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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggcacgattcgggcgtcgtttcgatccgtgaactctgagcacgttggtggacggtggtgggcggcggactaaaagtttggagctttgcgatcgcagAAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGCGGCGCTTTCTTGCCGCTCAAGGCTGCCGTGGGCTCCGGCGCGCCGGCGT

Basic information

species Zea mays
transcript GRMZM2G173882_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|211448523|gb|FK967261.1|FK967261
EST:     CGGCGCAGCTCTGGACGGGCGATTGCGGCCGCGAGGACGCGGAACCAGAG                         AAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGC
genomic: CGGCGCAGCTCTGGACGGGCGATTGCGGCCGCGAGGACGCGGAACCAGAGgtacggcacg ... gcgatcgcagAAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGC
EST: gi|31350353|gb|CD434710.1|CD434710
EST:     CGGCGCAGCTCTGGACCGTAGATTGCGGCCGCGAGGACGCGGAACCAGAG                         AAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCTCGCCGCCGGC
genomic: CGGCGCAGCTCTGGACGGGCGATTGCGGCCGCGAGGACGCGGAACCAGAGgtacggcacg ... gcgatcgcagAAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGC
EST: gi|31353132|gb|CD437489.1|CD437489
EST:     CGGCGCAGCTCTGGACGGGCGATTGCGGCCGCGAGGACGCGGAACCAGAG                         AAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGC
genomic: CGGCGCAGCTCTGGACGGGCGATTGCGGCCGCGAGGACGCGGAACCAGAGgtacggcacg ... gcgatcgcagAAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGC

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: 45 (upstream exon), 30 (downstream exon)
Score: 4

GGTGGCGGAGGAGGACGGCGCCGCCGGGGACAAGAGCAAGTGGATGAGCACGGCGCAGCTCTGGACGGGCGATTGCGGCCGCGAGGACGCGGAACCAGAGgtacggcacg ... gcgatcgcagAAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGCGGCGCTTTCTTGCCGCTCAAGGCTGCCGTGGGCTCCGGCGCGCCGGCGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 20

GGTGGCGGAGGAGGACGGCGCCGCCGGGGACAAGAGCAAGTGGATGAGCACGGCGCAGCTCTGGACGGGCGATTGCGGCCGCGAGGACGCGGAACCAGAGgtacggcacg ... gcgatcgcagAAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGCGGCGCTTTCTTGCCGCTCAAGGCTGCCGTGGGCTCCGGCGCGCCGGCGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 20

GGTGGCGGAGGAGGACGGCGCCGCCGGGGACAAGAGCAAGTGGATGAGCACGGCGCAGCTCTGGACGGGCGATTGCGGCCGCGAGGACGCGGAACCAGAGgtacggcacg ... gcgatcgcagAAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGCGGCGCTTTCTTGCCGCTCAAGGCTGCCGTGGGCTCCGGCGCGCCGGCGT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 13

GGTGGCGGAGGAGGACGGCGCCGCCGGGGACAAGAGCAAGTGGATGAGCACGGCGCAGCTCTGGACGGGCGATTGCGGCCGCGAGGACGCGGAACCAGAGgtacggcacg ... gcgatcgcagAAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGCGGCGCTTTCTTGCCGCTCAAGGCTGCCGTGGGCTCCGGCGCGCCGGCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttggtggacggtggtgggcggcggactaaaagtttggagctttgcgatcgcagAAGCAAGACAAGGAGAGGAGCTCGCCTGAGGCCAGGTCTCGCGCCGCCGGCGGCGCTTTCTTGCCGCTCAAGGCTGCCGTGGGCTCCGGCGCGCCGGCGT
                         gactaaa  putative branch site (score: 13)
                            taaaagttt  TA-rich tract