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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCGTTGACGACGCGGAGGACGACCAGCTCGCCTCCATGTCCACGGAGGATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGgtgagcgagcccagtcctagatccgatccctgcgggttcggaacttcggcgttagggtttgcttctgatctgtggggtttgtttggtttttctcttgccgcacccaggacgagttgcag

Basic information

species Zea mays
transcript GRMZM2G032505_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 1
GGCCGTTGACGACGCGGAGGACGACCAGCTCGCCTCCATGTCCACGGAGGATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGgtgagcgagcc-cagtcctagatccgatccctgcgggttcggaacttcggcgttagggtttgcttctgatctgtggggtttgtttggtttttctc----ttgccgcacccaggacgagttgcag------------------------------------
|||||| |||||||||||||||||||||||||||||||||||||||||||| ||| |||| ||||||||||| || |||||||||||||| ||||||||||  |||  ||| | |  ||   ||     ||          || |  |  |  |  |   |  ||   |  ||     |  | |   | |||       ||   |   || || ||  |    |                                    
GGCCGTGGACGACGCGGAGGACGACCAGCTCGCCTCCATGTCCACGGAGGACATCGTCCGTGCCTCCCGCCTACTCGACAACGAGATCCGCGTCCTCAAGgcaagcccgcctccgctctctctctctctcccctaaccctagatccccctccctccgaggtttttgccagttgcctcctccggtgaatctttgcttggattagggtttccgggtcgtctgatcggtttggggttttttttggtgtgattttggtgcgcag
















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|149101527|gb|EE187650.2|EE187650
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...
EST: gi|148951330|gb|EC897040.2|EC897040
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...
EST: gi|22473221|gb|BU037701.1|BU037701
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAG                         CGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAA
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGgtgagcgagc ... cgagttgcagCGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAA
EST: gi|149109720|gb|EE293507.2|EE293507
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...
EST: gi|149085416|gb|EE174922.2|EE174922
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...
EST: gi|22473395|gb|BU037875.1|BU037875
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAG                         CGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAA
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGgtgagcgagc ... cgagttgcagCGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAA
EST: gi|211077789|gb|FL088742.1|FL088742
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAG                         CGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAA
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGgtgagcgagc ... cgagttgcagCGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAA
EST: gi|148979721|gb|EE026794.2|EE026794
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...
EST: gi|149096589|gb|EE182348.2|EE182348
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...
EST: gi|74241694|gb|DT649608.1|DT649608
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...
EST: gi|60346168|gb|DN213141.1|DN213141
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...
EST: gi|149062853|gb|EE157572.2|EE157572
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTACAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-----A-AGgtgagcgagc ...
EST: gi|149077127|gb|EE165787.2|EE165787
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...
EST: gi|78179300|gb|DV549673.1|DV549673
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...
EST: gi|211077790|gb|FL088743.1|FL088743
EST:     ATATCATCCGGGMCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAG                         CGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAA
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGgtgagcgagc ... cgagttgcagCGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAA
EST: gi|149100563|gb|EE186648.2|EE186648
EST:     ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGGACGAGTTGCAG              
genomic: ATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCT------C-A-----AGgtgagcgagc ...

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 2 RNA-Seq libraries.


Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 23

GGCCGTTGACGACGCGGAGGACGACCAGCTCGCCTCCATGTCCACGGAGGATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGgtgagcgagc ... cgagttgcagCGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAAGAGAAAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 22

GGCCGTTGACGACGCGGAGGACGACCAGCTCGCCTCCATGTCCACGGAGGATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGgtgagcgagc ... cgagttgcagCGGACGAACCTGGAGTTGGAGTCGTTCAAGGAGAAGATTAAGGAAAACCAAGAGAAAATTAAGCTCAACAAGCAGCTGCCCTACCTCGTTGGCAACATCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCGTTGACGACGCGGAGGACGACCAGCTCGCCTCCATGTCCACGGAGGATATCATCCGGGCCTCCCGCCTTCTTGACAACGAGATCCGTGTCCTCAAGgtgagcgagcccagtcctagatccgatccctgcgggttcggaacttcggcgttagggtttgcttctgatctgtggggtttgtttggtttttctcttgccgcacccaggacgagttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC