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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaaaactacttccatccgcgcatgctgtgttcagagtttcgtcatgctttctgcctccaccatacatgttcagagtttcagaccaacgcgcgcgtgcatgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG

Basic information

species Zea mays
transcript GRMZM2G133844_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133844_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g72950.1 (Oryza sativa), 3'ss of exon 4
gtaatgaaaactacttccatccgcgcatgctgtgttcagagtttcgtcatgctttctgcctccaccatacatgttcagagtttcagaccaacgcgcgcgtgcatgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG
                              || ||     |   | ||||   |||||  |  |   |  |  ||  || ||    | |  |   |   ||  || |   |||||||||||||| || ||||| || |||||||||||||| ||||| |||||||||||||||
-----------------------------gtgagtcacctgccacttcatttcttctgtat--attttgtagatttggacttctgaatct-cattcatatgtttgga---cagATCGCTTGGGTTGGAATCCCAACTCCACCGGCATGGCTGCCAACTTACATGCTCATCAAG
















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|32842437|gb|CD982118.1|CD982118
EST:     CGGCCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: CGG-CGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|14529225|gb|BI096358.1|BI096358
EST:     CGGCGAGGTCTTGGATATCAGGAACTTCGAAGCAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: CGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|32842438|gb|CD982119.1|CD982119
EST:     CTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: CTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|32842276|gb|CD981957.1|CD981957
EST:     CTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: CTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|12971656|gb|BG267591.1|BG267591
EST:     CCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|37380814|gb|CF627243.1|CF627243
EST:     GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|18179821|gb|BM381031.1|BM381031
EST:     GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|37378226|gb|CF625789.1|CF625789
EST:     GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|16379515|gb|BI992998.1|BI992998
EST:     GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|28982421|gb|BQ539420.2|BQ539420
EST:     GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|13490470|gb|BG517234.1|BG517234
EST:     GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|4646657|gb|AI491495.2|AI491495
EST:     GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCNCCGGCATGGCTACCAACCTACATG
genomic: GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|13557973|gb|BG549329.1|BG549329
EST:     CTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: CTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
EST: gi|40334773|gb|CK368843.1|CK368843
EST:     GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTG                         ATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG
genomic: GCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATG

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: 41 (upstream exon), 49 (downstream exon)
Score: 11

AGTGGGACACCCGCCCTTCTACAAGGGGCTGGACTACATATACCAAGACCGCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 180

AGTGGGACACCCGCCCTTCTACAAGGGGCTGGACTACATATACCAAGACCGCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 27

AGTGGGACACCCGCCCTTCTACAAGGGGCTGGACTACATATACCAAGACCGCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 45

AGTGGGACACCCGCCCTTCTACAAGGGGCTGGACTACATATACCAAGACCGCGGCGAGGTCTTGGATATCAGGAACTTCGAAACAGGAGAATACGCCCTGgtaatgaaaa ... tgcatttcagATCGCTTGGGTGGGGATCCCGACGCCACCGGCATGGCTACCAACCTACATGCTCATCAAG