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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgcattataaggtttacctttattatagtatttatttatatcctcatcttagtttgttccctgcagatatttggctgaaaaggccaatgctatctggatataccttcattatgatccctatacaaaacataactacagctaggttgtctaatttttgttttattttgtttgtttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATTTCTTGATAAGGCTAAAGATATTACAGATCGACTCTTACCTGCTTGGGAT

Basic information

species Zea mays
transcript GRMZM2G130889_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 5
gttgcattataaggtttacctttattatagtatttatttatatcctcatcttagtttgttccctgcagatatttggctgaaaaggccaatgctatctggatataccttcattatgatccctatacaaaacataactacagctaggttgtct--aatttttgttttattttgtttgtttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATTTCTTGATAAGGCTAAAGATATTACAGATCGACTCTTACCTGCTTGGGAT
||||| |||||||||||||  || || |||||||| |||         |||||             | ||||||| ||     |  | ||||||| | |  | |||  ||||        | || || | | || || | |||| || |    | ||| |||||||||||       ||| ||||| ||||||||||| || || ||| |||| |||||||||||||| |||||||||||||| ||||| ||||||||||| || || ||  ||||||||||||||
gttgccttataaggtttactattgttgtagtattttttt---------tctta-------------aaatatttgacttctttgatcgatgctatgtaggcagacca-catt-------ttttagaacataaaagtatatctagttttttctaagtttctgttttatttt-------tatattcagAGTTGTTGGAGGCCTCCTCAGTGCATATGATCTATCTGGTGACAAAGTATTTCTTGAGAAGGCCAAAGATATTACTGACCGTCTACTACCTGCTTGGGAT
















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|148937008|gb|EC881178.2|EC881178
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
EST: gi|148934064|gb|EC878076.2|EC878076
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTTTT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
EST: gi|149108157|gb|EE292504.2|EE292504
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
EST: gi|211506494|gb|FL158303.1|FL158303
EST:     AGACTTTGACAAGGGATTATGATGCGAGTGTTTTTGAA-CGACCCATAGG                         GGTTGTTGGAGGTCTGC
genomic: AGACTTTGACAAGG-ATTATGATGCGAGTGTTTTTGAAACGACC-ATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGC
EST: gi|32929134|gb|CF033946.1|CF033946
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
EST: gi|148930753|gb|EC873061.2|EC873061
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
EST: gi|19058210|gb|BM736877.1|BM736877
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCA
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCA
EST: gi|18964229|gb|BM660885.1|BM660885
EST:     TTAGACTTTGACA-GGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATAC
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATAC
EST: gi|20300875|gb|BQ163818.1|BQ163818
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATAC
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATAC
EST: gi|32929269|gb|CF034081.1|CF034081
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
EST: gi|13178345|gb|BG349603.1|BG349603
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
EST: gi|149073799|gb|EE162117.2|EE162117
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGCTCATACGATCTATCT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCT
EST: gi|87151942|gb|DY396731.1|DY396731
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATAC
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATAC
EST: gi|78112348|gb|DV530742.1|DV530742
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACG
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACG
EST: gi|61119084|gb|DN560045.1|DN560045
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTGCATACGATCTAGCTGGTGATAAAGTATT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
EST: gi|20300848|gb|BQ163791.1|BQ163791
EST:     TTAGACTTTG-CAAGGATTATGATGCGAGTGTTTTTGAA-CGACCATAAG                         GGTTGTTGGAGGTCTGC
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGC
EST: gi|32928842|gb|CF033654.1|CF033654
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
EST: gi|60342116|gb|DN209089.1|DN209089
EST:     AACGA-CATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
genomic: AACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
EST: gi|87153018|gb|DY397807.1|DY397807
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATAC
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATAC
EST: gi|22490422|gb|BU050345.1|BU050345
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATAC
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATAC
EST: gi|32929345|gb|CF034157.1|CF034157
EST:     TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAG                         GGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT
genomic: TTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATT

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: 178

CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATTTCTTGATAAGGCTAAAGATATTACAGATCGACTCTTACCTGCTTGGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATTTCTTGATAAGGCTAAAGATATTACAGATCGACTCTTACCTGCTTGGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 243

CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATTTCTTGATAAGGCTAAAGATATTACAGATCGACTCTTACCTGCTTGGGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 285

CTGGGTGGCGGAGTCATTAGACTTTGACAAGGATTATGATGCGAGTGTTTTTGAAACGACCATAAGgttgcattat ... ttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATTTCTTGATAAGGCTAAAGATATTACAGATCGACTCTTACCTGCTTGGGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataactacagctaggttgtctaatttttgttttattttgtttgtttatcttcagGGTTGTTGGAGGTCTGCTTAGTTCATACGATCTATCTGGTGATAAAGTATTTCTTGATAAGGCTAAAGATATTACAGATCGACTCTTACCTGCTTGGGAT
                  gtctaat  putative branch site (score: 285)
                                            tttatcttc  putative PPT
                     taatttttgttttatt  TA-rich tract