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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgtctggcgaactgagcacgtaaacattctctgtctgagttgtagctaattcggctgatgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACTGAGCGCCGAGTATTTTGCCTTGGACCGTAGGAGGCTTGTAAAGTTTAGC

Basic information

species Zea mays
transcript GRMZM2G440916_T01
intron # 28
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|33097205|gb|CF057165.1|CF057165
EST:     CAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAG                         CTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACT
genomic: CAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAGgtacttgtct ... atgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACT
EST: gi|211323882|gb|FK953778.1|FK953778
EST:     CAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAG                         CTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACT
genomic: CAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAGgtacttgtct ... atgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACT
EST: gi|211323885|gb|FK953781.1|FK953781
EST:     CAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAG                         CTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCMNKT--ACACT
genomic: CAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAGgtacttgtct ... atgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACT
EST: gi|9732498|gb|BE511250.1|BE511250
EST:     CAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAG                         CTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACT
genomic: CAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAGgtacttgtct ... atgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACT
EST: gi|78075393|gb|DV503827.1|DV503827
EST:     CAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAG                         CTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACT
genomic: CAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAGgtacttgtct ... atgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACT

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: 130

TTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGCCTGCAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAGgtacttgtct ... atgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACTGAGCGCCGAGTATTTTGCCTTGGACCGTAGGAGGCTTGTAAAGTTTAGC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 23

TTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGCCTGCAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAGgtacttgtct ... atgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACTGAGCGCCGAGTATTTTGCCTTGGACCGTAGGAGGCTTGTAAAGTTTAGC


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 29

TTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGCCTGCAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAGgtacttgtct ... atgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACTGAGCGCCGAGTATTTTGCCTTGGACCGTAGGAGGCTTGTAAAGTTTAGC


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

TTCCTTCTGACGCCCAAGCTCCTACCTGATCTGGAGTACAGCGATGCCTGCAGCATTCTCAACATTATGAACGGCCCATGGATTGAGGAGCCAGCAAAAGgtacttgtct ... atgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACTGAGCGCCGAGTATTTTGCCTTGGACCGTAGGAGGCTTGTAAAGTTTAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagcacgtaaacattctctgtctgagttgtagctaattcggctgatgcatgcagCTTGGAGCTCCGGTGATTGTTGGAGGACAGTGGTCAGCGCAGCTGGACACTGAGCGCCGAGTATTTTGCCTTGGACCGTAGGAGGCTTGTAAAGTTTAGC
        taaacatt  TA-rich tract