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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctcccagccataccatgctcatcatagaatgttttacggttcattgattctgctaaggatttacggtcctggtattcctcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCTTGTCGTGACAAATGTAGTCTGGTCGACTCCACGTGGGATATAATGGTTT

Basic information

species Zea mays
transcript GRMZM2G088231_T01
intron # 10
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|110218295|gb|EC900193.1|EC900193
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTTTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|32929829|gb|CF034641.1|CF034641
EST:     CAAGGTGGCAACCCTCCTGGTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCAAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|78024492|gb|DV492879.1|DV492879
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|76021459|gb|DT948629.1|DT948629
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|16927525|gb|BM080594.1|BM080594
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|30032078|gb|CB833929.1|CB833929
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|32929709|gb|CF034521.1|CF034521
EST:     TGAACTTCAACTGATACAG                         TCTTTGATCAAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: TGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|28361707|gb|CB240063.1|CB240063
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCA
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCA
EST: gi|31664556|gb|CD573489.1|CD573489
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|213169775|gb|FM181432.1|FM181432
EST:     CAAGGTGGCAACCCTCCTGGTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCAAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|67039173|gb|CO465428.1|CO465428
EST:     CAAGGTGGCAACCCTCCTGGTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCAAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|32945536|gb|CF050355.1|CF050355
EST:     CAAGGTGGCAACCCTCCTGGTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCAAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|60397532|gb|DN230348.1|DN230348
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|149105350|gb|EE290850.2|EE290850
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|213172822|gb|FM192591.1|FM192591
EST:     CAAGGTGGCAACCCTCCTGGTGCTGGTGGTCTGAGCTTCAACTGATACAG                         TCTTTGATCAAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|33095867|gb|CF055861.1|CF055861
EST:     CAAGGTGGCAACCCTCCTGGTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCAAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|60346081|gb|DN213054.1|DN213054
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
EST: gi|28422583|gb|CB251938.1|CB251938
EST:     CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAG                         TCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT
genomic: CAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCT

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: 301

ACGCAATGGCTACTGCCGGGGAAGCTGCTCCTGCTGTTTTTGACTTTAACCAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCTTGTCGTGACAAATGTAGTCTGGTCGACTCCACGTGGGATATAATGGTTT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 112

ACGCAATGGCTACTGCCGGGGAAGCTGCTCCTGCTGTTTTTGACTTTAACCAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCTTGTCGTGACAAATGTAGTCTGGTCGACTCCACGTGGGATATAATGGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

ACGCAATGGCTACTGCCGGGGAAGCTGCTCCTGCTGTTTTTGACTTTAACCAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCTTGTCGTGACAAATGTAGTCTGGTCGACTCCACGTGGGATATAATGGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

ACGCAATGGCTACTGCCGGGGAAGCTGCTCCTGCTGTTTTTGACTTTAACCAAGGTGGCAACCCTCCTGCTGCTGGTGGTCTGAACTTCAACTGATACAGgttctcccag ... tcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCTTGTCGTGACAAATGTAGTCTGGTCGACTCCACGTGGGATATAATGGTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacggttcattgattctgctaaggatttacggtcctggtattcctcttttgcagTCTTTGATCGAAAGGGTGTTAATTCCCTCAGTGATGGGCTTGGCATTGGCTTGTCGTGACAAATGTAGTCTGGTCGACTCCACGTGGGATATAATGGTTT
        cattgat  putative branch site (score: 138)
                                       tattcctcttttgc  putative PPT
         attgatt  TA-rich tract