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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtctctctctagctagctagctttggttgcctgttgtgtgacatcaaaagtgacaacgagcagctctttcgacttcccaatcgggactcctcttttcccatttctctgatgcttcatcaaatatatatgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA

Basic information

species Zea mays
transcript GRMZM2G082502_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082502_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g36780.2 (Oryza sativa), 3'ss of exon 10
gttcgtctctctctagctagctagctttggttgcctgttgtgtgacatcaaaagtgacaacgagcagctctttcgacttcccaatcgggactcctcttttcccatttctctgatgcttcatcaaatatatatgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA
                         |||  | || || ||   ||  ||| |  |    ||     | | |   || | |  ||| |  ||||   ||||     ||  | |||  | ||| ||| ||         ||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||||| || |||||||| |||||| | |
----------------------gatttttatcgc-tgctg---gatttcagattttctcact----gttgtcctgaatgctaaattgatactcacatttt-----tttcccgattttgcatgaaaaatg-----gtgcagCTTCTAAAATAGTGTTCACAAATGGCTCTCAAGATCCATGGCGCCATGCCTCGAAACAGAAATCGTCGAAATATA

upper sequence: GRMZM2G082502_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 9
--------gttcgtctctctctagctagctagctttggttgcctgttgtgtgacatcaaaagtgacaacg-agcagc-tctttcgacttcccaatcgggactcctcttttcccatttc-tctgatgcttcatcaaat-atatatgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA
          | | || ||   |  |      |  ||    |   |    | |  | || | |        ||||   |  ||  |||    |      | | ||    |   |  |  | | |||  || |    | ||  |     |||| ||| |||||  | |||||||||||||| ||||| || ||||||||||| |||||||| |  |||||    || |
gtctagaaacttgcctatcctgaatttttatcccctgcccccaactcccttcattttaataatatttttatagcattatggttttactctgtacatactatttcttgaatatgacctgatttcatgtatcctattctgatgaacatggacagGTTCAAAAATAATATTTACAAATGGCTCACAAGATCCTTGGCGCCATGCATCCAAGCAAACTTCATCTCCTGATA
















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|71759256|gb|DR957193.1|DR957193
EST:     TCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTG                         CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCT
genomic: TCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTGgttcgtctct ... atgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCT
EST: gi|91055261|gb|EB165679.1|EB165679
EST:     TCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTG                         CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCT
genomic: TCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTGgttcgtctct ... atgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCT
EST: gi|18180479|gb|BM381689.1|BM381689
EST:     TCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTG                         CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCT
genomic: TCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTGgttcgtctct ... atgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCT
EST: gi|88750785|gb|DY534926.1|DY534926
EST:     TCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTG                         CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCT
genomic: TCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTGgttcgtctct ... atgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCT
EST: gi|8367939|gb|BE050884.1|BE050884
EST:     TCTCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTG                         CTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCT
genomic: TCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTGgttcgtctct ... atgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCT

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: 46 (upstream exon), 48 (downstream exon)
Score: 39

GTACCATTTGGACCTATGCAGACATGTCTTTGGGGAAGGCGTTTATCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTGgttcgtctct ... atgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA


Block sizes: 42 (upstream exon), 46 (downstream exon)
Score: 27

GTACCATTTGGACCTATGCAGACATGTCTTTGGGGAAGGCGTTTATCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTGgttcgtctct ... atgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 30

GTACCATTTGGACCTATGCAGACATGTCTTTGGGGAAGGCGTTTATCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTGgttcgtctct ... atgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 26

GTACCATTTGGACCTATGCAGACATGTCTTTGGGGAAGGCGTTTATCCCGATGTGTTCATGACGAACTTGTATTATGGAGGCACAAGAATCGCTGgttcgtctct ... atgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgggactcctcttttcccatttctctgatgcttcatcaaatatatatgcacacagCTTCTAAAATCGTGTTTACAAATGGCTCCCAAGACCCATGGCGCCATGCCTCCAAGCAGAAATCATCGAAAGACA
                      ctctgat  putative branch site (score: 26)
                               ttcatcaaatatatat  TA-rich tract