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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttcacattccggttgactagtgatgttggtgttgtttatcataaaacactcggaaacatgctgctgccttcattttggctttcgaccacttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTGCAGCACCCGCCAACGAGGAAGCTGGGCATGGACATGCTGAGGGAGCGAG

Basic information

species Zea mays
transcript GRMZM2G444692_T02
intron # 10
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|211272780|gb|FL461440.1|FL461440
EST:     TAGCTCGTAGCAACCGTTACGCTGAAAWAGCATTGTTTGTGTCAAACAAG                         ATTCTTGASCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTYTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|211085833|gb|FL083835.1|FL083835
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|211085836|gb|FL083838.1|FL083838
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|71433592|gb|DR814642.1|DR814642
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|71436759|gb|DR817809.1|DR817809
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|4804009|gb|AI665875.1|AI665875
EST:     ATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: ATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|116817309|gb|EC860144.1|EC860144
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|78024231|gb|DV492618.1|DV492618
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|33091123|gb|CF051117.1|CF051117
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|211085835|gb|FL083837.1|FL083837
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|60397571|gb|DN230387.1|DN230387
EST:     GCTG-AATAGCATTGTTTGTGTC-AACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: GCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|211085832|gb|FL083834.1|FL083834
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|71433593|gb|DR814643.1|DR814643
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|71428498|gb|DR809548.1|DR809548
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
EST: gi|14206626|gb|BG840304.1|BG840304
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCT
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCT
EST: gi|33094193|gb|CF054187.1|CF054187
EST:     TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAG                         ATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG
genomic: TAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTG

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: 48 (upstream exon), 45 (downstream exon)
Score: 72

GGCTGGGCTTAAGGCTCCTCACAACCTTTATGTGATGACGGCGACACTACTAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTGCAGCACCCGCCAACGAGGAAGCTGGGCATGGACATGCTGAGGGAGCGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

GGCTGGGCTTAAGGCTCCTCACAACCTTTATGTGATGACGGCGACACTACTAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTGCAGCACCCGCCAACGAGGAAGCTGGGCATGGACATGCTGAGGGAGCGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 68

GGCTGGGCTTAAGGCTCCTCACAACCTTTATGTGATGACGGCGACACTACTAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTGCAGCACCCGCCAACGAGGAAGCTGGGCATGGACATGCTGAGGGAGCGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 84

GGCTGGGCTTAAGGCTCCTCACAACCTTTATGTGATGACGGCGACACTACTAGCTCGTAGCAACCGTTACGCTGAAATAGCATTGTTTGTGTCAAACAAGgtcagtttat ... cttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTGCAGCACCCGCCAACGAGGAAGCTGGGCATGGACATGCTGAGGGAGCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacactcggaaacatgctgctgccttcattttggctttcgaccacttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTGCAGCACCCGCCAACGAGGAAGCTGGGCATGGACATGCTGAGGGAGCGAG
                                          ccacttcct  CT-rich tract
                         ttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttcacattccggttgactagtgatgttggtgttgtttatcataaaacactcggaaacatgctgctgccttcattttggctttcgaccacttcctgcagATTCTTGAGCCGTGTAAAGAACTGGCAATGCAACTTATGGAGCTGGGTCTGCAGCACCCGCCAACGAGGAAGCTGGGCATGGACATGCTGAGGGAGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG