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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCGAATGCATACATGAGCTGATCTGCAGCGGGAACAAGTTCCATTCGTGTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctcccttatcttgtcagaggcctaagctaatcgtttttataatatccacctttctcattgcatttgcttgtatctttcacatcatgcag

Basic information

species Zea mays
transcript GRMZM2G361398_T01
intron # 18
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|60355271|gb|DN222244.1|DN222244
EST:     GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAG                         TCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
genomic: GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
EST: gi|44900568|gb|CK827113.1|CK827113
EST:     GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAG                         TCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
genomic: GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
EST: gi|83278224|gb|DV942232.1|DV942232
EST:     GTGTTTTTCACCCAAATTACCCGAATTTGCTTCCAATCGGTTGTTATGAG                         TCCCTAGAGTTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
genomic: GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
EST: gi|33091637|gb|CF051631.1|CF051631
EST:     GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAG                         TCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
genomic: GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
EST: gi|83278911|gb|DV942919.1|DV942919
EST:     GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAG                         TCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
genomic: GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
EST: gi|24766351|gb|CA401505.1|CA401505
EST:     GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAG                         TCCCTAGAGCTTTGGGACATTAGGGAGAAGAACACGGTGACAATCAGCAAC
genomic: GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
EST: gi|60351102|gb|DN218075.1|DN218075
EST:     GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAG                         TCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
genomic: GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
EST: gi|78109474|gb|DV527890.1|DV527890
EST:     GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAG                         TCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC
genomic: GTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAAC

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), 47 (downstream exon)
Score: 107

CATCGAATGCATACATGAGCTGATCTGCAGCGGGAACAAGTTCCATTCGTGTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAACGCTCATGACGGCATGGTTGCTGCCCTAGCCGCGTCAAGTGCATCGGGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 42

CATCGAATGCATACATGAGCTGATCTGCAGCGGGAACAAGTTCCATTCGTGTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAACGCTCATGACGGCATGGTTGCTGCCCTAGCCGCGTCAAGTGCATCGGGGC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 33

CATCGAATGCATACATGAGCTGATCTGCAGCGGGAACAAGTTCCATTCGTGTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAACGCTCATGACGGCATGGTTGCTGCCCTAGCCGCGTCAAGTGCATCGGGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 32

CATCGAATGCATACATGAGCTGATCTGCAGCGGGAACAAGTTCCATTCGTGTGTTTTTCACCCAAATTACCCGAATTTGCTTATAATCGGTTGTTATGAGgcaagttctc ... catcatgcagTCCCTAGAGCTTTGGGACATAAGGGAGAAGAACACGGTGACAATCAGCAACGCTCATGACGGCATGGTTGCTGCCCTAGCCGCGTCAAGTGCATCGGGGC