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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatttgttcttcaataatttaagaatcataacagaacattagcggacgaatcttgcttcaccttttagacaaatacatactggcattggattgt...

Basic information

species Zea mays
transcript GRMZM2G132712_T03
intron # 31
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|6020890|gb|AW065818.1|AW065818
EST:     CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAG                         ATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA
genomic: CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA
EST: gi|60340338|gb|DN207311.1|DN207311
EST:     CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAG                         ATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA
genomic: CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA
EST: gi|5296205|gb|AI782885.1|AI782885
EST:     CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAG                         ATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA
genomic: CTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAA

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: 44 (upstream exon), 49 (downstream exon)
Score: 81

TTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

TTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

TTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 91

TTTTGATGGAGTAAGGATTCTGCGTCTGCAGAATGAAAGCCGATCTGATGCTGAGAAGATAACAAATACTTTCATCTTCAACACATTTGTATTTTGCCAGgtggagtatt ... tttatgccagATCTTCAATGAGTTCAATGCACGAAAACCCGAGGAAAAGAATGTCTTCAAAGGGGTCACGAAGAATCACCTGTTCATGGGAATAATCGGTATAACGACAG