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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacttttgtttagatttggcttcccttcaattggttaaccgtgaataagcccgctaacctgatgattcctagctacatatcctggcggcagtgagaaactgtctgccgccaaagccctcaacagttttttttagttttgctaagcctttttttttgcatgtaacaacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGTGAGC

Basic information

species Zea mays
transcript GRMZM2G179429_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179429_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g01320.1 (Oryza sativa), 3'ss of exon 7
gtgacttttgtttagatttggcttcccttcaattggttaaccgtgaataagcccgctaacctgatgattcctagctacatatcctggcggcagtgagaaactgtctgccgccaaagccctcaacagttttttttagttttgctaagcctttttttttgcatgtaacaacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGTGAGC
            ||  | |  ||    |   | | |  |||  |      |   |||| |   || |  |  ||   ||||| ||      | |  |  |     ||     ||    |||  ||   || ||| || | | |  ||     |||    |    || ||||||||| ||||||| || |||||||| |||||||||||||| ||||| || ||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||    
-----------gtatgtatcactcttttgtgacttga-aactattgtcttgt--gcta-ctgcatcagcctaagtggcatatgctttgcatattttggcatgacttgat---aagttactccgcaaccttgtttggtct-gatgggctgcccttt----acaataccacagATAGGCTATCTGGTGTCATGGATGATCGTGGGAAGTTCATATACATATCTACTGAGGAGATGAAGGCTGTCGCAGATTACATCAGGAAACAAGGGAGGGT----
















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|88754687|gb|DY538828.1|DY538828
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|31364129|gb|CD448484.1|CD448484
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGTGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|60357983|gb|DN224956.1|DN224956
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|76014912|gb|DT942082.1|DT942082
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|32165071|gb|CD670389.1|CD670389
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|91048409|gb|EB158827.1|EB158827
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGGGGTGATGGATGACCG
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGG-TGATGGATGACCG
EST: gi|31364620|gb|CD448975.1|CD448975
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGTGTGATGGATGACCGTGGGAAGTTCATCTACATC
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATC
EST: gi|211469382|gb|FL187167.1|FL187167
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGTGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|78112541|gb|DV530935.1|DV530935
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|211427421|gb|FL445183.1|FL445183
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGTGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|148932548|gb|EC876363.2|EC876363
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGTGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|71773570|gb|DR971468.1|DR971468
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|94472565|gb|EB701523.1|EB701523
EST:     GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
genomic: GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGA
EST: gi|148958245|gb|EC904458.2|EC904458
EST:     GACTGTATNCA-TCGGATTGTTACTCTGGAAAGCATGGATAG                         GTTATCTGGGGTGATGGATGACCGTGG
genomic: GACTGTAT-CAATCGGATTGTTACTCTGGAAAGCATGGGTATgtgacttttg ... caacagatagGTTATCTGGGGTGATGGATGACCGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacagttttttttagttttgctaagcctttttttttgcatgtaacaacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGTGAGC
                                       atgtaac  putative branch site (score: 3)
      ttttttttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacttttgtttagatttggcttcccttcaattggttaaccgtgaataagcccgctaacctgatgattcctagctacatatcctggcggcagtgagaaactgtctgccgccaaagccctcaacagttttttttagttttgctaagcctttttttttgcatgtaacaacagatagGTTATCTGGGGTGATGGATGACCGTGGGAAGTTCATCTACATCTCCACTGAAGAGATGAAGGCAGTTGCAGAGTACATTAGGAAGCAAGGGAGAGTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG