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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagcggaatttttgactaattttattttaagtctgaagaaatttgtctgaagctagttagtagtgtttggaattgtaacatatgctatcatcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG

Basic information

species Zea mays
transcript GRMZM2G179429_T01
intron # 5
splice site 3'
intron type U2

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:     TGTTTCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: TGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|31364620|gb|CD448975.1|CD448975
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|71757661|gb|DR955598.1|DR955598
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGATAG
EST: gi|71773570|gb|DR971468.1|DR971468
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|94472565|gb|EB701523.1|EB701523
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|71307150|gb|DR789746.1|DR789746
EST:     ACCTAGCTGCAGAGTTCAGGATGCGACCCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: ACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|91048409|gb|EB158827.1|EB158827
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|211427421|gb|FL445183.1|FL445183
EST:     AGTGTGTTCCCCTAGATGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|4688549|gb|AI637219.1|AI637219
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|76014913|gb|DT942083.1|DT942083
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCCGATTGTTACTC
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTC
EST: gi|148958245|gb|EC904458.2|EC904458
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATNCA-TCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTAT-CAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|71307153|gb|DR789747.1|DR789747
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATTCA-TCGGGAT-GTTACTCTGGAAAG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTAT-CAATCGG-ATTGTTACTCTGGAAAG
EST: gi|211469382|gb|FL187167.1|FL187167
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|31364129|gb|CD448484.1|CD448484
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|32165071|gb|CD670389.1|CD670389
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|60357983|gb|DN224956.1|DN224956
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|148956262|gb|EC902060.2|EC902060
EST:     GTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCCGA-CCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGAT
genomic: GTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGC-GAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGGAT
EST: gi|148932548|gb|EC876363.2|EC876363
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
EST: gi|78112541|gb|DV530935.1|DV530935
EST:     AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAG                         GACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
genomic: AGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 131

AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 156

AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 180

AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 229

AAGCAGAAGTGTGTTCCCCTAGAGGACCTAGCTGCAGAGTTCAGGATGCGAACCCAGgtacttcaaa ... tcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgaagctagttagtagtgtttggaattgtaacatatgctatcatcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG
                           ttgtaac  putative branch site (score: 229)
                         aattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagcggaatttttgactaattttattttaagtctgaagaaatttgtctgaagctagttagtagtgtttggaattgtaacatatgctatcatcatttgcagGACTGTATCAATCGGATTGTTACTCTGGAAAGCATGG

- - - - - - - - - - - - - - - - - gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catatgc