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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattgtttttagtcctcgattgtatcgtttgctagctactacagttggataacaaaatctttcctttgatcctttcgttttcgagtgaaattgtgcataatattttgttattaatgtaatgcttctgtaaccttttgttattatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAATCCACATCTTTTCTAAGATACGGGCATTTATCACGTGACAATGTAGCCC

Basic information

species Zea mays
transcript GRMZM2G014136_T01
intron # 12
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|78122591|gb|DV540975.1|DV540975
EST:     TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAG                         GAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
genomic: TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
EST: gi|31356814|gb|CD441171.1|CD441171
EST:     TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAG                         GAGGTACTGGGCTTGCTGAGATCTCTATATGTTATGGTGAACATAGATGAA
genomic: TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
EST: gi|78118416|gb|DV536802.1|DV536802
EST:     TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAG                         GAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
genomic: TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
EST: gi|24766737|gb|CA401884.1|CA401884
EST:     TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAG                         GAGGTACTGGGCTTGCTGAGATCTCTATATGTTATGGTGAACATAGATGAA
genomic: TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
EST: gi|5739931|gb|AI947621.1|AI947621
EST:     TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAG                         GAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
genomic: TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
EST: gi|211243697|gb|FL432248.1|FL432248
EST:     TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAG                         GAGGTACTGGGCTTGCTGAGATCACTATATGTTATGGTGAACATAGATGAA
genomic: TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
EST: gi|24768503|gb|CA403632.1|CA403632
EST:     AATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAG                         GAGGTCCTGGGCTTGCTGAGATCTCTATATGTTATGGTGAACATAGATGAA
genomic: AATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
EST: gi|78022584|gb|DV490971.1|DV490971
EST:     TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAG                         GAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA
genomic: TCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 34

TTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATCCTCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAATCCACATCTTTTCTAAGATACGGGCATTTATCACGTGACAATGTAGCCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 104

TTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATCCTCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAATCCACATCTTTTCTAAGATACGGGCATTTATCACGTGACAATGTAGCCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

TTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATCCTCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAATCCACATCTTTTCTAAGATACGGGCATTTATCACGTGACAATGTAGCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

TTATCAAGTTGCTGAAGACTTGGCTAGAGCGTTTACTGAGCGTACGATCCTCCAAATATTTTTGGAGGATGAGATGAATGTTCCTTCTGGTTCCCTAAAGgtatattgtt ... ttatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAATCCACATCTTTTCTAAGATACGGGCATTTATCACGTGACAATGTAGCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataatattttgttattaatgtaatgcttctgtaaccttttgttattatttccagGAGGTACTGGGCTTGCTGAGATCTCTATATGTCATGGTGAACATAGATGAATCCACATCTTTTCTAAGATACGGGCATTTATCACGTGACAATGTAGCCC
                                             ttatttcc  CT-rich tract
     tattttgttattaatg  TA-rich tract