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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttcagtatgcttcagtatttgcctatccgatgggtataatgctttattttgtgccaaggatcagtttgcagttttgataacttttaaatattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G022866_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|211302326|gb|FL459923.1|FL459923
EST:     TCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: TCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|45847020|gb|CN070963.1|CN070963
EST:     CTTATGGCGATGGAACTGTTCCAATTATGCTATCCCTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: CTTA-GGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|18167421|gb|BM337260.1|BM337260
EST:     TCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: TCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|78076799|gb|DV505233.1|DV505233
EST:     GGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: GGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|149086438|gb|EE175981.2|EE175981
EST:     TCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: TCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|71774726|gb|DR972604.1|DR972604
EST:     TCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: TCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
EST: gi|5706290|gb|AI942066.1|AI942066
EST:     TTGGTCTGTTGACA                         GCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
genomic: TTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG

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), 49 (downstream exon)
Score: 65

GTTTCTTCCTATAAGTGACCTTACTGACCTCACTCACTTATGCTTGTTTTTCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

GTTTCTTCCTATAAGTGACCTTACTGACCTCACTCACTTATGCTTGTTTTTCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

GTTTCTTCCTATAAGTGACCTTACTGACCTCACTCACTTATGCTTGTTTTTCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 78

GTTTCTTCCTATAAGTGACCTTACTGACCTCACTCACTTATGCTTGTTTTTCTTAGGCGATGGAACTGTTCCAATTATGCTATCACTTGGTCTGTTGACAgtaagtaaac ... tattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttgtgccaaggatcagtttgcagttttgataacttttaaatattttttagGCAATTACAGCAGGGCTTGCTACTCTTGGTCGTATTGGAAAG
                               tgataac  putative branch site (score: 78)
                                             tatttttt  putative PPT
                          agttttgataactttt  TA-rich tract