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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaggaggaaagaaaaatgcttctctcttactgaaattaatgtcaagcatgagttgctagctttttgctaaagttttctcctaaataatttgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATG

Basic information

species Zea mays
transcript GRMZM2G149704_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 4
----------caaggaggaaagaaaaatgcttctctcttactgaaattaatgtcaagcatgagttgctagctttttgctaaagttttctcctaaataatttgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATG
            ||     ||   || |||||||        ||  ||||   |||  ||  | | ||  | ||||    || |            |  | ||| |||||||| |||| |||||||||||| |||||||| ||  | ||||| | ||| ||||||||||||||||| | ||| ||  ||||||||||||| || |||
acaccctttctcagacactaaaccaagtgcttcttagggctggattttaaccccaatgatttggtactgacattttctggaaat----------gcacctggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG
















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|78080588|gb|DV509000.1|DV509000
EST:     ATGGATAATACACCGCCAGTGGTAGAACCCCCAGGCAAACCTAAATATAG                         GCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAA
genomic: ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAA
EST: gi|211045637|gb|FL292676.1|FL292676
EST:     ATGGATAATACACCGCCAGTGGTAGAACCYNCAAGCAAACCTAAATATAG                         GCATGACTACTACAACAGTGCCAC
genomic: ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACAGTGCCAC
EST: gi|89757539|gb|DY687098.1|DY687098
EST:     ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAG                         GCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAA
genomic: ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAA
EST: gi|149076474|gb|EE165099.2|EE165099
EST:     ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAG                         GCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAA
genomic: ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAA
EST: gi|29947233|gb|CB816549.1|CB816549
EST:     ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAG                         GCATGACTACTACAACA
genomic: ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACA
EST: gi|149104781|gb|EE290244.2|EE290244
EST:     ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAG                         GCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAA
genomic: ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAA
EST: gi|148975634|gb|EE025764.2|EE025764
EST:     ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAG                         GCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAA
genomic: ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAA
EST: gi|31612314|gb|CD568936.1|CD568936
EST:     ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAG                         GCATGACTACTACAACA
genomic: ATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACA

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: 189

TCGAGGCTCCTGTAGCTGCTACTGTTGAGGACAAGGAGGATGTCGCAAATATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

TCGAGGCTCCTGTAGCTGCTACTGTTGAGGACAAGGAGGATGTCGCAAATATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

TCGAGGCTCCTGTAGCTGCTACTGTTGAGGACAAGGAGGATGTCGCAAATATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 58

TCGAGGCTCCTGTAGCTGCTACTGTTGAGGACAAGGAGGATGTCGCAAATATGGATAATACACCGCCAGTGGTAGAACCCCCAAGCAAACCTAAATATAGgtaattaggg ... tgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatgagttgctagctttttgctaaagttttctcctaaataatttgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATG
                                 tcctaaa  putative branch site (score: 58)
                                    taaataatttgtgat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaggaggaaagaaaaatgcttctctcttactgaaattaatgtcaagcatgagttgctagctttttgctaaagttttctcctaaataatttgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - -aagaaaa
- - - - - - - - -tgcttct
- - - - - - - - - - - - - cttactg
- - - - - - - - - - - - - - - - - - - - - - aagcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgctagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgct