Sequence
atgc intronic sequence ATGC exonic sequencegttagcattagtagaatatttttgggtagaaactgtagtcatttgatgtatctataagtcattgttgtttatttttgcttgattcggcactgtacagGCTGGTAATATCCTTATTGATGGTGCTGGGGTAGTGAAGCTTGGAGACTTTGGTGTTTCTGCTTGTATGTTTGATAGAGGTGACAGGCAAAGATCTAGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G413544_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g37480.1 (Oryza sativa), 3'ss of exon 2
gttagcattagtagaatatttttgggtagaaactgtagtcatttgatgtatctataagtcattgttgtttatttttgcttgattcggcactgtacagGCTGGTAATATCCTTATTGATGGTGCTGGGGTAGTGAAGCTTGGAGACTTTGGTGTTTCTGCTTGTATGTTTGATAGAGGTGACAGGCAAAGATCTAGGA
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--------------gttagcttctgtcaaatattgtaatcatctgatttga-tgttatttacttcaatttatctttgctcaatgtgacacttggcagGCCGGCAATATCCTTGTTGATAATGCTGGTATAGTGAAGCTTGGGGACTTCGGCGTGTCTGCTTGTATGTTTGATAGAGGTGATCGACAAAGATCTAGGA
upper sequence: GRMZM2G413544_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S39_232V6.1 (Physcomitrella patens), 3'ss of exon 2
gttagcattagtagaatatttttgggtagaaactgtagtcatttgatgtatcta--taagtcattgttgtttatttt---tgcttgattcggcactgtacagGCTGGTAATATCCTTATTGATGGTGCTGGGGTAGTGAAGCTTGGAGACTTTGGTGTTTCTGCTTGTATGTTTGATAGAGGTGACAGGCAAAGATCTAGGA
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-gcaggtcaaaaatatttattctaggtgtggtctcgatggaccgcatgcaaatgagtatttactcacaatgtatttggtgcacttcgtttactatt-ttcagGCTGGGAACATATTAGTTGATTCAAATGGATCTGTGAAGCTTGGAGACTTTGGTGTTTCAGCATGCATGTTTGACACTGGTGATAGACAGCGGTCTAGGA
upper sequence: GRMZM2G413544_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S407_24V6.1 (Physcomitrella patens), 3'ss of exon 2
gttagcattagtagaatatttttgggtagaaactgtagtcatttgatgtatctataagtcattgttgtttatttttgc------ttgattcggcactgtacagGCTGGTAATATCCTTATTGATGGTGCTGGGGTAGTGAAGCTTGGAGACTTTGGTGTTTCTGCTTGTATGTTTGATAGAGGTGACAGGCAAAGATCTAGGA
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---agggtagataaactatattatctgaggtgttgtttccaacggctgcgtgtaaatagtgttacttgcactttatgtggtgcattttgttggctgttttcagGCAGGAAACATATTAGTTGACTCAAACGGATCTGTGAAGCTTGGAGACTTTGGTGTTTCAGCATGTATGTTCGACACTGGTGATAGACAGCGGTCCAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatgtatctataagtcattgttgtttatttttgcttgattcggcactgtacagGCTGGTAATATCCTTATTGATGGTGCTGGGGTAGTGAAGCTTGGAGACTTTGGTGTTTCTGCTTGTATGTTTGATAGAGGTGACAGGCAAAGATCTAGGA
gcttgat putative branch site (score: 5)
attgttgtttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcattagtagaatatttttgggtagaaactgtagtcatttgatgtatctataagtcattgttgtttatttttgcttgattcggcactgtacagGCTGGTAATATCCTTATTGATGGTGCTGGGGTAGTGAAGCTTGGAGACTTTGGTGTTTCTGCTTGTATGTTTGATAGAGGTGACAGGCAAAGATCTAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG