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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtttgcaacccaccgccacgccttcttctccccccgcgatctacccggcccgggcgccgttgctgctactgctattactaatactactaccgcgtcgtagcggaggcagGGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGGCGTCCTCGCGCTCTTCGACGTCGACGGCACCCTCACAGCGCCGCGCAAG

Basic information

species Zea mays
transcript GRMZM2G165535_T05
intron # 1
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|71771666|gb|DR969603.1|DR969603
EST:     CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATT                         G
genomic: CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcag-
EST: gi|71771666|gb|DR969603.1|DR969603
EST:     CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATT                         G
genomic: CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcag-
EST: gi|71771666|gb|DR969603.1|DR969603
EST:     CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATT                         G
genomic: CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcag-
EST: gi|71771666|gb|DR969603.1|DR969603
EST:     CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATT                         G
genomic: CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcag-
EST: gi|71771666|gb|DR969603.1|DR969603
EST:     CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATT                         G
genomic: CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcag-
EST: gi|148950412|gb|EC895979.2|EC895979
EST:     CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATT                         GGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGG
genomic: CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcagGGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGG
EST: gi|148943663|gb|EC888727.2|EC888727
EST:     CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATT                         GGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGG
genomic: CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcagGGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGG
EST: gi|76280415|gb|DV019983.1|DV019983
EST:     CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATT                         GGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGG
genomic: CCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcagGGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGG

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: 47 (upstream exon), 49 (downstream exon)
Score: 132

TGCATTCCCTTGCGCGGGACGCGACAACTCCACGCTACACAGTTCACACGCCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcagGGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGGCGTCCTCGCGCTCTTCGACGTCGACGGCACCCTCACAGCGCCGCGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 293

TGCATTCCCTTGCGCGGGACGCGACAACTCCACGCTACACAGTTCACACGCCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcagGGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGGCGTCCTCGCGCTCTTCGACGTCGACGGCACCCTCACAGCGCCGCGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 339

TGCATTCCCTTGCGCGGGACGCGACAACTCCACGCTACACAGTTCACACGCCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcagGGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGGCGTCCTCGCGCTCTTCGACGTCGACGGCACCCTCACAGCGCCGCGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

TGCATTCCCTTGCGCGGGACGCGACAACTCCACGCTACACAGTTCACACGCCAAGCGAGGGCCGCATCTAGATCCGCGCCGCCGAGCTGACTTGACTATTgcaagtttgc ... gcggaggcagGGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGGCGTCCTCGCGCTCTTCGACGTCGACGGCACCCTCACAGCGCCGCGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgccgttgctgctactgctattactaatactactaccgcgtcgtagcggaggcagGGACTTGAGGAGCGGGTGGGTTGCGATGGCCGCTGCGGGGAGGAATGCGGGCGTCCTCGCGCTCTTCGACGTCGACGGCACCCTCACAGCGCCGCGCAAG
                     tactaat  putative branch site (score: 203)
                  tattactaatacta  TA-rich tract