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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacattttgtttgcagttagttgtatcctgacatagttgttcactatgacttggactaatttgatttgccatatcaatattttccagtaatgtggcctctggcttcatagaaaatcaactgctaatggcttaaaataatgctgctgttattgattttaagcatgatctaatattcctctgtttttcttagTTATACGGAGAGCCCCACATGAATTCAAGATTGCTTGCCTGGAG

Basic information

species Zea mays
transcript GRMZM2G099481_T01
intron # 7
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|78083912|gb|DV512305.1|DV512305
EST:     GCCTGTTGTAATTTCACCTGATGGCTTGTTTCCTTCACTCTACCGAGAAG                         TTATACGGAGAGCCCCACATGAATTCAAGATTGCTTGCCTGGAG
genomic: GCCTGTTGTAATTTCACCTGATGGCTTGTTTCCTTCACTCTACCGAGAAGgtgacatttt ... tttttcttagTTATACGGAGAGCCCCACATGAATTCAAGATTGCTTGCCTGGAG




















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: 48 (upstream exon), 48 (downstream exon)
Score: 69

GATGGGAAAGCACTACCCAATGGGCCTGTTGTAATTTCACCTGATGGCTTGTTTCCTTCACTCTACCGAGAAGgtgacatttt ... tttttcttagTTATACGGAGAGCCCCACATGAATTCAAGATTGCTTGCCTGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 74

GATGGGAAAGCACTACCCAATGGGCCTGTTGTAATTTCACCTGATGGCTTGTTTCCTTCACTCTACCGAGAAGgtgacatttt ... tttttcttagTTATACGGAGAGCCCCACATGAATTCAAGATTGCTTGCCTGGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 103

GATGGGAAAGCACTACCCAATGGGCCTGTTGTAATTTCACCTGATGGCTTGTTTCCTTCACTCTACCGAGAAGgtgacatttt ... tttttcttagTTATACGGAGAGCCCCACATGAATTCAAGATTGCTTGCCTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

GATGGGAAAGCACTACCCAATGGGCCTGTTGTAATTTCACCTGATGGCTTGTTTCCTTCACTCTACCGAGAAGgtgacatttt ... tttttcttagTTATACGGAGAGCCCCACATGAATTCAAGATTGCTTGCCTGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgctgctgttattgattttaagcatgatctaatattcctctgtttttcttagTTATACGGAGAGCCCCACATGAATTCAAGATTGCTTGCCTGGAG
                             atctaat  putative branch site (score: 123)
                                   tattcctctgtttttc  CT-rich tract
         tgttattgattttaa  TA-rich tract