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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttcagctcttgaacgagtcccatacattttgtgattcatttctttaaggtactgaagtattgtttgctctgatgcagCGTGAACTTCCATTCTACTATCCCGGACAG

Basic information

species Zea mays
transcript GRMZM2G091419_T01
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|148985729|gb|EE029744.2|EE029744
EST:     ATTACTTCCCTGGCAGACGAAAAAGAGGTAAGGACTACAGTGAGGATATG                         CGTGAACTTCCATTCTACTATCCCGGACAG
genomic: ATTACTTCCCTGGCAGACGAAAAAGAGGTAAGGACTACAGTGAGGATATGgtaggttcag ... tctgatgcagCGTGAACTTCCATTCTACTATCCCGGACAG




















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), 30 (downstream exon)
Score: 35

TTTGATCAGGATTACTTCCCTGGCAGACGAAAAAGAGGTAAGGACTACAGTGAGGATATGgtaggttcag ... tctgatgcagCGTGAACTTCCATTCTACTATCCCGGACAG


Block sizes: 49 (upstream exon), 30 (downstream exon)
Score: 167

TTTGATCAGGATTACTTCCCTGGCAGACGAAAAAGAGGTAAGGACTACAGTGAGGATATGgtaggttcag ... tctgatgcagCGTGAACTTCCATTCTACTATCCCGGACAG


Block sizes: 46 (upstream exon), 21 (downstream exon)
Score: 4

TTTGATCAGGATTACTTCCCTGGCAGACGAAAAAGAGGTAAGGACTACAGTGAGGATATGgtaggttcag ... tctgatgcagCGTGAACTTCCATTCTACTATCCCGGACAG


Block sizes: 48 (upstream exon), 30 (downstream exon)
Score: 39

TTTGATCAGGATTACTTCCCTGGCAGACGAAAAAGAGGTAAGGACTACAGTGAGGATATGgtaggttcag ... tctgatgcagCGTGAACTTCCATTCTACTATCCCGGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacattttgtgattcatttctttaaggtactgaagtattgtttgctctgatgcagCGTGAACTTCCATTCTACTATCCCGGACAG
                                            ctctgat  putative branch site (score: 39)
                                        tttgctct  CT-rich tract
           attcatttctttaa  TA-rich tract