Sequence
atgc intronic sequence ATGC exonic sequence...ttgttaaattctttttacaaccctgtttctatcaagtttggatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0357g00070.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
ttgttaaattctttttacaaccctgtttctatcaagtttggatttgg-atacattacatgtgcctctagtaattgctgatg-aaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA
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-agatgaggacatggctggatgtt-ttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
upper sequence: Vv00s0357g00070.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g36000.1 (Oryza sativa), 3'ss of exon 3
ttgttaaattctttttacaaccctgtttctatcaagtttggatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgg--gtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA
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atgagaacatgcgtgctcgatcttaggtatttcc--tctggtctagcatcagcaagacaactccctgcctagtgacaaaatagtttttaccttgatgtgcagGCAATGGCCCAGGTTGGAGGTCTGGTTATGTTGCAACCTGAAGTTGGTGGATCTCGAGAGAACTTCTTTTTTGCAGGGATTGATAAAGTGAGATTTCGTA
upper sequence: Vv00s0357g00070.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
ttgttaaattctttttacaaccctgtttctatcaagtttggatttggat-acattacatgtgcctctagtaattgctgatgaaagtggttggtgggtc------cagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA
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-------atatatataatgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagtaactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
upper sequence: Vv00s0357g00070.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G055667_T01 (Zea mays), 3'ss of exon 3
ttgttaaattctttttacaaccctgtttctatcaagtttggatttggatacattacatgtgcctctagtaattgctgatgaaagtggt-tggtgggt--ccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA
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---gcatttttttttcctgaagacattaaagctacctattgtctcaagcaaactttctggttgacttgtacgtactggacaattttttaccatgatttttcagGCAATGGCCCAGGTCGGAGGAATAGTGATGTTGCAGCCTGAAGTGGGTGGATCTCGAGAGAACTTCTTTTTTGCGGGGATCGATAAAGTGAGGTTCCGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA
tgctgat putative branch site (score: 3)
tagtaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttaaattctttttacaaccctgtttctatcaagtttggatttggatacattacatgtgcctctagtaattgctgatgaaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA
- - - - - - - - acaaccc
- - - - - - - - - - - - - - ctatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ttacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg