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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCCATTCAAGGGATTGGGTTTGGAACACTTAAATGGCTCGAGCCCTGTTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatcatagttagttttttacttctaatacatccctggaacaacataaaactctaatgtttgagtggatttgttcacatgaatag

Basic information

species Zea mays
transcript GRMZM2G014136_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014136_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g24704.1 (Oryza sativa), 5'ss of exon 10
GCAGCCATTCAAGGGATTGGGTTTGGAACACTTAAATGGCTCGAGCCCTGTTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatcatag-ttagttttttacttctaatacatccctggaacaacataaaactctaatgtttgagtggatttgttcacatgaatag
 || ||||||||||||||||| ||||||||||| |||||  |  ||||||||||||||||| | ||||||||| ||| | |||| |||||||  ||||||||| ||||| |||  ||||||| |||| | ||  | ||  |||  |  | | ||  || ||     ||  ||  |||||     |||||||
TCAACCATTCAAGGGATTGGGCTTGGAACACTTGAATGGTCCTTGCCCTGTTATTCCTGATTATCTGACAAGTGGCACACTAAGAAGCTCCAGTTTCCAGgtatagaataataacttagtttcttacatttataagatagctgtcatgagacaactcttta-----tgtatgcctttgtgatggtgaatag
















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|213191931|gb|FM185346.1|FM185346
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32922953|gb|CF027765.1|CF027765
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|78122591|gb|DV540975.1|DV540975
EST:     AAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: AAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32922640|gb|CF027452.1|CF027452
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32923445|gb|CF028257.1|CF028257
EST:     TTATTCCTGATAAGCTGCCAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32921856|gb|CF026668.1|CF026668
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32920309|gb|CF025121.1|CF025121
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32922125|gb|CF026937.1|CF026937
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32923051|gb|CF027863.1|CF027863
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|31356814|gb|CD441171.1|CD441171
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|78118416|gb|DV536802.1|DV536802
EST:     CCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: CCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|61119686|gb|DN560647.1|DN560647
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAG
EST: gi|32921929|gb|CF026741.1|CF026741
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32922523|gb|CF027335.1|CF027335
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32922152|gb|CF026964.1|CF026964
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32923374|gb|CF028186.1|CF028186
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32922298|gb|CF027110.1|CF027110
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32922571|gb|CF027383.1|CF027383
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
EST: gi|32922304|gb|CF027116.1|CF027116
EST:     TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAG                         ATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG
genomic: TTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAG

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), 49 (downstream exon)
Score: 70

GCAGCCATTCAAGGGATTGGGTTTGGAACACTTAAATGGCTCGAGCCCTGTTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 351

GCAGCCATTCAAGGGATTGGGTTTGGAACACTTAAATGGCTCGAGCCCTGTTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGA


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

GCAGCCATTCAAGGGATTGGGTTTGGAACACTTAAATGGCTCGAGCCCTGTTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 190

GCAGCCATTCAAGGGATTGGGTTTGGAACACTTAAATGGCTCGAGCCCTGTTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatc ... acatgaatagATGGACCTGTTCTGCTTAAGGGAGAGAGATTTACTGAAGCAGTTTGTAGAGGAGGTTTCTCTCCATCTTGCACAAGGCGAAAGCAGAGAAAAGGCTTTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCCATTCAAGGGATTGGGTTTGGAACACTTAAATGGCTCGAGCCCTGTTATTCCTGATAAGCTGACAAGTAGCATATTAAGGAGCTCCAAGTTCCAGgtaaagaatcatagttagttttttacttctaatacatccctggaacaacataaaactctaatgtttgagtggatttgttcacatgaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT