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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcatttttaccttgggaacattattcaatcttatttcgtttacaatgaatttgtattcttcctcgtatatattcaaactatatatgatcttcgtga...

Basic information

species Zea mays
transcript GRMZM2G066051_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066051_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 5'ss of exon 6
GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcatttttaccttgggaacattat--tcaatcttatttcgtttacaatgaat-ttgtattcttcctcgtatat--------attcaaactatatatgatct---tcgtga------------------------------------------------------
|||||  |||||||||||||||| |||||||| |||||||| || || |||||||| ||||| || |||||||| |||| | ||| ||  | ||||    |   | |||||  | | |||||| || | | ||||          |||||     | |||| | |   | || |                                                      
GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGGgtgagtatttttac-ttggcatcatcattgttaatccatgtcgatgtacaaacactgttgtatcctgctttgtatgccacttataattcagttagtgtatggtttaaattgtaacatcttttctgctattgtagtctcatgtctttatcatctttctttcttctgcag
















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|37401622|gb|CF638179.1|CF638179
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|18660671|gb|BM500986.1|BM500986
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|148999213|gb|EE036132.2|EE036132
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|149082295|gb|EE171480.2|EE171480
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|7844268|gb|AW787490.1|AW787490
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGAATGG                         GTCTTTGAAGAATTTAACTCTAGGGTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|6194845|gb|AW146949.1|AW146949
EST:     CAAGGCATAAAGCAACCGNGGCTGAATTTCTATCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTG
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTG
EST: gi|111192096|gb|EE290232.1|EE290232
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTTTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|149041351|gb|EE046989.2|EE046989
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|78107218|gb|DV525636.1|DV525636
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|33467028|gb|CF244077.1|CF244077
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTTTAGGTTGCTGTCATCACCCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|60354560|gb|DN221533.1|DN221533
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|5895944|gb|AW037190.1|AW037190
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|6445388|gb|AW179351.1|AW179351
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|6056599|gb|AW091004.1|AW091004
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|3157331|gb|AA979953.1|AA979953
EST:     GCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: GCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|5525422|gb|AI861315.1|AI861315
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTTTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|24769447|gb|CA404576.1|CA404576
EST:     CAAGGCATAAAGCACCCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|60350125|gb|DN217098.1|DN217098
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|211020659|gb|FL429513.1|FL429513
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATTATTGG                         TTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA
EST: gi|71328879|gb|DR801122.1|DR801122
EST:     CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG                         TTCTTTGAAGAATTTAACTTTAGGTTGCTGTCATCAACCAACTACATAACA
genomic: CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACA

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: 98

GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACAAAAAGGCAAGCTATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACAAAAAGGCAAGCTATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACAAAAAGGCAAGCTATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcattt ... cattccttagTTCTTTGAAGAATTTAACTCTAGGTTGCTGTCATCAACCAACTACATAACAAAAAGGCAAGCTATCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGGgtcagcatttttaccttgggaacattattcaatcttatttcgtttacaatgaatttgtattcttcctcgtatatattcaaactatatatgatcttcgtga

- - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcctcg