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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgtccattccccgctgtctgccatccaattatgtttacaaaaaccgttgtgacatccagacatccagatccagtggtgtttgaaaaaaaaaatgttccgtattgtagacaattgagatgctgctaacattaaggcctttcacctttgcagTCTGGAGGTTGATCTCCCCAGTCGTATTGAGGAACCAACTTGCCAATGAAGAGTTGATGCCACACAGGCCTACAGTATAGTTTTGATGATATAGAGAAAA

Basic information

species Zea mays
transcript GRMZM2G018756_T02
intron # 11
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|166684894|gb|EG164892.1|EG164892
EST:     TGGTTCGCGGCTAGCATATACC                         TCTGGAGGTTGATCT-CCCAGTCGTATTGAGGAACCAACTTGCCAATGAAG
genomic: TGGTTCGCGGCTAGCATATACCgtgagtcgtc ... acctttgcagTCTGGAGGTTGATCTCCCCAGTCGTATTGAGGAACCAACTTGCCAATGAAG
EST: gi|76010754|gb|DT937924.1|DT937924
EST:     AAGTACATGGGTGAAGATCATCAACGAGTGGTTCGCGGCTAGCATATACC                         TTTGGAGGTTGATCTCCCCAGTCGTATTGAGGAACCAACTTGCCAATGAAG
genomic: AAGTACATGGGTGAAGATCATCAACGAGTGGTTCGCGGCTAGCATATACCgtgagtcgtc ... acctttgcagTCTGGAGGTTGATCTCCCCAGTCGTATTGAGGAACCAACTTGCCAATGAAG

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: 40 (upstream exon), 42 (downstream exon)
Score: 15

GTGGAGCATAGATGTTGGATGGGCAAGTACATGGGTGAAGATCATCAACGAGTGGTTCGCGGCTAGCATATACCgtgagtcgtc ... acctttgcagTCTGGAGGTTGATCTCCCCAGTCGTATTGAGGAACCAACTTGCCAATGAAGAGTTGATGCCACACAGGCCTACAGTATAGTTTTGATGATATAGAGAAAA


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 15

GTGGAGCATAGATGTTGGATGGGCAAGTACATGGGTGAAGATCATCAACGAGTGGTTCGCGGCTAGCATATACCgtgagtcgtc ... acctttgcagTCTGGAGGTTGATCTCCCCAGTCGTATTGAGGAACCAACTTGCCAATGAAGAGTTGATGCCACACAGGCCTACAGTATAGTTTTGATGATATAGAGAAAA


Block sizes: 40 (upstream exon), 37 (downstream exon)
Score: 2

GTGGAGCATAGATGTTGGATGGGCAAGTACATGGGTGAAGATCATCAACGAGTGGTTCGCGGCTAGCATATACCgtgagtcgtc ... acctttgcagTCTGGAGGTTGATCTCCCCAGTCGTATTGAGGAACCAACTTGCCAATGAAGAGTTGATGCCACACAGGCCTACAGTATAGTTTTGATGATATAGAGAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgtattgtagacaattgagatgctgctaacattaaggcctttcacctttgcagTCTGGAGGTTGATCTCCCCAGTCGTATTGAGGAACCAACTTGCCAATGAAGAGTTGATGCCACACAGGCCTACAGTATAGTTTTGATGATATAGAGAAAA
                         tgctaac  putative branch site (score: 2)
                                       cctttcacctttgc  putative PPT
                            taacattaa  TA-rich tract