Sequence
atgc intronic sequence ATGC exonic sequencegtgagatagattcaggttcttgtctcgacacatgagatggattcacgtagcttgcttattattattgattattctactgtttttgccttctgcaattcttcctattggcatgagtatttggaattctagagtattgttcccatccagatagattatctctgcctaataaattctgcccattgattattgcagTAAGCTGGAGTCCGAGGTTCTCAAGGATGTCGTCTCCCAGATAGTTCAGGATGCCAAGAAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G074769_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g44450.2 (Oryza sativa), 3'ss of exon 1
gtgagatagattcaggttcttgtctcgacacatgagatggattcacgtagcttgcttattattattgattattctactgtttttgccttctgcaattcttcctattggcatgagtatttggaattctagagtattgttcccatccagatagattatctctgcctaataaattctgcccattgattattgcagTAAGCTGGAGTCCGAGGTTCTCAAGGATGTCGTCTCCCAGATAGTTCAGGATGCCAAGAAGAA---TAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
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----------------------------------------------------------------------------tagattatgtctg----aatataggttactg--atcggtataagaaatgctcgttctttgtttcc-------tgaacaaaattcacgtgctgagct-tgcgtgatca--attgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGAATCCAAGGAGAAGGGCAGGAAGTTCACCGAGACCGTTGAGCTTCAGATT---
upper sequence: GRMZM2G074769_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagatagattcaggttcttgtctcgacacatgagatggattcacgtagcttgcttattattattgattattctactgtttttgccttctgcaattcttcctattggcatgagtatttggaattctagagtattgttcccatccagatagattatctctgcctaataaattctgcccattgattattgcagTAAGCTGGAGTCCGAGGTTCTCAAGGATGTCGTCTCCCAGATAGTTCAGGATGCCAAG---AAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
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-------------------------------------------------------------------------------atggggagttttagggtttttagtag-ggtttga---ttggtagctacaacctactagtcgaatt-acacgtttaacggtcgtgttatg----ctgctctcgg----ctgcagTAAGCTTCAGAGCGATGTCCTCAGGGAGGCCATCACTCAGATTACCACTGCCGCTAAGGAGAAGAATAGGAAGTTCACAGAGACTGTGGAGCTTCAGATC---
upper sequence: GRMZM2G074769_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagatagattcaggttcttgtctcgacacatgagatggattcacgtagcttgcttattattattgattattctactgtttttgccttctgcaattcttcctattggcatgagtatttggaattctagagtattgttcccatccagatagattatctctgcctaataaattctgcccattgattattgcagTAAGCTGGAGTCCGAGGTTCTCAAGGATGTCGTCTCCCAGATAGTTCAGGATGCCAAGAAGAATA---GGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
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----------------------------------------------------------------------------tgagttctgctttggaaatttagttcctgtggtgagttgtttaatggttgttaggtttaatttgtagct-gacggac-------gtggaatgattttttcggac--------gcagTAAGCTCCAGAGCGATGTCCTCCGGGAGGCCATTACGCAGATCACCACTGCGGCCAAGGAGAAGAACCGGAAGTTCACTGAAACTGTAGAGCTTCAGATT---
upper sequence: GRMZM2G074769_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagatagattcaggttcttgtctcgacacatgagatggattcacgtagcttgcttattattattgattattctactgtttttgccttctgcaattcttcctattggcatgagtatttggaattctagagtattgttcccatccagata-gattatctctgcctaataaattctgcccattgattattgcagTAAGCTGGAGTCCGAGGTTCTCAAGGATGTCGTCTCCCAGATAGTTCAGGATGCCAAG---AAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
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---------------------------------------------------------------------------------------------gtcaggtaacacgaatatgaaatcttggaaattaggtttacgactctggtactgttttgatgatatggaactgaaatagagtttaatgtattctcaacagTAAGCTTCAGAGTGATGTTCTGAGGGAGGCGATCACTCAGATCGTGGCTGCAGCCAAGGAGAAGAATAGGAAGTTCACAGAGACTGTTGAACTTCAGATC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcccatccagatagattatctctgcctaataaattctgcccattgattattgcagTAAGCTGGAGTCCGAGGTTCTCAAGGATGTCGTCTCCCAGATAGTTCAGGATGCCAAGAAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
taataaattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagatagattcaggttcttgtctcgacacatgagatggattcacgtagcttgcttattattattgattattctactgtttttgccttctgcaattcttcctattggcatgagtatttggaattctagagtattgttcccatccagatagattatctctgcctaataaattctgcccattgattattgcagTAAGCTGGAGTCCGAGGTTCTCAAGGATGTCGTCTCCCAGATAGTTCAGGATGCCAAGAAGAATAGGAAGTTCACTGAGACTGTTGAGCTTCAGATTAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT