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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtaattttttctacattttttataatgttctaaaaaaactgttgctaccggtttactaactgcctttttggatattttatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT

Basic information

species Zea mays
transcript GRMZM5G835235_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 9
gtgtaat-tttttctacattttttataatgttctaaaaaaactgttgctaccggtttactaactgcctttttggatattttatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT
||| ||  | | ||||  | | || | ||  | | |  || |      || | | | | ||||    | | |  |      || ||| |||||||| | |||||| |||| ||||||||||||||||| |||||| |||| ||||||||||| || || || ||||||||||||
gtgcaaagtctatctatttctgttgttatactttcagcaatcgtccagtatcaggtgattaaccatatatgtaaa------atattt-agGTATTCCATAAAAGGTTGCCTCCAGAAGCTGTTGATCTTGTCTCTAGGCTGCTCCAGTACTCACCCAACCTAAGATGCACTGCT
















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|32859083|gb|CD998764.1|CD998764
EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|32865498|gb|CF005180.1|CF005180
EST:     AATCAAAGCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: AATCAAAGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|33093876|gb|CF053870.1|CF053870
EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|20803001|gb|BQ294051.1|BQ294051
EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|78544269|gb|DV621767.1|DV621767
EST:     AGCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: AGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|22543122|gb|BU093560.1|BU093560
EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|60349422|gb|DN216395.1|DN216395
EST:     ATTGCACAGAGTTTAAGTTCCCACAAATCAAAGCACACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|18172726|gb|BM348114.1|BM348114
EST:     GTTTAAGTTCCCACAAATC-AAGNCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: GTTTAAGTTCCCACAAATCAAAG-CTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|30087357|gb|CB885563.1|CB885563
EST:     CTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: CTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|32865481|gb|CF005163.1|CF005163
EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|32865499|gb|CF005181.1|CF005181
EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|18170275|gb|BM340115.1|BM340115
EST:     TCAAAGCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: TCAAAGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
EST: gi|26456580|gb|CA828163.1|CA828163
EST:     ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAG                         GTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA
genomic: ATTACACAGAGTTTAAGTTCCCACAAATCAAAGCTCACCCATGGCACAAGgtgtaatttt ... tatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaactgttgctaccggtttactaactgcctttttggatattttatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT
                     tactaac  putative branch site (score: 0)
                                          ttttatctttc  putative PPT
                                tttttggatattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtaattttttctacattttttataatgttctaaaaaaactgttgctaccggtttactaactgcctttttggatattttatctttcagGTATTCAACAAAAGGATGCCGCCAGAAGCTGTTGATCTGGTCTCTCGGCTACTCCAGTACTCCCCAAATCTGAGATGCACTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG