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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtagtttaactgcaccttgccattcttttaccttctctcctctcagtcgtcccttggtggtgtggtgttggtcctctgtttggttcgcgcccgatcctgttcgagatgacggccattaacttgggtgtcggttgtttgtttgttaatttggccgctggacggggtgtgtacgtactgcgcagGCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGAACGACAAGATCCGGTGCGAGAACATCGCCATGCGGGAGGCGCTCCGGAGCGTCATCT

Basic information

species Zea mays
transcript GRMZM2G126646_T01
intron # 2
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|149077901|gb|EE166629.2|EE166629
EST:     AGCCCCGGCAGATCAAGTTCTGGTTCCAGAACCGCCGGACGCAGATGAAG                         GCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGAACGACAAG
genomic: AGCCCCGGCAGATCAAGTTCTGGTTCCAGAACCGCCGGACGCAGATGAAGgtgtgtagtt ... tactgcgcagGCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGAACGACAAG
EST: gi|149077902|gb|EE166630.2|EE166630
EST:     AGCCCCGGCAGATCAAGTTCTGGTTCCAGAACCGCCGGACGCAGATGAAG                         GCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGAACGACAAG
genomic: AGCCCCGGCAGATCAAGTTCTGGTTCCAGAACCGCCGGACGCAGATGAAGgtgtgtagtt ... tactgcgcagGCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGAACGACAAG
EST: gi|211467804|gb|FL339447.1|FL339447
EST:     AGCCCCAGCAGATCAAGTTCTGGTTCCAGAACCGCCGGACGCAGATGAAG                         GCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGACCGACAAG
genomic: AGCCCCGGCAGATCAAGTTCTGGTTCCAGAACCGCCGGACGCAGATGAAGgtgtgtagtt ... tactgcgcagGCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGAACGACAAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 21

GCACCCGGACGAGAACCAGCGGATGCAGCTGAGCAGGGAGCTGGGGCTGGAGCCCCGGCAGATCAAGTTCTGGTTCCAGAACCGCCGGACGCAGATGAAGgtgtgtagtt ... tactgcgcagGCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGAACGACAAGATCCGGTGCGAGAACATCGCCATGCGGGAGGCGCTCCGGAGCGTCATCT


Block sizes: 49 (upstream exon), 16 (downstream exon)
Score: 2

GCACCCGGACGAGAACCAGCGGATGCAGCTGAGCAGGGAGCTGGGGCTGGAGCCCCGGCAGATCAAGTTCTGGTTCCAGAACCGCCGGACGCAGATGAAGgtgtgtagtt ... tactgcgcagGCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGAACGACAAGATCCGGTGCGAGAACATCGCCATGCGGGAGGCGCTCCGGAGCGTCATCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 6

GCACCCGGACGAGAACCAGCGGATGCAGCTGAGCAGGGAGCTGGGGCTGGAGCCCCGGCAGATCAAGTTCTGGTTCCAGAACCGCCGGACGCAGATGAAGgtgtgtagtt ... tactgcgcagGCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGAACGACAAGATCCGGTGCGAGAACATCGCCATGCGGGAGGCGCTCCGGAGCGTCATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggttgtttgtttgttaatttggccgctggacggggtgtgtacgtactgcgcagGCGCAGCACGAGCGCCAGGACAACTGCTTCCTGCGCGCGGAGAACGACAAGATCCGGTGCGAGAACATCGCCATGCGGGAGGCGCTCCGGAGCGTCATCT
             tgttaat  putative branch site (score: 6)
       tttgtttgttaattt  TA-rich tract