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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaatttccatattttcaggatgtccatgcattgttaccaattttctacaagtgaagcttgtgtgagtttagctttctgttctgaatgtacactttttttctgtatcacatggcacag

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 13
splice site 5'
intron type U2

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|211174464|gb|FL381682.1|FL381682
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|32836432|gb|CD976110.1|CD976110
EST:     CTGGGATGTTGCANCTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|32844741|gb|CD984422.1|CD984422
EST:     CAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|67027757|gb|CO456506.1|CO456506
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCA-CCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|32838372|gb|CD978050.1|CD978050
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|32935034|gb|CF039846.1|CF039846
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|211459151|gb|FL411539.1|FL411539
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|211215524|gb|FL427999.1|FL427999
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|32844417|gb|CD984098.1|CD984098
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|67019408|gb|CO448157.1|CO448157
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGAATAATGTNGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|211214717|gb|FL394674.1|FL394674
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|67037452|gb|CO464268.1|CO464268
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|32838758|gb|CD978439.1|CD978439
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|67010832|gb|CO439581.1|CO439581
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA
EST: gi|32837235|gb|CD976913.1|CD976913
EST:     CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGTTACTCTATCTGGACATA
genomic: CTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATA

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: 49 (upstream exon), 49 (downstream exon)
Score: 657

GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 706

GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 538

GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1167

GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaa ... catggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGACTGGGATGTTGCAACTACGTTTGCTTTTCTACAGAAGTATGGTCTTACCGgtaatataaatttccatattttcaggatgtccatgcattgttaccaattttctacaagtgaagcttgtgtgagtttagctttctgttctgaatgtacactttttttctgtatcacatggcacag

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