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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagagacttctgactgtcatccattttcttaagaaattcataggagatgtcatgtaaaaggccatcaaacctaattgtcaaacagcatcacctgttggcctcaaattttgtag

Basic information

species Zea mays
transcript GRMZM2G066578_T01
intron # 7
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|211117536|gb|FL480259.1|FL480259
EST:     TCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATCGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
genomic: TCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
EST: gi|76018387|gb|DT945557.1|DT945557
EST:     CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATGGTCTAGATGCTTTTGAGCAGTTTAAGGCACAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
EST: gi|12058339|gb|BF729405.2|BF729405
EST:     CAGAAGATGCAGCTGAGAACCTTTTGGTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCA
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCA
EST: gi|211362136|gb|FL332732.1|FL332732
EST:     CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATGGTCTARATGCTTCTGAGCAGTTTAAGGCACAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
EST: gi|8577333|gb|BE129970.1|BE129970
EST:     CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGCTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
EST: gi|78091932|gb|DV520306.1|DV520306
EST:     CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
EST: gi|7844522|gb|AW787744.1|AW787744
EST:     CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAG
EST: gi|211355369|gb|FL034995.1|FL034995
EST:     CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATCGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
EST: gi|211355368|gb|FL034994.1|FL034994
EST:     CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTNATTGGGGATCGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
EST: gi|211355370|gb|FL034996.1|FL034996
EST:     CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATCGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
EST: gi|78180792|gb|DV551165.1|DV551165
EST:     CAGAAGATGCAGCTGAGAACC-TTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
EST: gi|89757800|gb|DY687246.1|DY687246
EST:     CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATGGTCTAGATGCTTTTGAGCAGTTTAAGGCACAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
EST: gi|78179861|gb|DV550234.1|DV550234
EST:     CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAG                         GTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG
genomic: CAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 105

GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAGAAAGGGACCCAGTTTATCCCATATTCACAGTTTCCACCAAGAATGGCAC


Block sizes: 41 (upstream exon), 9 (downstream exon)
Score: 1

GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAGAAAGGGACCCAGTTTATCCCATATTCACAGTTTCCACCAAGAATGGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2069

GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagaga ... aattttgtagGTGTGGTTAATTGGGGATGGTCTAGATGCTTCTGAGCAGTTTAAGGCACAGAAAGGGACCCAGTTTATCCCATATTCACAGTTTCCACCAAGAATGGCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGTAATGACCAACAAGCAGGATTACCATTTTCTTAAGCCTAACATGGCAGAAGATGCAGCTGAGAACCTTTTGTTTTCAAAGACAACTACTGCAAAGgttaaagagacttctgactgtcatccattttcttaagaaattcataggagatgtcatgtaaaaggccatcaaacctaattgtcaaacagcatcacctgttggcctcaaattttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG