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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaataatgaagtcacttcttcatttaccatgtcatggtggaactagcatattttataaaccggtgtgcttctctgaccaaaaagattattatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG

Basic information

species Zea mays
transcript GRMZM5G886883_T03
intron # 4
splice site 3'
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|71305066|gb|DR788670.1|DR788670
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|78109684|gb|DV528100.1|DV528100
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|148947131|gb|EC892444.2|EC892444
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|93014964|gb|EB640484.1|EB640484
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|149000423|gb|EE037594.2|EE037594
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|148992844|gb|EE033671.2|EE033671
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|148982611|gb|EE028409.2|EE028409
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|149088271|gb|EE177365.2|EE177365
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|148996312|gb|EE035595.2|EE035595
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|149000477|gb|EE037653.2|EE037653
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|67031282|gb|CO460031.1|CO460031
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTANAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|71767172|gb|DR965109.1|DR965109
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|60339883|gb|DN206856.1|DN206856
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
EST: gi|149078105|gb|EE166854.2|EE166854
EST:     AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAAC                         GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
genomic: AAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG

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), 46 (downstream exon)
Score: 70

CTGCATATGAAGAACAAAGTTCTTTAAGCCATGGCAAATATGCTTACCCAAAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 144

CTGCATATGAAGAACAAAGTTCTTTAAGCCATGGCAAATATGCTTACCCAAAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 150

CTGCATATGAAGAACAAAGTTCTTTAAGCCATGGCAAATATGCTTACCCAAAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 130

CTGCATATGAAGAACAAAGTTCTTTAAGCCATGGCAAATATGCTTACCCAAAGAATGGTGGTCAAATTTCAAAAGAGTCGTTGAGGCATCAATCAAAAACgtgcgcttat ... ttatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcatattttataaaccggtgtgcttctctgaccaaaaagattattatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG
                           ctctgac  putative branch site (score: 130)
                                   aaaaagattattatct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaataatgaagtcacttcttcatttaccatgtcatggtggaactagcatattttataaaccggtgtgcttctctgaccaaaaagattattatctgcagGTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - taccatg
- - - - - - - - - - - - - - - - - catggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaga