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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtcgacagttgcaattatactacgttgcgtgcatttctttctctctcttttttttttggtcacatgtacaagtacaaagaaagagtgaactgactgacaagtgttttggaaaaagGCCAGAGGCCAGCTGCTCGGGGAAGACGGAGTGCGCGTGCACAGCATGGTTCTCCCTGGTCTCGTCTCCAGCACGTCGATCAACTTCTCTGGCCCAGGAG

Basic information

species Zea mays
transcript GRMZM2G044247_T01
intron # 7
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|149088345|gb|EE177444.2|EE177444
EST:     CAGACCTTGGTCAGATATACAACAGGGAAGATATGGATTCCAGCAGTCCA                         GCCAGAGGCCAGCTGCTCGGGGA
genomic: CAGACCTTGGTCAGATATACAACAGGGAAGATATGGATTCCAGCAGTCCAgtaagtgtcg ... ttggaaaaagGCCAGAGGCCAGCTGCTCGGGGA
EST: gi|76285579|gb|DV025147.1|DV025147
EST:     CAGACCTTGGTCAGATATACAACAGGGAAGATATGGATTCCAGCAGTCCA                         GCCAGAGGCCAGCTGCTCGGGGAAGACGGAGTGCGCGTGCACAGCATGGTT
genomic: CAGACCTTGGTCAGATATACAACAGGGAAGATATGGATTCCAGCAGTCCAgtaagtgtcg ... ttggaaaaagGCCAGAGGCCAGCTGCTCGGGGAAGACGGAGTGCGCGTGCACAGCATGGTT
EST: gi|148949802|gb|EC895289.2|EC895289
EST:     CAGACCTTGGTCAGATATACAACAGGGAAGATATGGATTCCAGCAGTCCA                         GCCAGAAGCCAGCTGCTCGGGGAAGACGGAGTGCGCGTGCACAGCATGGTT
genomic: CAGACCTTGGTCAGATATACAACAGGGAAGATATGGATTCCAGCAGTCCAgtaagtgtcg ... ttggaaaaagGCCAGAGGCCAGCTGCTCGGGGAAGACGGAGTGCGCGTGCACAGCATGGTT

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 3 RNA-Seq libraries.


Block sizes: 11 (upstream exon), 39 (downstream exon)
Score: 1

GATCTTCCATCGCAAGATGCAATCCAGATTGCAAACAACATATCAGACCTTGGTCAGATATACAACAGGGAAGATATGGATTCCAGCAGTCCAgtaagtgtcg ... ttggaaaaagGCCAGAGGCCAGCTGCTCGGGGAAGACGGAGTGCGCGTGCACAGCATGGTTCTCCCTGGTCTCGTCTCCAGCACGTCGATCAACTTCTCTGGCCCAGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

GATCTTCCATCGCAAGATGCAATCCAGATTGCAAACAACATATCAGACCTTGGTCAGATATACAACAGGGAAGATATGGATTCCAGCAGTCCAgtaagtgtcg ... ttggaaaaagGCCAGAGGCCAGCTGCTCGGGGAAGACGGAGTGCGCGTGCACAGCATGGTTCTCCCTGGTCTCGTCTCCAGCACGTCGATCAACTTCTCTGGCCCAGGAG


Block sizes: 43 (upstream exon), 41 (downstream exon)
Score: 18

GATCTTCCATCGCAAGATGCAATCCAGATTGCAAACAACATATCAGACCTTGGTCAGATATACAACAGGGAAGATATGGATTCCAGCAGTCCAgtaagtgtcg ... ttggaaaaagGCCAGAGGCCAGCTGCTCGGGGAAGACGGAGTGCGCGTGCACAGCATGGTTCTCCCTGGTCTCGTCTCCAGCACGTCGATCAACTTCTCTGGCCCAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatgtacaagtacaaagaaagagtgaactgactgacaagtgttttggaaaaagGCCAGAGGCCAGCTGCTCGGGGAAGACGGAGTGCGCGTGCACAGCATGGTTCTCCCTGGTCTCGTCTCCAGCACGTCGATCAACTTCTCTGGCCCAGGAG
                               gactgac  putative branch site (score: 18)
               aaagaaa  TA-rich tract