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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatttgtcttgaaacattacgtacctgaagtatttgtttgtttgtccaactcttgacacatttctttttacttctctggttttagACATTCAGTTACCTGAATTTCGGCTTGAGCCATCTCCACGTCCAGTACAAGAGAACAAGGATAATAGAAGACCAAAAGCACAAGTTAGCAATAGAAATAG

Basic information

species Zea mays
transcript GRMZM2G074818_T01
intron # 6
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|29130575|gb|CB381279.1|CB381279
EST:     TGCACCAAACACCTTTGATGCTTTTGCAGATGATGCACCCCTAAATTTTG                         ACATTCAGTTACCTGAATTTCGGCTTGAGCCATCTCCACGTCCAGTACAAG
genomic: TGCACCAAACACCTTTGATGCTTTTGCAGATGATGCACCCCTAAATTTTGgttagtattt ... ctggttttagACATTCAGTTACCTGAATTTCGGCTTGAGCCATCTCCACGTCCAGTACAAG




















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: 49 (upstream exon), 45 (downstream exon)
Score: 86

ACAACTTCTGCTGGTCGACAAGTACCTGGGAGATCCATTTCCAATTTACGTGCACCAAACACCTTTGATGCTTTTGCAGATGATGCACCCCTAAATTTTGgttagtattt ... ctggttttagACATTCAGTTACCTGAATTTCGGCTTGAGCCATCTCCACGTCCAGTACAAGAGAACAAGGATAATAGAAGACCAAAAGCACAAGTTAGCAATAGAAATAG


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 7

ACAACTTCTGCTGGTCGACAAGTACCTGGGAGATCCATTTCCAATTTACGTGCACCAAACACCTTTGATGCTTTTGCAGATGATGCACCCCTAAATTTTGgttagtattt ... ctggttttagACATTCAGTTACCTGAATTTCGGCTTGAGCCATCTCCACGTCCAGTACAAGAGAACAAGGATAATAGAAGACCAAAAGCACAAGTTAGCAATAGAAATAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 9

ACAACTTCTGCTGGTCGACAAGTACCTGGGAGATCCATTTCCAATTTACGTGCACCAAACACCTTTGATGCTTTTGCAGATGATGCACCCCTAAATTTTGgttagtattt ... ctggttttagACATTCAGTTACCTGAATTTCGGCTTGAGCCATCTCCACGTCCAGTACAAGAGAACAAGGATAATAGAAGACCAAAAGCACAAGTTAGCAATAGAAATAG


Block sizes: 23 (upstream exon), 38 (downstream exon)
Score: 5

ACAACTTCTGCTGGTCGACAAGTACCTGGGAGATCCATTTCCAATTTACGTGCACCAAACACCTTTGATGCTTTTGCAGATGATGCACCCCTAAATTTTGgttagtattt ... ctggttttagACATTCAGTTACCTGAATTTCGGCTTGAGCCATCTCCACGTCCAGTACAAGAGAACAAGGATAATAGAAGACCAAAAGCACAAGTTAGCAATAGAAATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgtttgtttgtccaactcttgacacatttctttttacttctctggttttagACATTCAGTTACCTGAATTTCGGCTTGAGCCATCTCCACGTCCAGTACAAGAGAACAAGGATAATAGAAGACCAAAAGCACAAGTTAGCAATAGAAATAG
                    tcttgac  putative branch site (score: 5)
                              tttctttttacttctc  putative PPT
                             atttctttttactt  TA-rich tract