Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgcatttccatattgcctcctctacacccaagttattttcaaatgtgagctggtgtcaatttcttactcttctgtgaagTGGTTATCTTGCACCCGAGTACGCCATGAGGGGTCATATGACCGAGAAAGTTGATGTGTTTGCATTTGGAGTGGTCATATTGGAGACTCTAGCTGGAAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G155837_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os04g52640.1 (Oryza sativa), 3'ss of exon 22
----------gtaagtgcatttccatattgcct----cctctacacccaagttattttcaa-atgtgagctggtgtcaat-ttcttactcttctgtgaagTGGTTATCTTGCACCCGAGTACGCCATGAGGGGTCATATGACCGAGAAAGTTGATGTGTTTGCATTTGGAGTGGTCATATTGGAGACTCTAGCTGGAAGG
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catacaaaccccttacataatgtcaaattacataagcagtttacatattatttttttttaatacatgtgaaggtaatgatgtttttttggctctttccagTGGTTATCTTGCACCTGAGTACGCCATGAGAGGACATATGACTGAGAAAGTTGATGTGTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGCCGG
upper sequence: GRMZM2G155837_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 22
gtaagtgcatttccatattgcctcctctacacccaagttattttcaaatgtgagctggtgtcaatttcttac-tcttctgtgaagTGGTTATCTTGCACCCGAGTACGCCATGAGGGGTCATATGACCGAGAAAGTTGATGTGTTTGCATTTGGAGTGGTCATATTGGAGACTCTAGCTGGAAGG
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gtaagtacattccatctgttccacctttatgt-----ttacaatcatatttatgttaatggtatttttgggtatcctttgtccagCGGTTATCTTGCACCTGAGTATGCCATGAGAGGTCATATGACTGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGACGG
upper sequence: GRMZM2G155837_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os04g52606.2 (Oryza sativa), 3'ss of exon 19
gtaagtgcatttccatattgcctcctctacacc--caagttattttcaaatgtgagctggtgtcaatttc--ttactcttctgtgaagTGGTTATCTTGCACCCGAGTACGCCATGAGGGGTCATATGACCGAGAAAGTTGATGTGTTTGCATTTGGAGTGGTCATATTGGAGACTCTAGCTGGAAGG
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gtaagttcattccatctttcgcaccttcatgtttacaaattattttcgtacctgtgctaacgggatttatggcttttcttttatctagTGGTTATCTTGCACCTGAGTATGCTATGAGAGGTCGTTTGACCGAGAAAGTTGATGTCTTTGCATTTGGCGTGGTCTTATTGGAGACTTTAGCTGGCCGA
upper sequence: GRMZM2G155837_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os04g52630.1 (Oryza sativa), 3'ss of exon 20
gtaagtgcatttccatattgcctcctctacacc--caagttattttcaaatgtgagctggtgtcaatttct-tactcttctgtgaagTGGTTATCTTGCACCCGAGTACGCCATGAGGGGTCATATGACCGAGAAAGTTGATGTGTTTGCATTTGGAGTGGTCATATTGGAGACTCTAGCTGGAAGG
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gtaagttcattccatctttctcacctttgtctttacaaactacggagtacta-aagctaatgagatttttggctctcctttgtccagTGGTTATCTTGCACCTGAGTATGCCATGAGAGGCCGTATGACTGAGAAAGTTGATGTCTTCGCATTTGGCGTGGTCTTATTGGAGATTTTAGCTGGCCGA
upper sequence: GRMZM2G155837_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os04g52614.1 (Oryza sativa), 3'ss of exon 18
gtaagtgcatttccatattgcctcctctacacccaagttattttcaaatgtgagctggtgtcaatttctta----ctcttctgtgaagTGGTTATCTTGCACCCGAGTACGCCATGAGGGGTCATATGACCGAGAAAGTTGATGTGTTTGCATTTGGAGTGGTCATATTGGAGACTCTAGCTGGAAGG
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gtaagtacattccttctttcccacctttatgtttacaat-ttttcatacttatgttggcggtggcttttttggctctcctttgtccagCGGTTATCTTGCACCTGAGTACGCCATGAGAGGCCATATGACCGAGAAAGTTGACGTCTTTGCATTTGGCGTG--------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacccaagttattttcaaatgtgagctggtgtcaatttcttactcttctgtgaagTGGTTATCTTGCACCCGAGTACGCCATGAGGGGTCATATGACCGAGAAAGTTGATGTGTTTGCATTTGGAGTGGTCATATTGGAGACTCTAGCTGGAAGG
ttcttac putative branch site (score: 2)
tttcttactcttctgt CT-rich tract
aagttattttcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgcatttccatattgcctcctctacacccaagttattttcaaatgtgagctggtgtcaatttcttactcttctgtgaagTGGTTATCTTGCACCCGAGTACGCCATGAGGGGTCATATGACCGAGAAAGTTGATGTGTTTGCATTTGGAGTGGTCATATTGGAGACTCTAGCTGGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG