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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagtcaaagggcaacctgaagcttatttatcttatatgatgtgaaactcctttgtttttcattgtttctagttaaaaaaatatgttgttctgacactagGAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCATGCCTTGTAAGGGAATATTAAGGTTCTGTGCCATGTCACTTCCG

Basic information

species Zea mays
transcript GRMZM2G037624_T01
intron # 9
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|6022628|gb|AW067440.1|AW067440
EST:     TTTTATCATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTG                         GAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCAT
genomic: TTTTATCATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTGgtttgtataa ... ctgacactagGAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCAT
EST: gi|60398284|gb|DN231100.1|DN231100
EST:     CATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTG                         GAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCAT
genomic: CATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTGgtttgtataa ... ctgacactagGAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCAT
EST: gi|71449425|gb|DR830475.1|DR830475
EST:     TTTTATCATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTG                         GAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCAT
genomic: TTTTATCATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTGgtttgtataa ... ctgacactagGAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCAT
EST: gi|149009603|gb|EE154023.2|EE154023
EST:     TTTTATCATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTG                         GAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCAT
genomic: TTTTATCATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTGgtttgtataa ... ctgacactagGAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCAT

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: 44 (upstream exon), 45 (downstream exon)
Score: 38

GTTAATATGTTAGTGGGGGAACCCTTTTATCATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTGgtttgtataa ... ctgacactagGAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCATGCCTTGTAAGGGAATATTAAGGTTCTGTGCCATGTCACTTCCG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 37

GTTAATATGTTAGTGGGGGAACCCTTTTATCATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTGgtttgtataa ... ctgacactagGAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCATGCCTTGTAAGGGAATATTAAGGTTCTGTGCCATGTCACTTCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 29

GTTAATATGTTAGTGGGGGAACCCTTTTATCATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTGgtttgtataa ... ctgacactagGAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCATGCCTTGTAAGGGAATATTAAGGTTCTGTGCCATGTCACTTCCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 17

GTTAATATGTTAGTGGGGGAACCCTTTTATCATGGAAGTGAAGGGATGCTGCCATGGCAAAATCTGCGTTTCTGgtttgtataa ... ctgacactagGAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCATGCCTTGTAAGGGAATATTAAGGTTCTGTGCCATGTCACTTCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcctttgtttttcattgtttctagttaaaaaaatatgttgttctgacactagGAATGAAAGGACTCTGCTTGATCCGTTGCTCTCTGAGGATGCATTCATCATGCCTTGTAAGGGAATATTAAGGTTCTGTGCCATGTCACTTCCG
                                           ttctgac  putative branch site (score: 17)
                                        ttgttct  CT-rich tract
          tttttcattgtttcta  TA-rich tract