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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgctcttcatacacaacctaacattaatctcttgtttgataaatcaatatactgaatgatacttaagatctctttgataaatatgatggagctgatgctaaaattacccccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAGGTATGTTCCATAGCATTCCAGCACGTA

Basic information

species Zea mays
transcript GRMZM2G152775_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152775_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------gtaagtttgctcttcatacacaacctaacattaatctcttgtttgataaatcaatatactgaatgatacttaagatctctttgataaatatgatggagctgatgctaaaattaccccct-tgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAGGTATGTTCCATAGCATTCCAGCACGTA
                                                           ||| | | || ||  ||  ||||    | | | |  | |  ||   |||  || |  |||    | ||||    || |  ||| |    | |||  |||  |||||||| || ||| |  | |||||||| |||||||| ||||||||||| || ||||||||||||||||| ||||||||| | |||||||||||||||                           
gtaagtttgttcttgtgtaattataatatatctattaatgctctctccttttaagctaagtaggatggcactgaatgaacaataataaacttagatttcattaattaacacagtgaactagtagttactgtgaatat--ttgctgtgcaagat--agcccatgctaaattttccctcgatttgcagAATTCAGCTTGGGCAACCAGCTACTGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG---------------------------

upper sequence: GRMZM2G152775_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 3
gtaagtt-tgctcttcatac--acaacctaacattaatctcttgtttgataaatcaatatactgaatgatacttaagatctctttgataaatatgatggagctgatgctaaaattaccccct-tgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAGGTATGTTCCATAGCATTCCAGCACGTA
||||||| | | ||| |  |  | |     |  || |        || ||| || | | | ||    | ||||  | |  |  |||||    | ||   || | |||||||| || ||| |  | | |||||| |||||||| || ||||||||||| ||||||||||||||||| ||||||||| | |||||||||||||||                           
gtaagttgtccccttgaagcgaataggaagaagttgaatgaactcttcatatat-attgttctactagttactggaaacat--ttgatgtgcaagac--agttcatgctaaattttccctccattttcagAATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG---------------------------
















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|211427386|gb|FK988649.1|FK988649
EST:     ATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCCAC-AACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAG
genomic: ATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCC-ACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAG
EST: gi|89252178|gb|DY623964.1|DY623964
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCACCACAC                         AATCCAGCTTGGGACAACCAGCTACCGTTAAAG
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGG-ACAACCAGCTACCGTTAAAG
EST: gi|211424798|gb|FK988647.1|FK988647
EST:     ATACACAAGTYCATTTCGGATTATGTACGCTATTTCCTCYACCAACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAG
genomic: ATACACAAGT-CATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAG
EST: gi|211419584|gb|FK988617.1|FK988617
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGANAACCAGCTACCGTTTAAGTTGCWGCCAACTTGATTAG
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAG
EST: gi|211422177|gb|FK988623.1|FK988623
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTNAAGTTGCAGCCAACTTGATTAG
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAG
EST: gi|211422175|gb|FK988621.1|FK988621
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTAA
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAA
EST: gi|32826830|gb|CD966508.1|CD966508
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACC
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACC
EST: gi|148946911|gb|EC892193.2|EC892193
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAG
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAG
EST: gi|76925303|gb|DV170371.1|DV170371
EST:     GATACCCAAGTCATTTCGGATTATGTACGCTATTTCCTCC-CCAACACAC                         AATCCAGCTTGGACAAC
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAAC
EST: gi|211419574|gb|FK988607.1|FK988607
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAG
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAG
EST: gi|32808848|gb|CD961082.1|CD961082
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTA
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTA
EST: gi|32826298|gb|CD965976.1|CD965976
EST:     GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC                         AATCCAGCTTGGACAACCAGCTACCGTTA
genomic: GATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTA

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: 316

GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAGGTATGTTCCATAGCATTCCAGCACGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAGGTATGTTCCATAGCATTCCAGCACGTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 195

GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAGGTATGTTCCATAGCATTCCAGCACGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

GCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACACgtaagtttgc ... ccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAGGTATGTTCCATAGCATTCCAGCACGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatctctttgataaatatgatggagctgatgctaaaattacccccttgtgcagAATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAGGTATGTTCCATAGCATTCCAGCACGTA
                               tgctaaa  putative branch site (score: 239)
                                       ttaccccctt  CT-rich tract
        tttgataaatatgat  TA-rich tract