Sequence
atgc intronic sequence ATGC exonic sequence...tgctattatatacattcatgatacatttgattgctttaggtttttctgccttccgttattaaaagctattgtatgctgtgttgcctgtattaatttttagGTGGCACAATCACCTTAATCCTGCCATAAACAAGGAGGCATGGACTCAAGAAGAAGAGTTGGCATTGGTTCGTGCTCATCAGATATATGGAAACAAGTGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 5
--tgctattatatacattcatgatacatttgattgctttaggtttt-tctgccttccgttattaaaagctattgtatgctgtgttgcctgtattaatttttagGTGGCACAATCACCTTAATCCTGCCATAAACAAGGAGGCATGGACTCAAGAAGAAGAGTTGGCATTGGTTCGTGCTCATCAGATATATGGAAACAAGTGG
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tatgctaatttatttcttaatg-tgcatgccattatttttaatcgagtatcattactgtggattctacgtcttaaa-gatggactatcta-atctgcatttagGTGGCACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
upper sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g12860.1 (Oryza sativa), 3'ss of exon 5
tgctattatatacattcatgatacatttgattgctttaggtttttctgccttccgttattaaaagctattgtatgc--------tgtgttgcctgtattaatttttagGTGGCACAATCACCTTAATCCTGCCATAAACAAGGAGGCATGGACTCAAGAAGAAGAGTTGGCATTGGTTCGTGCTCATCAGATATATGGAAACAAGTGG
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-----taactttgtttcttaatatgcatggtagcatta--tttttaatttgagtatcattacaatgtattggatgccttacagatgtatcatcta-atctgcatttagGTGGTACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
upper sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 3
tgctattatata-cat-tcatgatacatttgattgctttaggtttttctgccttccgttattaaaagctattgtatgctgtgttgcctgtattaatttttagGTGGCACAATCACCTTAATCCTGCCATAAACAAGGAGGCATGGACTCAAGAAGAAGAGTTGGCATTGGTTCGTGCTCATCAGATATATGGAAACAAGTGG
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aggcatcatatggtatgtctttgcaaattcattcaattatgggtactataaatgtgttaactgtagtttctctaaccatggattagcttatctgattc--agGTGGCACAATCATCTTAACCCAGCCATAAACAAGGAGGCATGGACGCAAGAAGAGGAGATTACTCTTATTCATGCTCATAGGATGTATGGAAATAAATGG
upper sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S120_159V6.2 (Physcomitrella patens), 3'ss of exon 4
-------tgctattatatacattcatgatacatttg-----attg-ctttaggtttttctgccttccgttattaaaagctat-tgtatgctgtgttgcctgtattaatt------tttagGTGGCACAATCACCTTAATCCTGCCATAAACAAGGAGGCATGGACTCAAGAAGAAGAGTTGGCATTGGTTCGTGCTCATCAGATATATGGAAACAAGTGG
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gtgggctcacgaggacctaaattgtgggttctattatcaaaactgtcctcagggtttcttgttttgtcgcacggttgaccttatgtagcctgtctgactgcagttcgttgaatgattcagGTGGCACAATCATCTCAATCCCAGTATAAAGCGCGAGGCTTGGACTCAACAAGAGGATTTGGCATTGATCCGTGCTCATCAACTATATGGAAACAAGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgccttccgttattaaaagctattgtatgctgtgttgcctgtattaatttttagGTGGCACAATCACCTTAATCCTGCCATAAACAAGGAGGCATGGACTCAAGAAGAAGAGTTGGCATTGGTTCGTGCTCATCAGATATATGGAAACAAGTGG
tattaat putative branch site (score: 2)
ttttt CT-rich tract
tgtattaattttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctattatatacattcatgatacatttgattgctttaggtttttctgccttccgttattaaaagctattgtatgctgtgttgcctgtattaatttttagGTGGCACAATCACCTTAATCCTGCCATAAACAAGGAGGCATGGACTCAAGAAGAAGAGTTGGCATTGGTTCGTGCTCATCAGATATATGGAAACAAGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - cattcat
- - - - - - - - - - - - - -tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -attaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctgt