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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgtgtgtgctttcattgaactctctctctctctatatatatacatatcttttgcttcaactaaactagatctcttttgattctgtatttggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACAGCAG

Basic information

species Zea mays
transcript GRMZM2G062289_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062289_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g31830.1 (Oryza sativa), 3'ss of exon 2
gttgtgtgtgctttcattgaactctctctctctctatatatatacatatcttt-tgcttcaactaaactagatctcttttgattctgtat------ttggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACAGCAG
           |    | ||| |   |       ||||||  ||| | || ||   ||  || | |     | ||   |   |||| |||      ||   || ||||| || |||||||||||||||||||||||||||||||| ||||||||||||||||
-------aatttcctgtggaaattcatgctgtattatatacttacttgtccttgcactataattgagtagcaccttactcccttctttatgttttgttttcttccagGGCTTAGTTGACATGAACAAGCCTCCTGAAATGATATCCGGCAATATGACAGCAG
















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|211035874|gb|FL217659.1|FL217659
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|211035875|gb|FL217660.1|FL217660
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|211420452|gb|FL472942.1|FL472942
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTGGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|211101991|gb|FL255798.1|FL255798
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|60349122|gb|DN216095.1|DN216095
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|18175649|gb|BM350886.1|BM350886
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|211035871|gb|FL217656.1|FL217656
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|211035870|gb|FL217655.1|FL217655
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|211101993|gb|FL255800.1|FL255800
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|60339491|gb|DN206464.1|DN206464
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|211104465|gb|FL255813.1|FL255813
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGAGCTTCGTCATCACG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|4624432|gb|AI615265.1|AI615265
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|9794648|gb|BE552956.1|BE552956
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCTTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|211035876|gb|FL217661.1|FL217661
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|18162322|gb|BM332161.1|BM332161
EST:     AGACCACCCACTTATGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|211104468|gb|FL255816.1|FL255816
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|14548408|gb|BI096737.1|BI096737
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|211035873|gb|FL217658.1|FL217658
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA
EST: gi|9824845|gb|BE575152.1|BE575152
EST:     AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCG                         GGTTTGGTTGACATGAGCAAGCCTCCTGAAATGATATCTGGCAATATGACA
genomic: AGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACA

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), 47 (downstream exon)
Score: 211

CCCCATGGCGACGGCGCTCAAATCGTTCCTGAACAGCCCCGTCGGCCCCAAGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 601

CCCCATGGCGACGGCGCTCAAATCGTTCCTGAACAGCCCCGTCGGCCCCAAGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 691

CCCCATGGCGACGGCGCTCAAATCGTTCCTGAACAGCCCCGTCGGCCCCAAGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 577

CCCCATGGCGACGGCGCTCAAATCGTTCCTGAACAGCCCCGTCGGCCCCAAGACCACCCACTTCTGGGGCCCTGTCGCCAACTGGGGCTTCGTCATCGCGgtacgcctct ... tggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcttttgcttcaactaaactagatctcttttgattctgtatttggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACAGCAG
                              ttttgatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtgtgtgctttcattgaactctctctctctctatatatatacatatcttttgcttcaactaaactagatctcttttgattctgtatttggtttgcagGGTTTGGTTGACATGAACAAGCCTCCTGAAATGATATCTGGCAATATGACAGCAG

- - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - ttttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactaa