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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttcctattaatgccattttgtgctccatatccctagagtcacacttatatttcttgtcaaatgccttgtatactcatacataatttattttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGGCCTTAAGGATTACATATCACATGCTTCTGAAATCATG

Basic information

species Zea mays
transcript GRMZM2G086484_T02
intron # 2
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|87156040|gb|DY400829.1|DY400829
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|211283774|gb|FL132376.1|FL132376
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGGTTCA-TTGCAGCTGCAAAATCATCCAGCTGGACTTTTGGGAGGAC
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGG-TTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTT-GGGAGGAC
EST: gi|31361452|gb|CD445809.1|CD445809
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|33467333|gb|CF244382.1|CF244382
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAAC
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAAC
EST: gi|22546264|gb|BU098575.1|BU098575
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|149014128|gb|EE043668.2|EE043668
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|71311913|gb|DR792440.1|DR792440
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|71448533|gb|DR829583.1|DR829583
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|211283778|gb|FL132380.1|FL132380
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|50334338|gb|CO529464.1|CO529464
EST:     GCGGAGGCTGCTACCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|211283773|gb|FL132375.1|FL132375
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|28987141|gb|CB351484.1|CB351484
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|76915806|gb|DV166129.1|DV166129
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|94473209|gb|EB702167.1|EB702167
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|94473338|gb|EB702296.1|EB702296
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|78105254|gb|DV523672.1|DV523672
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|88757793|gb|DY541934.1|DY541934
EST:     GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
EST: gi|26558697|gb|CA830932.1|CA830932
EST:     GGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAG                         CTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG
genomic: GGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGG

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), 48 (downstream exon)
Score: 143

CTTCCCATCAGCATGTGATGGCAGGACCCGCTAGTTTAGATCCTCGGCGGGCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGGCCTTAAGGATTACATATCACATGCTTCTGAAATCATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 74

CTTCCCATCAGCATGTGATGGCAGGACCCGCTAGTTTAGATCCTCGGCGGGCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGGCCTTAAGGATTACATATCACATGCTTCTGAAATCATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 99

CTTCCCATCAGCATGTGATGGCAGGACCCGCTAGTTTAGATCCTCGGCGGGCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGGCCTTAAGGATTACATATCACATGCTTCTGAAATCATG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 44

CTTCCCATCAGCATGTGATGGCAGGACCCGCTAGTTTAGATCCTCGGCGGGCGGAGGCTGCTAGCAAACATGTGAGGGCACTTAATACCCAGTTTGCAAGgtgtgttcct ... ttttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGGCCTTAAGGATTACATATCACATGCTTCTGAAATCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttatatttcttgtcaaatgccttgtatactcatacataatttattttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGGCCTTAAGGATTACATATCACATGCTTCTGAAATCATG
                                         tttatttt  CT-rich tract
                          tatactcatacataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttcctattaatgccattttgtgctccatatccctagagtcacacttatatttcttgtcaaatgccttgtatactcatacataatttattttgagcagCTGGGTTCAATTGCAGCTGCAAAATCATCCAGCTGAACTTTGGGAGGACGGCCTTAAGGATTACATATCACATGCTTCTGAAATCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA