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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgtttcagtagaatattcttgatctcctgttcttttgacactagggaggaaatagtttgactttgatattgatgtttgccttgtatgtagATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG

Basic information

species Zea mays
transcript GRMZM2G381395_T01
intron # 15
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|91877942|gb|EB407899.1|EB407899
EST:     CTCTTGGGCTCCCAGTTGTACAACCATATCGCAAACTTGGGAGGCATCTT                         ATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG
genomic: CTCTTGGGCTCCCAGTTGTACAACCATATCGCAAACTTGGGAGGCATCTTgtaggtgttt ... ttgtatgtagATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG
EST: gi|6031435|gb|AW076337.1|AW076337
EST:     AACTTGGGAGGCATCTT                         ATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG
genomic: AACTTGGGAGGCATCTTgtaggtgttt ... ttgtatgtagATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG
EST: gi|74240732|gb|DT648646.1|DT648646
EST:     CTCTTGGGCTCCCAGTTGTACAACCATATCGCAAACTTGGGAGGCATCTT                         ATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG
genomic: CTCTTGGGCTCCCAGTTGTACAACCATATCGCAAACTTGGGAGGCATCTTgtaggtgttt ... ttgtatgtagATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG
EST: gi|31354501|gb|CD438858.1|CD438858
EST:     CTCTTGGGCTCCCAGTTGTACAACCATATCGCAAACTTGGGAGGCATCTT                         ATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG
genomic: CTCTTGGGCTCCCAGTTGTACAACCATATCGCAAACTTGGGAGGCATCTTgtaggtgttt ... ttgtatgtagATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG

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), 48 (downstream exon)
Score: 150

GTAATTGCTTGTGAAAATGAACCAGTGAGATGGACGACTCCTCTTGGGCTCCCAGTTGTACAACCATATCGCAAACTTGGGAGGCATCTTgtaggtgttt ... ttgtatgtagATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 73

GTAATTGCTTGTGAAAATGAACCAGTGAGATGGACGACTCCTCTTGGGCTCCCAGTTGTACAACCATATCGCAAACTTGGGAGGCATCTTgtaggtgttt ... ttgtatgtagATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 109

GTAATTGCTTGTGAAAATGAACCAGTGAGATGGACGACTCCTCTTGGGCTCCCAGTTGTACAACCATATCGCAAACTTGGGAGGCATCTTgtaggtgttt ... ttgtatgtagATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 47

GTAATTGCTTGTGAAAATGAACCAGTGAGATGGACGACTCCTCTTGGGCTCCCAGTTGTACAACCATATCGCAAACTTGGGAGGCATCTTgtaggtgttt ... ttgtatgtagATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacactagggaggaaatagtttgactttgatattgatgtttgccttgtatgtagATTAAAACGTCATTGCAGGTTTTGACCCTTCAGCGGGAGACGGATAAG
                               tattgat  putative branch site (score: 47)
                                       tttgcctt  CT-rich tract
              aaatagttt  TA-rich tract