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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAACAGGATGAAATACTTCTTATGAAGTGCAATTTCATGTCCTGGATGTTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtaccaaatcaaatcaaatcaaatggaaacactgtagattgcttgatttctattaggccccttgtgatgccaaatttcccttcattgttggagatgcag

Basic information

species Zea mays
transcript GRMZM2G025042_T01
intron # 5
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|148953492|gb|EE152999.2|EE152999
EST:     TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTT                         GCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTNCA-GCCCAA
genomic: TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATT-CAAGCCCAA
EST: gi|211220756|gb|FL455709.1|FL455709
EST:     TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTT                         GCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
genomic: TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
EST: gi|37388244|gb|CF631329.1|CF631329
EST:     TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTT                         GCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
genomic: TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
EST: gi|37386201|gb|CF630281.1|CF630281
EST:     TGTTGGATCCTACGATGCATTTTTCGCCATATTT                         GCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
genomic: TGTTGTATCCTACGATGCA-TTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
EST: gi|88748691|gb|DY532832.1|DY532832
EST:     TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTT                         GCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
genomic: TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
EST: gi|76014839|gb|DT942009.1|DT942009
EST:     TCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTTCGC-ATATTT                         GCTGGACCTCGGGTGAATTCCA-TGACTTTTATGTGCCATTCAAGCCCAA-
genomic: TCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTT-CGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
EST: gi|211220755|gb|FL455708.1|FL455708
EST:     TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTT                         GCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
genomic: TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
EST: gi|148995059|gb|EE034374.2|EE034374
EST:     TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTT                         GCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
genomic: TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
EST: gi|76013875|gb|DT941045.1|DT941045
EST:     TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTT                         GCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
genomic: TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
EST: gi|211385110|gb|FL405372.1|FL405372
EST:     TCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTTCGC-ATATTT                         A
genomic: TCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTT-CGCCATATTTgtaagtacca ... ggagatgcag-
EST: gi|211385110|gb|FL405372.1|FL405372
EST:     TCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTTCGC-ATATTT                         A
genomic: TCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTT-CGCCATATTTgtaagtacca ... ggagatgcag-
EST: gi|211385110|gb|FL405372.1|FL405372
EST:     TCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTTCGC-ATATTT                         A
genomic: TCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTT-CGCCATATTTgtaagtacca ... ggagatgcag-
EST: gi|211220757|gb|FL455710.1|FL455710
EST:     TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTT                         GCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
genomic: TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
EST: gi|78117325|gb|DV535712.1|DV535712
EST:     TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTT                         GCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA
genomic: TTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAA

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), 41 (downstream exon)
Score: 22

GATAACAGGATGAAATACTTCTTATGAAGTGCAATTTCATGTCCTGGATGTTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAATTGAAGCTTCTCTACTACAAAACAATATGTTGGGTCCAGCTACGTTATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GATAACAGGATGAAATACTTCTTATGAAGTGCAATTTCATGTCCTGGATGTTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAATTGAAGCTTCTCTACTACAAAACAATATGTTGGGTCCAGCTACGTTATT


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 44

GATAACAGGATGAAATACTTCTTATGAAGTGCAATTTCATGTCCTGGATGTTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAATTGAAGCTTCTCTACTACAAAACAATATGTTGGGTCCAGCTACGTTATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

GATAACAGGATGAAATACTTCTTATGAAGTGCAATTTCATGTCCTGGATGTTCCCTAGTCCATTCCATGTTGTATCCTACGATGCATTTTCGCCATATTTgtaagtacca ... ggagatgcagGCTGGACCTCCGGTGAATTCCAATGACTTTTATGTGCCATTCAAGCCCAAATTGAAGCTTCTCTACTACAAAACAATATGTTGGGTCCAGCTACGTTATT