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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggttctcctattatgaacatttgttatgctgcactgtagttgtggtctgatgggaacccttgtacagaattcgcaattttgagtataatgtaagtcttgaatgatgtgtcaaactgaagtagggagatagaatgtaggaggcatattcactctattctattgttgtatacgtgcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATCATTCTTACGTGAAGAGCACCACTCATACTCAGGAGTCGGGACAGATTTG

Basic information

species Zea mays
transcript GRMZM2G024733_T01
intron # 13
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|71432684|gb|DR813734.1|DR813734
EST:     CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTTTTCTTCAGTACAAAG                         AACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
genomic: CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
EST: gi|93017162|gb|EB642682.1|EB642682
EST:     CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAG                         AACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
genomic: CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
EST: gi|93017161|gb|EB642681.1|EB642681
EST:     CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTTTTCTTCAGTACAAAG                         AACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
genomic: CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
EST: gi|71426413|gb|DR807463.1|DR807463
EST:     CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAG                         AACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
genomic: CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
EST: gi|60396257|gb|DN229126.1|DN229126
EST:     CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAG                         AACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
genomic: CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
EST: gi|5706171|gb|AI941947.1|AI941947
EST:     CGGCAAAGCAGATAAAGCCTGACAGGAATGGTTTTTTCTTCAGTACAAAG                         AACTGAAACTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
genomic: CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
EST: gi|76288324|gb|DV027892.1|DV027892
EST:     CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAG                         AACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
genomic: CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
EST: gi|71764376|gb|DR962313.1|DR962313
EST:     CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTTTTCTTCAGTACAAAG                         AACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
genomic: CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
EST: gi|113820774|gb|DW944425.1|DW944425
EST:     CTTCAGTACAAAG                         AACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
genomic: CTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
EST: gi|78026532|gb|DV494919.1|DV494919
EST:     CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAG                         AACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC
genomic: CGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATC

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: 46 (upstream exon), 49 (downstream exon)
Score: 81

CAGTTCCTTTATTTCCATTATCGGAAGCAAAGGGAGCTTTCAGATGAGCACGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATCATTCTTACGTGAAGAGCACCACTCATACTCAGGAGTCGGGACAGATTTG


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

CAGTTCCTTTATTTCCATTATCGGAAGCAAAGGGAGCTTTCAGATGAGCACGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATCATTCTTACGTGAAGAGCACCACTCATACTCAGGAGTCGGGACAGATTTG


Block sizes: 37 (upstream exon), 47 (downstream exon)
Score: 14

CAGTTCCTTTATTTCCATTATCGGAAGCAAAGGGAGCTTTCAGATGAGCACGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATCATTCTTACGTGAAGAGCACCACTCATACTCAGGAGTCGGGACAGATTTG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 45

CAGTTCCTTTATTTCCATTATCGGAAGCAAAGGGAGCTTTCAGATGAGCACGACAAAGCAGATAAAGCCTGACAGAAATGGTTTCTTCTTCAGTACAAAGgtctggttct ... gcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATCATTCTTACGTGAAGAGCACCACTCATACTCAGGAGTCGGGACAGATTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaatgtaggaggcatattcactctattctattgttgtatacgtgcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATCATTCTTACGTGAAGAGCACCACTCATACTCAGGAGTCGGGACAGATTTG
                         tattctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggttctcctattatgaacatttgttatgctgcactgtagttgtggtctgatgggaacccttgtacagaattcgcaattttgagtataatgtaagtcttgaatgatgtgtcaaactgaagtagggagatagaatgtaggaggcatattcactctattctattgttgtatacgtgcgtatgcagAACTGAAGCTGAAATGAGTACCTCATACAACTGGCTCTGGGTAGCAGCATCATTCTTACGTGAAGAGCACCACTCATACTCAGGAGTCGGGACAGATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA