Sequence
atgc intronic sequence ATGC exonic sequence...tgtatccatatagatttatttagtttatttttaccaaagaatttctcttgtgggtctgttctttatttctttacacataacaacaacgctaatatggcagGCGGTTTCAAGGCAATTCATTCCAAGGTCCACTTCCAAGCACTCTTGCTAATCTTGTTCAGCTAACAAGCTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g52606.2 (Oryza sativa), 3'ss of exon 7
--------tgtatccatatagatttatttagtttattt-ttaccaaagaatttctcttgtgggtctgttctttatttctttacacataacaacaacgctaatatggcagGCGGTTTCAAGGCAATTCATTCCAAGGTCCACTTCCAAGCACTCTTGCTAATCTTGTTCAGCTAACAAGCTT
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aagtttgcccttttttcttagcactactagtttaatttgccactgaataaatgataatttaaattaacaaactact-ctttctacat--ctatgaatctc------tagGCGGTTGCAAGGGAATTCTTTTCAAGGTCCACTTCCAGCCACTCTTTCTAATCTTGTCCAATTAACAAACTT
upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g52640.3 (Oryza sativa), 3'ss of exon 8
-tgtatccatatagatttatttagtttatttttaccaaagaatttctcttgtgggtctgttctttatt-tctttacacataacaacaacgctaatatggcagGCGGTTTCAAGGCAATTCATTCCAAGGTCCACTTCCAAGCACTCTTGCTAATCTTGTTCAGCTAACAAGCTT
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ttttcctccttttgttttactagagttgagaca--ctactagtttaatgtatcactaaataaatgataatctaaatgacaaactacatctatgaatctgtagGCGGTTTCAAGGAAATTCTTTTCAAGGTCCACTTCCAGCTAATCTTTCTAATCTTGTCCAATTAACAAACTT
upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g52614.1 (Oryza sativa), 3'ss of exon 8
tgtatccatatagatttatttagtttatttttaccaaagaatttctcttgtgggtctgttctttatt-tctttacacataacaacaacgctaatatggcagGCGGTTTCAAGGCAATTCATTCCAAGGTCCACTTCCAAGCACTCTTGCTAATCTTGTTCAGCTAACAAGCTT
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-ttttaagcaaagaattgatctgttcttttatcactactagtttaatgtatcaataattaaatgatgatttgaatgactaattacatctatcaatctgtagGCGGTTTCAAGGCAATTCTTTTCAAGGTCCAATTCCCGCTGCTCTTTCTAATCTTGTCCAATTATCAAGCTT
upper sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 8
--------tgtatccatatagatttatttagt-ttatttttaccaaagaatttctcttgtgggtctgttctttatttctttacacataacaacaacgctaatatggcagGCGGTTTCAAGGCAATTCATTCCAAGGTCCACTTCCAAGCACTCTTGCTAATCTTGTTCAGCTAACAAGCTT
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ttcctttttttaatcaaagagttcttcctgctatcatttctagtttgatgtttcagtaaaaaagatgatttgaatgact--------agttacagctatgatctg-tagGCGGTTTCAAGGCAATTCTTTTCAAGGTCCAATTCCTTCTGCTCTTTCTAATCTTGTCCAACTATCAAGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgtgggtctgttctttatttctttacacataacaacaacgctaatatggcagGCGGTTTCAAGGCAATTCATTCCAAGGTCCACTTCCAAGCACTCTTGCTAATCTTGTTCAGCTAACAAGCTT
cgctaat putative branch site (score: 3)
ttctttatttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtatccatatagatttatttagtttatttttaccaaagaatttctcttgtgggtctgttctttatttctttacacataacaacaacgctaatatggcagGCGGTTTCAAGGCAATTCATTCCAAGGTCCACTTCCAAGCACTCTTGCTAATCTTGTTCAGCTAACAAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
tgtatcc
- - - - - - - - - - - - - - - - - caaagaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacaac