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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctccgttcttttttatttgtcgcggtttagttcaaaaatgaattagcgggcgacaaatatttgagaacggaggtagtactatggcaacctactatgttaatacttggtattcttactaaaatgtgtattcatgcaaaacttactattatcgttgtcacag

Basic information

species Zea mays
transcript GRMZM2G014116_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 5
GTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctccgttcttttttatttgtcgcggtttagttcaaaaatgaattagcgggcgacaaatatttgagaacggaggtagtactatggcaacctactatgttaatacttggtattcttactaaaatgtgtattcatgcaaaacttactattatcgttgtcacag
||||||||||||||||| ||||||||||| || || ||||| |||||||| ||||||||||                 |  |   |   |  || |  ||| ||            |||||    || |  | |   |  |||| |    |   |  |                                                                  
GTTGAAACATTTGGCTCCATGGCAAAGACAGAAAAGATTGCATTCATTCTAGAGCAGgtatgaag-------------aaatacagtaataaagcttgaaattg----------ttacaaaagcctgggttctggaatcttactgtaatcatg-atcacag---------------------------------------------------------------

upper sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 5'ss of exon 5
GTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgta----ttccctccgttcttttttatttgtcgcggttta-gttcaaaaatgaattagcgggcgacaaatatttgagaacggaggtagtactatggcaacctactatgttaatacttggtattcttactaaaatgtgtattcatgcaaaacttactattatcgttgtcacag
|| || ||||||||  |||||||||| || ||||||||||||||||||||||| || |||    || |     |  |||  ||||| |   | |||  | |      |   ||   |   |    || || | ||    |  || |  | ||  ||| |   | |                                                                
GTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCTTTCATTCTTGAACAAgtaagactttctgttatcttttcatatttcttaagctttgtgctttgtgctttgttcttgtttg---tatgtt-gtgattctaattattggtgtgtaaacttctgaag----------------------------------------------------------------

upper sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S58_256V6.1 (Physcomitrella patens), 5'ss of exon 5
GTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctccgttcttttttatttgtcgcggtttagttcaaaaatgaattagcgggcgacaaatatttgagaacggaggtagtactatggcaacctactatgttaatacttggtattcttactaaaatgtgtattcatgcaaaacttactattatcgttgtcacag
|| || || || ||  ||||||||||||| |||||||||||||||||||| |||||||||            || ||   ||  |||  |   ||      ||    ||||  |       |||||  |||||    |    || |  ||   |  ||  ||   | |   || || || || ||||  | ||   |                           
GTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAGgtaagg-----aaatttcttggctttacgctatgctgt------atatgctagctcg-------tatttaggaacgatactgaagcttt--cagtttggtactttccgaatcattactcatattagaatg-atgttgcag---------------------------

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|17931575|gb|BM268535.1|BM268535
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|31358688|gb|CD443045.1|CD443045
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|211388540|gb|FL326080.1|FL326080
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|211427058|gb|FL201071.1|FL201071
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|32942192|gb|CF047011.1|CF047011
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|18166644|gb|BM336483.1|BM336483
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|31355001|gb|CD439358.1|CD439358
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|7216589|gb|AW562711.1|AW562711
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|113588935|gb|DW753644.1|DW753644
EST:     CATTTGGCTCTATGGCAAAGACGGNGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGG
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGG
EST: gi|31355164|gb|CD439521.1|CD439521
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|61236504|gb|DN586255.1|DN586255
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGTCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|31355423|gb|CD439780.1|CD439780
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|14202839|gb|BG836516.1|BG836516
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|211429638|gb|FL201075.1|FL201075
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|18161887|gb|BM331726.1|BM331726
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|18168671|gb|BM338511.1|BM338511
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|9953978|gb|BE640561.1|BE640561
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGTCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|31350034|gb|CD434391.1|CD434391
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|213188018|gb|FM188229.1|FM188229
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|32808457|gb|CD960691.1|CD960691
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|26457612|gb|CA829195.1|CA829195
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|71448354|gb|DR829404.1|DR829404
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|213183945|gb|FM195837.1|FM195837
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|31354458|gb|CD438815.1|CD438815
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|31910184|gb|CD651297.1|CD651297
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCC
EST: gi|211427049|gb|FL201062.1|FL201062
EST:     CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG                         GTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACA
genomic: CATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACA

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: 309

GTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCCAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAAAGGAAAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 323

GTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCCAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAAAGGAAAAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 203

GTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCCAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAAAGGAAAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 298

GTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctc ... gttgtcacagGTCCGGCTATGCCTGGATCGGCAAGATTTTGTCAGAGCACAAATTTTATCCAGGAAAATCAGTACTAGAGTATTTGACGCAGATCCATCAAAGGAAAAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAGgtattccctccgttcttttttatttgtcgcggtttagttcaaaaatgaattagcgggcgacaaatatttgagaacggaggtagtactatggcaacctactatgttaatacttggtattcttactaaaatgtgtattcatgcaaaacttactattatcgttgtcacag

- - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG