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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggccaaaacttctattcacctggttatgacttaccccctcgctggtgttttcaactgtggtgtcggaaacagttcattactgttcctgctaatctagactgaagtctctgttacag

Basic information

species Zea mays
transcript GRMZM2G069008_T01
intron # 6
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|78087423|gb|DV515816.1|DV515816
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTCCCATCCCCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|15215527|gb|BI431332.1|BI431332
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|148991429|gb|EE032931.2|EE032931
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|45847993|gb|CN071936.1|CN071936
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|149074764|gb|EE163194.2|EE163194
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|6012345|gb|AW061701.1|AW061701
EST:     TTACGGCNCTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCCCCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|148942502|gb|EC887517.2|EC887517
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCCCCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|91054277|gb|EB164695.1|EB164695
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|29544119|gb|CB604499.1|CB604499
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|149096585|gb|EE182343.2|EE182343
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|149111714|gb|EE190861.2|EE190861
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|78082236|gb|DV510648.1|DV510648
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|113703128|gb|EE680632.1|EE680632
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACTGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|29543762|gb|CB604142.1|CB604142
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
EST: gi|31355362|gb|CD439719.1|CD439719
EST:     TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCG                         GGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC
genomic: TTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGAC

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

GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGACGAGGAGACCATAAGATCGCTCCAGGGGAAGGAAACCGGGCTGCGCGACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 80

GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGACGAGGAGACCATAAGATCGCTCCAGGGGAAGGAAACCGGGCTGCGCGACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGACGAGGAGACCATAAGATCGCTCCAGGGGAAGGAAACCGGGCTGCGCGACC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 70

GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggcc ... tctgttacagGGTGGCTGCGACGAAGAGATTGGCCTGTTCCTGTACAGGGGCCGCGTTGACGAGGAGACCATAAGATCGCTCCAGGGGAAGGAAACCGGGCTGCGCGACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGAAGAAGAGACTGGTATAAAGCTGAATATAGAAGACATGGTTGATCTTACGGCACTGCTGGACCCTGCTACTGGAGGTCGAATGCTACCATCACCGgtaactggccaaaacttctattcacctggttatgacttaccccctcgctggtgttttcaactgtggtgtcggaaacagttcattactgttcctgctaatctagactgaagtctctgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG