Sequence
atgc intronic sequence ATGC exonic sequencegtaagaggccaagacttcagcattttttttccatatagtctccaaggaaatatgaccctaagtgttacttgttactgactctggttttatctcccttcgttttattatattgatttttttgggacatctgtttatgcagCTGCTTTTGGTTGACAAAAAGATCACAAATGCAAGGGATCTCATTAATGTTTTGGAAGATGCCATCAAAGGGGGATATCCAATCTTGATAATTGCGGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 6
gtaagaggccaagacttcagcattttttttccatatagtctccaaggaaatatgaccctaagtgt---tacttgttactgactctggttttatctcccttcgttttattatattgatttttttgggacatctgtttatgcagCTGCTTTTGGTTGACAAAAAGATCACAAATGCAAGGGATCTCATTAATGTTTTGGAAGATGCCATCAAAGGGGGATATCCAATCTTGATAATTGCGGAAG
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----------------------------------------------gtagcttcagcctgagcacacataccc-ctgctgtatgctgctttaatctgtttcagtttcttattgcactatgttt----ccactattttt-cagCTTCTTTTGGTGGACAAAAAAATCACCAACGCAAGGGATCTTATCAATGTTTTGGAGGAGGCCATAAGAGGTGCATACCCAATTCTGATAATTGCTGAGG
upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G065023_T01 (Zea mays), 3'ss of exon 1
gtaagaggccaagacttcagcattttttttccatatagtctccaaggaaatatgaccctaagtgttacttgttactgactctggtt-ttatctcccttcgttttattatattgatttttttgggacatctgtttatgcagCTGCTTTTGGTTGACAAAAAGATCACAAATGCAAGGGATCTCATTAATGTTTTGGAAGATGCCATCAAAGGGGGATATCCAATCTTGATAATTGCGGAAG
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------------------------------------aacctattggggggtgggggtaagacagttcctaggca--aacaacagttgctttcctgtttcagactattaatgctattgtctttcatcttca--ttgttcagCTGCTTTTGGTTGATAATAAAATCACCAATGCAAGGGATCTTATCAACGTTTTGGAAGAAGCCATCAGAGGTGCATACCCAATCCTGATAATTGCAGAGG
upper sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 5
-------------gtaagaggccaagact------tcagcattttttttccatatagtctccaaggaaata--------tgaccc---------taagtgttacttgttactgactctggttttatctcccttc--gttttattatattgatttttttggg--acatctgt-ttatgcagCTGCTTTTGGTTGACAAAAAGATCACAAATGCAAGGGATCTCATTAATGTTTTGGAAGATGCCATCAAAGGGGGATATCCAATCTTGATAATTGCGGAAG
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gtaactgtaaaatatgagatatcaattcttttttttttgctgtttattgctttcctgtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTTTTGGAAGAAGCCATCAGAGGTGCATACCCAATCCTGATAATTGCAGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatctcccttcgttttattatattgatttttttgggacatctgtttatgcagCTGCTTTTGGTTGACAAAAAGATCACAAATGCAAGGGATCTCATTAATGTTTTGGAAGATGCCATCAAAGGGGGATATCCAATCTTGATAATTGCGGAAG
tattgat putative branch site (score: 3)
tctgttt putative PPT
ttcgttttattatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaggccaagacttcagcattttttttccatatagtctccaaggaaatatgaccctaagtgttacttgttactgactctggttttatctcccttcgttttattatattgatttttttgggacatctgtttatgcagCTGCTTTTGGTTGACAAAAAGATCACAAATGCAAGGGATCTCATTAATGTTTTGGAAGATGCCATCAAAGGGGGATATCCAATCTTGATAATTGCGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG