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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataattttttctatccagatgatatttggctgatgtatccctgctacatgattaattgctatctttgatacag

Basic information

species Zea mays
transcript GRMZM2G066440_T01
intron # 11
splice site 5'
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|211094279|gb|FL470654.1|FL470654
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|111991228|gb|EE332430.1|EE332430
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|16919952|gb|BM074437.1|BM074437
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|24764480|gb|CA399644.1|CA399644
EST:     AACAGCAGCCAGAACAATCAGACAGGTGACAATCCGAGCTTTCCACCCAG                         CTCCAGTAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|32907008|gb|CF011821.1|CF011821
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|60396317|gb|DN229186.1|DN229186
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|62550542|gb|DN830962.1|DN830962
EST:     AACATTCAGACGGGTGACAATCCGAACTTCCCACCCAG                         CTCCAGCAAGAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|32919364|gb|CF024176.1|CF024176
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|37401565|gb|CF638149.1|CF638149
EST:     AACAGCAGCCAGAACAATCAGACAGGTGACAATCCGAGCTTTCCACCCAG                         CTCCAGTAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|60341740|gb|DN208713.1|DN208713
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGGTTCT
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAGGTTCT
EST: gi|116823588|gb|EC867128.1|EC867128
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|13515771|gb|BG518047.1|BG518047
EST:     AGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|33095213|gb|CF055207.1|CF055207
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|149072974|gb|EE161235.2|EE161235
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|50336101|gb|CO531227.1|CO531227
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|32921823|gb|CF026635.1|CF026635
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
EST: gi|78120607|gb|DV538991.1|DV538991
EST:     AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAG                         CTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG
genomic: AACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG

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), 45 (downstream exon)
Score: 296

CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 103

CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 104

CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 105

CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataa ... tttgatacagCTCCAGCAACAATCAGTCCGGGGATGGTCTCAGTTTTCATGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGGTAACAGCAGCCAGAACAATCAGACGGGTGACAATCCGAGCTTCCCACCCAGgtatgtataattttttctatccagatgatatttggctgatgtatccctgctacatgattaattgctatctttgatacag

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