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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtactaacgatgaccgtattgtagttgctgaattggaattactgtactaacgatgaccgcatgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA

Basic information

species Zea mays
transcript GRMZM5G864319_T01
intron # 11
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|78092060|gb|DV520434.1|DV520434
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|33104324|gb|CF064284.1|CF064284
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|13382067|gb|BG458742.1|BG458742
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|32835294|gb|CD974972.1|CD974972
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|149044449|gb|EE047570.2|EE047570
EST:     GGCAGTAAACTGTGCCCAGAACATAGCCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|32834719|gb|CD974397.1|CD974397
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|113703173|gb|EE680677.1|EE680677
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|60395837|gb|DN228707.1|DN228707
EST:     AACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: AACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|19436236|gb|BM952646.1|BM952646
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|60356985|gb|DN223958.1|DN223958
EST:     CCAGAACATAGGCCAAGCAGCAAACCAAGAGGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: CCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|213179269|gb|FM196444.1|FM196444
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|9732140|gb|BE510892.1|BE510892
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|22490101|gb|BU050024.1|BU050024
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|19351144|gb|BM895676.1|BM895676
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|33101745|gb|CF061705.1|CF061705
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|18655285|gb|BM500090.1|BM500090
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCNCCTGATTTGCTAGAGGCNTGCAGTAGCTCACAT
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCC-CCTGATTTGCTAGAGGC-TGCAGTAGCTCACAT
EST: gi|60358249|gb|DN225222.1|DN225222
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|14204220|gb|BG837897.1|BG837897
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
EST: gi|87153521|gb|DY398310.1|DY398310
EST:     GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAG                         GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC
genomic: GGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCC

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), 47 (downstream exon)
Score: 265

CTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGGCTCTCAGGATGGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 716

CTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGGCTCTCAGGATGGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 957

CTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGGCTCTCAGGATGGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 908

CTTAACCCTGTTGCCATACAAGAGGCGTTTGAAGCCAGGGCTCTCAGGATGGCAGTAAACTGTGCCCAGAACATAGGCCAAGCAGCAAACCAAGAAGAAGgtagtactaa ... tgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtagttgctgaattggaattactgtactaacgatgaccgcatgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA
                            tactaac  putative branch site (score: 908)
                    aattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtactaacgatgaccgtattgtagttgctgaattggaattactgtactaacgatgaccgcatgccttgcagGTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA