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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGCCCACAATATGGCTGAGGATGTAAGGATCCAATACGACGACCAAGAAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaattctttaacccaaatctagataatttcctcgattatgtgaagcaacagttttccatatgttgtagatgtagttatttgctctgttatcaattgctgatttggattcgaaaagaagaagaatgcatcattattctttttgttttgtcaaaaaaaatccag

Basic information

species Zea mays
transcript GRMZM2G426275_T04
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G426275_T04 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g58590.1 (Oryza sativa), 5'ss of exon 17
GAAAGCCCACAATATGGCTGAGGATGTAAGGATCCAATACGACGACCAAGAAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaattctttaacccaaatct-------agataatttcctcg----attatgtgaagcaacagttttccatatgttgtagatgtagttatttgctctgttatcaattgctgatttggattcgaaaagaagaagaatgcatcattattctttttgttttgtcaaaaaaaatccag
||||||||||||||||| || ||||||||||||||| ||  |||| || ||||  || |||| |||||||||||||||||||||||| ||||||||||||||  ||| |||||| |||| | | |       | |||||   || |    | || || |||  ||| ||||   | || |||       | |  ||| |  |                                                                            
GAAAGCCCACAATATGGATGCGGATGTAAGGATCCAGTATAACGATCAGGAAGACTTTGAGCGGATAGCTCGTCAATTTGGAATATTTGAAGAATGGAAGgt--ttacttctttgaccccatttttattcataaataatgctcttgtcaaagtaggtcaagtgacaattttgtgtctgatgttttcagtggtgattgttagg----------------------------------------------------------------------------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|149082838|gb|EE172062.2|EE172062
EST:     TAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: TAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|76011179|gb|DT938349.1|DT938349
EST:     AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|8318693|gb|BE025258.1|BE025258
EST:     AAGGTTTTGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|89757376|gb|DY687005.1|DY687005
EST:     AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|78123462|gb|DV541846.1|DV541846
EST:     AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|16379214|gb|BI992824.1|BI992824
EST:     GGTTTCGAGCAGATAGCTCGTCAATTTGGAGTATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACACC
genomic: GGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|32789075|gb|CD941311.1|CD941311
EST:     AAGGTTTTGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|60342158|gb|DN209131.1|DN209131
EST:     AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|71439956|gb|DR821006.1|DR821006
EST:     AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|86471523|gb|DY237893.1|DY237893
EST:     AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|148986616|gb|EE030387.2|EE030387
EST:     AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
EST: gi|76285203|gb|DV024771.1|DV024771
EST:     AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAG                         GATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC
genomic: AAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaatt ... aaaaatccagGATGGCATCCCAAGAACGGCTTACAAAGGAGTGGTGGTCTTCCGGTACAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGCCCACAATATGGCTGAGGATGTAAGGATCCAATACGACGACCAAGAAGGTTTCGAGCAGATAGCTCGTCAATTTGGAATATTCGAAGAATGGAAGgtgtttaattctttaacccaaatctagataatttcctcgattatgtgaagcaacagttttccatatgttgtagatgtagttatttgctctgttatcaattgctgatttggattcgaaaagaagaagaatgcatcattattctttttgttttgtcaaaaaaaatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG