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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGTCAGCGAAACTAACTTAAGTCGACAATCAGCTCAAGTACATAAAATGCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctcgcactagaacacagtttctactattttactaaaatgtgcagtaaatcttatcggcacgatttcctgtatgcag

Basic information

species Zea mays
transcript GRMZM5G833124_T01
intron # 13
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|211226568|gb|FL435981.1|FL435981
EST:     GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|32849291|gb|CD988972.1|CD988972
EST:     ACTTGAACCTG                         GAGCGTCAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: ACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|31363448|gb|CD447805.1|CD447805
EST:     GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|16916759|gb|BM072978.1|BM072978
EST:     GCACCAAATTGTCATGAGTCCTGATCCGGCAGGAACAGTACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|32846021|gb|CD985702.1|CD985702
EST:     ACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: ACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|17931896|gb|BM268856.1|BM268856
EST:     GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|84977310|gb|DW475732.1|DW475732
EST:     GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGG-TGCTGACTCAGGA-G
genomic: GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|37374924|gb|CF623866.1|CF623866
EST:     GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|84969714|gb|DW468143.1|DW468143
EST:     GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|32937580|gb|CF042399.1|CF042399
EST:     GCACCAAATTGTCATGAGTCCTGATCCTGAAGGAACAGTACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|93281684|gb|EB673948.1|EB673948
EST:     GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
EST: gi|76016960|gb|DT944130.1|DT944130
EST:     GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTG                         GAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG
genomic: GCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAG

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: 68

TGAGTCAGCGAAACTAACTTAAGTCGACAATCAGCTCAAGTACATAAAATGCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAGGGTCCGTGAAGGCTCCAAACTGCGGAAGATCGACTAACAATCAGCTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

TGAGTCAGCGAAACTAACTTAAGTCGACAATCAGCTCAAGTACATAAAATGCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAGGGTCCGTGAAGGCTCCAAACTGCGGAAGATCGACTAACAATCAGCTCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 101

TGAGTCAGCGAAACTAACTTAAGTCGACAATCAGCTCAAGTACATAAAATGCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAGGGTCCGTGAAGGCTCCAAACTGCGGAAGATCGACTAACAATCAGCTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

TGAGTCAGCGAAACTAACTTAAGTCGACAATCAGCTCAAGTACATAAAATGCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctc ... ctgtatgcagGAGCGTTAGATCGCAACAACCACCATGACAGGGGGGTGCTGACTCAGGAAGGGTCCGTGAAGGCTCCAAACTGCGGAAGATCGACTAACAATCAGCTCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGTCAGCGAAACTAACTTAAGTCGACAATCAGCTCAAGTACATAAAATGCACCAAATTGTCATGAGTCCTGATCCTGCAGGAACAGTACTTGAACCTGgttagttctcgcactagaacacagtttctactattttactaaaatgtgcagtaaatcttatcggcacgatttcctgtatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG