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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCCGCATTAGTTTTTGAGGGTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtgcgatgcaagtattttctgcatgtgccactgtcgctattgcttgccatttcttcctttttatttggagagcacgattgcctttttcttctctctgcgagtggaacatattgtttcagagcatgcattcgtatgacaaatcattttattgctctgatggtttcaacag

Basic information

species Zea mays
transcript AC234528.1_FGT005
intron # 10
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 10
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 5'ss of exon 10
GTCCCGCATTAGTTTTTGAGGGTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtgcgatgcaagtattttctgcatgtgccactgtcgc-tattgcttgccatttcttcctttttatttggagagcacgattgcctttttcttctctctgcgagtggaacatattgtttcagagcatgcattcgtatgacaaatcattttattgctctgatggtttcaacag
| || ||| |||| ||||||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||    || |||           | |||| | |    |  |||  ||  || |||       | |  |  | |     || ||       || ||   |    ||                                                                  
GCCCTGCACTAGTGTTTGAGGGTGAAGAATCTATGATTACAGCTATATCAGAAAACCCAGCGAATTTCAAGgtaatatgattaatccaaa----------aggtgcaatttggacacattcttttgcaattcagaggcctgaaatacaaaatttcatagcaaccagttt-tccaagtatttg------------------------------------------------------------------
















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:     CCAGCGAATTTCAAG                         GGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
genomic: CCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
EST: gi|24765717|gb|CA400876.1|CA400876
EST:     GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAG                         GGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
genomic: GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
EST: gi|71320321|gb|DR796908.1|DR796908
EST:     GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAG                         GGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
genomic: GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
EST: gi|101400106|gb|EB821895.1|EB821895
EST:     AAAACCCAGCGAATTTCAAG                         GGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
genomic: AAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
EST: gi|31405687|gb|CD484419.1|CD484419
EST:     GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAG                         GGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
genomic: GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
EST: gi|89250573|gb|DY622359.1|DY622359
EST:     GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAG                         GGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
genomic: GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
EST: gi|31363513|gb|CD447870.1|CD447870
EST:     GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAG                         GGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
genomic: GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
EST: gi|31358397|gb|CD442754.1|CD442754
EST:     GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAG                         GGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
genomic: GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
EST: gi|37395981|gb|CF635277.1|CF635277
EST:     GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAG                         GGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
genomic: GTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
EST: gi|32850063|gb|CD989744.1|CD989744
EST:     GCTATCTCAGANAACCCAGCGAATTTCAAG                         GGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG
genomic: GCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATG

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), 46 (downstream exon)
Score: 80

GTCCCGCATTAGTTTTTGAGGGTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 93

GTCCCGCATTAGTTTTTGAGGGTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 51

GTCCCGCATTAGTTTTTGAGGGTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAA


Block sizes: 47 (upstream exon), 37 (downstream exon)
Score: 30

GTCCCGCATTAGTTTTTGAGGGTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtg ... gtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCCGCATTAGTTTTTGAGGGTGAAGAATCCATGATCACAGCTATCTCAGAAAACCCAGCGAATTTCAAGgtaatatgtgcgatgcaagtattttctgcatgtgccactgtcgctattgcttgccatttcttcctttttatttggagagcacgattgcctttttcttctctctgcgagtggaacatattgtttcagagcatgcattcgtatgacaaatcattttattgctctgatggtttcaacag

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