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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatgcacaggctttggagttcttgatgtttcctgtttgtgtaaactcaaacgccgaggattttattgaagcaataaaagGGCCAGATGCTATTATTGTTGGCTATATCAGACAGTTTGTCATCAAGCCTTTGTCTGGATTCCTTTTTGGCACTCTTATGGAGTACTAAGCCACACTGAA

Basic information

species Zea mays
transcript GRMZM5G883871_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|211291951|gb|FL254575.1|FL254575
EST:     TCTATATCAGTTGCCAATCATAAGAAACAAATCTTATTATTGCACTCCAG                         GGCCAGATGCTATTTATTGT-GGCTATATCAGACAGTTTGTCATCAAGCCT
genomic: TCTATATCAGTTGCCAATCATAAGAAACAAATCTTATTATTGCACTCCAGgtattatgca ... gcaataaaagGGCCAGATGCTATT-ATTGTTGGCTATATCAGACAGTTTGTCATCAAGCCT




















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: 44 (upstream exon), 49 (downstream exon)
Score: 6

CAAGTTGTGGTGGAGAAGGGCGACGACCCCATGACAACATGGGGTGAATTTCTATATCAGTTGCCAATCATAAGAAACAAATCTTATTATTGCACTCCAGgtattatgca ... gcaataaaagGGCCAGATGCTATTATTGTTGGCTATATCAGACAGTTTGTCATCAAGCCTTTGTCTGGATTCCTTTTTGGCACTCTTATGGAGTACTAAGCCACACTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 7

CAAGTTGTGGTGGAGAAGGGCGACGACCCCATGACAACATGGGGTGAATTTCTATATCAGTTGCCAATCATAAGAAACAAATCTTATTATTGCACTCCAGgtattatgca ... gcaataaaagGGCCAGATGCTATTATTGTTGGCTATATCAGACAGTTTGTCATCAAGCCTTTGTCTGGATTCCTTTTTGGCACTCTTATGGAGTACTAAGCCACACTGAA


Block sizes: 32 (upstream exon), 33 (downstream exon)
Score: 3

CAAGTTGTGGTGGAGAAGGGCGACGACCCCATGACAACATGGGGTGAATTTCTATATCAGTTGCCAATCATAAGAAACAAATCTTATTATTGCACTCCAGgtattatgca ... gcaataaaagGGCCAGATGCTATTATTGTTGGCTATATCAGACAGTTTGTCATCAAGCCTTTGTCTGGATTCCTTTTTGGCACTCTTATGGAGTACTAAGCCACACTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttcctgtttgtgtaaactcaaacgccgaggattttattgaagcaataaaagGGCCAGATGCTATTATTGTTGGCTATATCAGACAGTTTGTCATCAAGCCTTTGTCTGGATTCCTTTTTGGCACTCTTATGGAGTACTAAGCCACACTGAA
 tcttgat  putative branch site (score: 3)
                                  attttattgaa  TA-rich tract