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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAAGCTCTAACCTTCTATAAATCCAGTACATTTGAAGTTGATGTTTTGTATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacccttacacagtgtgcatgttattagataattctgttgttatttgctataacgtgctaaaatatgtgtag

Basic information

species Zea mays
transcript GRMZM2G063676_T01
intron # 3
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|21809991|gb|BQ668309.1|BQ668309
EST:     ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACA                         ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
genomic: ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
EST: gi|32931548|gb|CF036360.1|CF036360
EST:     ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACA                         ATTGGACCTTTCCAACCCTCCAAAGGTGAGAAGGCCAAACTGAAAGTTAAA
genomic: ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
EST: gi|71307557|gb|DR789997.1|DR789997
EST:     ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACA                         ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
genomic: ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
EST: gi|18648899|gb|BM497718.1|BM497718
EST:     ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACA                         ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
genomic: ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
EST: gi|18654531|gb|BM499336.1|BM499336
EST:     ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACA                         ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
genomic: ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
EST: gi|31355297|gb|CD439654.1|CD439654
EST:     ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACA                         ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
genomic: ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
EST: gi|18654532|gb|BM499337.1|BM499337
EST:     ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACA                         ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
genomic: ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
EST: gi|32933060|gb|CF037872.1|CF037872
EST:     ACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACA                         ATTGGACCTTTCCAACCCTCCAAAGGTGAGAAGGCCAAACTGAAAGTTAAA
genomic: ACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
EST: gi|18654538|gb|BM499343.1|BM499343
EST:     ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACA                         ATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA
genomic: ATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAA

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), 49 (downstream exon)
Score: 292

TAAAGCTCTAACCTTCTATAAATCCAGTACATTTGAAGTTGATGTTTTGTATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 159

TAAAGCTCTAACCTTCTATAAATCCAGTACATTTGAAGTTGATGTTTTGTATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

TAAAGCTCTAACCTTCTATAAATCCAGTACATTTGAAGTTGATGTTTTGTATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 198

TAAAGCTCTAACCTTCTATAAATCCAGTACATTTGAAGTTGATGTTTTGTATGTGGACACATGCGACTCGCAAATTCCACAGAAGATAAGCACTTACACAgtaagcaacc ... atatgtgtagATTGGACCTTTCCAACCCTCCAAAGGTGAGAGGGCCAAACTGAAAGTTAAAGTGCGTCTCAACATCCACGGGATTGTCACAGTTGATTCAGCTATG