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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCGGTGCACATACCGAGCATATGATGCCATGGATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtggtgcactcaaactctaagttgaatccgtgttacataaggaaaaattctgattttttgatacatgaaacatactgtttgtagtcatggcatc...

Basic information

species Zea mays
transcript GRMZM2G133749_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133749_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT4G21520.1 (Arabidopsis thaliana), 5'ss of exon 6
CTCCGGTGCACATACCGAGCATATGATGCCATGGATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtggtgcactcaaactctaagttgaatccgtgttac-ataaggaaaaattctgattttttgatacatgaaacatactgtttgtagtcatggcatc--
|| || ||||||||||| || |||||||| ||||||||||||||||||||| ||||  ||   |||||| ||   ||| | ||||| |        |||  |  ||||||||| |||| | || | | | || |||    |||||    |     |         ||  ||| || ||| | |   
CTTCGATGCACATACCGGGCCTATGATGCTATGGATGAAATAACTGCTGCATTTTCAGTTGGATTCAATCCTGATGGAACCAAgtaagcaaaa---acttca--tctaagttgtatccatcttcccacacggtaaagaattgattaaaagtggtctatgttcatttgcctgt-gttatgtctttag
















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|78120250|gb|DV538634.1|DV538634
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
EST: gi|78110507|gb|DV528917.1|DV528917
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
EST: gi|71437477|gb|DR818527.1|DR818527
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
EST: gi|71449230|gb|DR830280.1|DR830280
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
EST: gi|31558468|gb|CD527680.1|CD527680
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTATAAGA
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGA
EST: gi|76287082|gb|DV026650.1|DV026650
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
EST: gi|60394554|gb|DN227424.1|DN227424
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
EST: gi|211132517|gb|FL346748.1|FL346748
EST:     GAAATACCTGCTGCACCTTTCGATTTCTTTCATTTTCT-CAGGGATCTAA                         GCTATTTGCTGGGATACA-CAAAGCT
genomic: GAAATAACTGCTGCAC-TTTCGATTTCTTTCAATT-CTTCAGG-ATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGG-ATACAACAAAGCT
EST: gi|37418378|gb|CF646857.1|CF646857
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
EST: gi|78084101|gb|DV512494.1|DV512494
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
EST: gi|94478312|gb|EB707270.1|EB707270
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCATTTCTTCCGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTA
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTA
EST: gi|78112774|gb|DV531168.1|DV531168
EST:     GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAA                         GCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC
genomic: GATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCC

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: 97

CTCCGGTGCACATACCGAGCATATGATGCCATGGATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCCTGGCAGAGACTTTGATCAGTATTCTTTACTCAAGGGGGGTGAAGGACCA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 37

CTCCGGTGCACATACCGAGCATATGATGCCATGGATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCCTGGCAGAGACTTTGATCAGTATTCTTTACTCAAGGGGGGTGAAGGACCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 39

CTCCGGTGCACATACCGAGCATATGATGCCATGGATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCCTGGCAGAGACTTTGATCAGTATTCTTTACTCAAGGGGGGTGAAGGACCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 49

CTCCGGTGCACATACCGAGCATATGATGCCATGGATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtgg ... tattttacagGCTATTTGCTGGATACAACAAAGCTATAAGAGTGTTTGATGTTCATCGGCCTGGCAGAGACTTTGATCAGTATTCTTTACTCAAGGGGGGTGAAGGACCA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCGGTGCACATACCGAGCATATGATGCCATGGATGAAATAACTGCTGCACTTTCGATTTCTTTCAATTCTTCAGGATCTAAgtatgtgtggtgcactcaaactctaagttgaatccgtgttacataaggaaaaattctgattttttgatacatgaaacatactgtttgtagtcatggcatc

- - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaaaa