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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctctgaacttttgctctgtaactgtgaccctcaataaaaaaaattcagttaaaggaataggtcccgttgaccgagctcttcgattctctctgaatgcagATAGCTACACTGGTAGCTGTATACGCGGACTGGGGGTTCACTTCGATCGAAGGCATTGGATGGGGCTGGGCTGGTGTGGTGTGGCTCTACAACCTCGTCT

Basic information

species Zea mays
transcript GRMZM2G068259_T01
intron # 19
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|37388839|gb|CF631634.1|CF631634
EST:     TTGAGCGCCCGGGCTTTCTACTAGTGTTTGCCTTCCTGGTCGCGCAGCTG                         ATAGCTACACTGGTAGCTGTATACGCGGACTGGGGGTTCACTTCGATCGAA
genomic: CTGAGCGCCCGGGCTTTCTACTAGTGTTTGCCTTCCTGGTCGCGCAGCTGgtatgctctc ... ctgaatgcagATAGCTACACTGGTAGCTGTATACGCGGACTGGGGGTTCACTTCGATCGAA
EST: gi|6601730|gb|AW256126.1|AW256126
EST:     CTGAGCGCCCGGGCTTTCTACTAGTGTTTGCCTTCCTGGTCGCGCAGCTG                         ATAGCTACACTGGTAGCTGTATACGCGGACTGGGGGTTCACTTCGATCGAA
genomic: CTGAGCGCCCGGGCTTTCTACTAGTGTTTGCCTTCCTGGTCGCGCAGCTGgtatgctctc ... ctgaatgcagATAGCTACACTGGTAGCTGTATACGCGGACTGGGGGTTCACTTCGATCGAA

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: 42 (upstream exon), 47 (downstream exon)
Score: 41

CATCAGCCAAGCTCTCATCTTCGTGACGAGGTCTCGCAGCTGGTCATTCGCTGAGCGCCCGGGCTTTCTACTAGTGTTTGCCTTCCTGGTCGCGCAGCTGgtatgctctc ... ctgaatgcagATAGCTACACTGGTAGCTGTATACGCGGACTGGGGGTTCACTTCGATCGAAGGCATTGGATGGGGCTGGGCTGGTGTGGTGTGGCTCTACAACCTCGTCT


Block sizes: 30 (upstream exon), 35 (downstream exon)
Score: 7

CATCAGCCAAGCTCTCATCTTCGTGACGAGGTCTCGCAGCTGGTCATTCGCTGAGCGCCCGGGCTTTCTACTAGTGTTTGCCTTCCTGGTCGCGCAGCTGgtatgctctc ... ctgaatgcagATAGCTACACTGGTAGCTGTATACGCGGACTGGGGGTTCACTTCGATCGAAGGCATTGGATGGGGCTGGGCTGGTGTGGTGTGGCTCTACAACCTCGTCT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 19

CATCAGCCAAGCTCTCATCTTCGTGACGAGGTCTCGCAGCTGGTCATTCGCTGAGCGCCCGGGCTTTCTACTAGTGTTTGCCTTCCTGGTCGCGCAGCTGgtatgctctc ... ctgaatgcagATAGCTACACTGGTAGCTGTATACGCGGACTGGGGGTTCACTTCGATCGAAGGCATTGGATGGGGCTGGGCTGGTGTGGTGTGGCTCTACAACCTCGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagttaaaggaataggtcccgttgaccgagctcttcgattctctctgaatgcagATAGCTACACTGGTAGCTGTATACGCGGACTGGGGGTTCACTTCGATCGAAGGCATTGGATGGGGCTGGGCTGGTGTGGTGTGGCTCTACAACCTCGTCT
                    cgttgac  putative branch site (score: 19)
                               ctcttcgattctctct  putative PPT