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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctgaattctgagaagtctttccgatgtctagtttctggtgtgtatgtatgtatgtatatatatatctatgcactgagttggaaataatatgcaatgtacatggcatttctcctaatgctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA

Basic information

species Zea mays
transcript GRMZM2G044629_T01
intron # 3
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|149081508|gb|EE170644.2|EE170644
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|211249747|gb|FL285802.1|FL285802
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCC-TAAGGGATGTTTCA
EST: gi|149015643|gb|EE045441.2|EE045441
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|40337292|gb|CK371362.1|CK371362
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|149100896|gb|EE186991.2|EE186991
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|149014175|gb|EE043721.2|EE043721
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|148958334|gb|EC904558.2|EC904558
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|211249750|gb|FL285805.1|FL285805
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTA
EST: gi|71429565|gb|DR810615.1|DR810615
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|148982619|gb|EE028417.2|EE028417
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|211249751|gb|FL285806.1|FL285806
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|149090039|gb|EE179333.2|EE179333
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|78115803|gb|DV534191.1|DV534191
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|148956834|gb|EC902742.2|EC902742
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|91052249|gb|EB162667.1|EB162667
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|149014877|gb|EE044588.2|EE044588
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|148943648|gb|EC888712.2|EC888712
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|71757247|gb|DR955184.1|DR955184
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|148990989|gb|EE032426.2|EE032426
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|94477177|gb|EB706135.1|EB706135
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|31354041|gb|CD438398.1|CD438398
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
EST: gi|76282035|gb|DV021603.1|DV021603
EST:     AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAG                         GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
genomic: AAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA

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: 191

GGAGGGCAGGTCTGCAGAGGACAAAGAAAGATGGTGGAAGAAGGGGTTGAAAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 302

GGAGGGCAGGTCTGCAGAGGACAAAGAAAGATGGTGGAAGAAGGGGTTGAAAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 340

GGAGGGCAGGTCTGCAGAGGACAAAGAAAGATGGTGGAAGAAGGGGTTGAAAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 622

GGAGGGCAGGTCTGCAGAGGACAAAGAAAGATGGTGGAAGAAGGGGTTGAAAGCCATCTCGGAGGGGAAGCTGGCCGTTGTCCTTTTGGCCGGTGGTCAGgtactctgaa ... ctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagttggaaataatatgcaatgtacatggcatttctcctaatgctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA
                                     tcctaat  putative branch site (score: 622)
         aaataatatgcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactctgaattctgagaagtctttccgatgtctagtttctggtgtgtatgtatgtatgtatatatatatctatgcactgagttggaaataatatgcaatgtacatggcatttctcctaatgctgtgcgcagGGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA