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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGGTAATCGACGTTGACCTTACCGAGCAGCAGCTCGAAGAAAGACGGAGGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagcttaaacgttgtctgcgttgttggcatcagagtaatccttggctccgtgctgaatgtctcttctccatgtattattgcag

Basic information

species Zea mays
transcript AC234528.1_FGT005
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC234528.1_FGT005 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 5'ss of exon 13
GAGGGTAATCGACGTTGACCTTACCGAGCAGCAGCTCGAAGAAAGACGGAGGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagctta--------aacgttgtctgcgttgttggcatcagagtaatccttggctccgtgctgaatgtctcttctccatgtattattgcag
||| ||||| || ||||| || || ||     |||| ||||||||||||||||||||||| || |||||| ||||| |  || ||||||| |||||||||||||||   | ||         || ||  |     || | |||| ||| |   | ||||    |  |   ||  || |  ||| | ||| |||||||
GAGAGTAATTGATGTTGAACTGACTGAAGCTGAGCTGGAAGAAAGACGGAGGAAATGGACGCCGCCGCCACACAAGGCTGCCCGTGGAGCGCTTTGGAAGgtactactacatacattatatcacattaacattcctggtcgcataagattggcctttggtaatgaac---atcgctgtaatccttttatcattgcag
















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|30031654|gb|CB833505.1|CB833505
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|17970195|gb|BM276959.1|BM276959
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|24765717|gb|CA400876.1|CA400876
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|71760179|gb|DR958116.1|DR958116
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|71320321|gb|DR796908.1|DR796908
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|87153700|gb|DY398489.1|DY398489
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|18385075|gb|BM418274.1|BM418274
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|6695730|gb|AW288808.1|AW288808
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|101400106|gb|EB821895.1|EB821895
EST:     GGAAATGGACCCCACCCCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|91051076|gb|EB161494.1|EB161494
EST:     ATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: ATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|211216218|gb|FL457818.1|FL457818
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTYTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|31405687|gb|CD484419.1|CD484419
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|9255082|gb|BE345550.1|BE345550
EST:     CACCGCCATACAAGTCGACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: CACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|17970153|gb|BM276918.1|BM276918
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGC
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGC
EST: gi|211151454|gb|FL261068.1|FL261068
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|22489566|gb|BU049489.1|BU049489
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|89250573|gb|DY622359.1|DY622359
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCCTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|31363513|gb|CD447870.1|CD447870
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|91051077|gb|EB161495.1|EB161495
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|31358397|gb|CD442754.1|CD442754
EST:     NGAAATGGACCCCACCGCCATACAAGTCGACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|211474969|gb|FL438610.1|FL438610
EST:     GAAATGGACCCCACCGCCATACCAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GAAATGGACCCCACCGCCATA-CAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|17921817|gb|BM259468.1|BM259468
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|24764655|gb|CA399819.1|CA399819
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|17921490|gb|BM259141.1|BM259141
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|37395981|gb|CF635277.1|CF635277
EST:     GGAAATGGACCCCACCGCCATACAAGTCGACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG
EST: gi|60354975|gb|DN221948.1|DN221948
EST:     GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAG                         TACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAATAG
genomic: GGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAG

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: 47 (upstream exon), 47 (downstream exon)
Score: 248

GAGGGTAATCGACGTTGACCTTACCGAGCAGCAGCTCGAAGAAAGACGGAGGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAGGATGTGTTACATTCTGTTAGGTTGTGCACATGATGTGTTTGTCAATCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 117

GAGGGTAATCGACGTTGACCTTACCGAGCAGCAGCTCGAAGAAAGACGGAGGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAGGATGTGTTACATTCTGTTAGGTTGTGCACATGATGTGTTTGTCAATCAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 111

GAGGGTAATCGACGTTGACCTTACCGAGCAGCAGCTCGAAGAAAGACGGAGGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAGGATGTGTTACATTCTGTTAGGTTGTGCACATGATGTGTTTGTCAATCAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 111

GAGGGTAATCGACGTTGACCTTACCGAGCAGCAGCTCGAAGAAAGACGGAGGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagc ... attattgcagTACATCAAGCTTGTGGCTCCAGCGTCTAGAGGATGCGTCACTGATGAGTAGGATGTGTTACATTCTGTTAGGTTGTGCACATGATGTGTTTGTCAATCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGGTAATCGACGTTGACCTTACCGAGCAGCAGCTCGAAGAAAGACGGAGGAAATGGACCCCACCGCCATACAAGTCCACCTGTGGAGCTCTTTGGAAGgtactatagcttaaacgttgtctgcgttgttggcatcagagtaatccttggctccgtgctgaatgtctcttctccatgtattattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG