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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTATCCAGGAGCAAATAACAAGGGTTCTTCTGGAGCGTCTAATAGTGAACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacctgtttcttttcatgcggttgattaaaatattgcaaacactatcactaaatgtacctttcttgtgttag

Basic information

species Zea mays
transcript GRMZM5G862538_T01
intron # 10
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|60351141|gb|DN218114.1|DN218114
EST:     ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAG                         AATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
genomic: ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
EST: gi|19351618|gb|BM896150.1|BM896150
EST:     ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAG                         AATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
genomic: ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
EST: gi|32934851|gb|CF039663.1|CF039663
EST:     ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAG                         AATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
genomic: ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
EST: gi|37401645|gb|CF638191.1|CF638191
EST:     ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAG                         AATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
genomic: ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
EST: gi|58029766|gb|CX725193.1|CX725193
EST:     ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAG                         AATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
genomic: ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
EST: gi|84351374|gb|DW245779.1|DW245779
EST:     ACCGCCCCCATCCGTGGGGGTTACTTATTACTTCCATTGAATTGATAAAG                         AATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
genomic: ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
EST: gi|31352508|gb|CD436865.1|CD436865
EST:     ACCGCCCCCATCCTTGGGGGTTACTTATTCCTTCCATTGAATTGATAAAG                         AATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
genomic: ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG
EST: gi|67027758|gb|CO456507.1|CO456507
EST:     ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATANAG                         AATCCGCGTTACAACTTTTGGGACCGGTCTTTTACACATAGTGCACCTGAG
genomic: ACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAG

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), 46 (downstream exon)
Score: 51

GATTATCCAGGAGCAAATAACAAGGGTTCTTCTGGAGCGTCTAATAGTGAACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAGATTGAGAAACTGTTTGAGTCAGTGGCTAGGTCCTGCGGCGCAAAAGCTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 49

GATTATCCAGGAGCAAATAACAAGGGTTCTTCTGGAGCGTCTAATAGTGAACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAGATTGAGAAACTGTTTGAGTCAGTGGCTAGGTCCTGCGGCGCAAAAGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

GATTATCCAGGAGCAAATAACAAGGGTTCTTCTGGAGCGTCTAATAGTGAACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAGATTGAGAAACTGTTTGAGTCAGTGGCTAGGTCCTGCGGCGCAAAAGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 74

GATTATCCAGGAGCAAATAACAAGGGTTCTTCTGGAGCGTCTAATAGTGAACCGCCCCCATCCTTGGGGGTTACTTATTACTTCCATTGAATTGATAAAGgtatgtgacc ... cttgtgttagAATCCGCGTTACAACTTTTGGAACCGGTCTTTTACACATAGTGCACCTGAGATTGAGAAACTGTTTGAGTCAGTGGCTAGGTCCTGCGGCGCAAAAGCTG