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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtcgtgccatgttgttcgcccgatccatgatctgtccctgctgttgtttccctccacgtgtagtgtatctctcatctggtggtggtttttgagcttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTGGTGCTCGGTGTGATCCTCGGCGCGCACACTCACGAGAAACGTTCCATGA

Basic information

species Zea mays
transcript GRMZM2G157675_T02
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|28188247|gb|CB179857.1|CB179857
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|211162572|gb|FL132731.1|FL132731
EST:     TATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGCTCGCCGTG
genomic: TATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|38229508|gb|CF919821.1|CF919821
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|28188031|gb|CB179641.1|CB179641
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG
EST: gi|7138105|gb|AW499432.1|AW499432
EST:     AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGC                         AAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGGTCATGCTCGCCGTG
genomic: AGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTG

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: 27 (upstream exon), 23 (downstream exon)
Score: 1

CCCCAACAGCATTCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTGGTGCTCGGTGTGATCCTCGGCGCGCACACTCACGAGAAACGTTCCATGA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 2

CCCCAACAGCATTCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTGGTGCTCGGTGTGATCCTCGGCGCGCACACTCACGAGAAACGTTCCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 320

CCCCAACAGCATTCTCGTCGTCACCATCAACGGCATCGGCCTCGTCATCGAGGCCGTCTACCTCACTATCTTCTTCCTCTATTCCGACAGCCAGAAGCGCgtgagtgtcg ... cttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTGGTGCTCGGTGTGATCCTCGGCGCGCACACTCACGAGAAACGTTCCATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctccacgtgtagtgtatctctcatctggtggtggtttttgagcttaatgcagAAGAAGGCGTTCGCGATCCTGGCCGTGGAGATTCTGTTCATGGTCGCCGTGGTGCTCGGTGTGATCCTCGGCGCGCACACTCACGAGAAACGTTCCATGA
                                            gcttaat  putative branch site (score: 320)
                                     tttttga  TA-rich tract