatgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtttgaaagtgtcccatttttaaggctagttttcctgttcgtctcagtgacactgcaaattcttcatcattcacaatgttatgattttgatcttgcagCTATACCTGGGGATTGGGAAATATGGGACAACTTGGGCATTGTTCTCTGCAATACGGGGATAAGGAGCTGGTACCAAGGCGAGTAGTTGCTCTTGATGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - -tgtccca
- - - - - - - - - - - - - - - - -ttcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - cactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaatg