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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagttcttctattgtcacaaatatctacttataatgtggctaggtattaattcatcacttatatttttgcaggag

Basic information

species Zea mays
transcript GRMZM2G109383_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 9
TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagt--tcttctattgtcacaaatatctacttataatgtggctaggtattaattcatcacttatatttttgcaggag
||||||||| |||||||||||||| ||  |||| || | || |||||||||||||||||||||||||| |||||||||| ||||||| ||||| ||||| |||||  ||  ||||||||  |||||| | |  |  || ||| | | | ||| || |||| | |||| ||||||| |||   
TTATGATGCTCTCCATGGTGTTGCTGGGACTTACGCAACACGCATCTTTGTGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgttttcttctatcatcacaatt-tgaaaatagaatttagattggtgttcattctttacttgtatttttacag---

upper sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 10
TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgt-----------aatgagttcttctat---tgtcacaaa--tatctactt--ataatgtggctaggtattaat---tcatcacttatatttttgcaggag-------------
|||||||||||| ||||| ||||  ||||||||||| || |  || ||||| ||||||||||||||  | ||||||||| || |||| || || || || ||            |||   | ||   |   |||   |||  |||| |  |  ||||| |    |  ||  |||   |  | | || | ||||||   ||              
TTATGATGCACTGCATGGAGTTGGTGGAGCTTATGCAAAGCGAATATTTGTTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacag
















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|67018536|gb|CO447285.1|CO447285
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAGA                        
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|67018536|gb|CO447285.1|CO447285
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAGA                        
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|31363628|gb|CD447985.1|CD447985
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAGA                        
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|31363628|gb|CD447985.1|CD447985
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAGA                        
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|67025909|gb|CO454658.1|CO454658
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... tttgcaggagGA---CTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|31353391|gb|CD437748.1|CD437748
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAGA                        
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|31353391|gb|CD437748.1|CD437748
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAGA                        
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|32910896|gb|CF015708.1|CF015708
EST:     GAATTGTGTCCCGAAAGA                        
genomic: GAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|32910896|gb|CF015708.1|CF015708
EST:     GAATTGTGTCCCGAAAGA                        
genomic: GAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|67022599|gb|CO451348.1|CO451348
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAGA                        
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|67022599|gb|CO451348.1|CO451348
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAGA                        
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|60351436|gb|DN218409.1|DN218409
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTAT
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... tttgcaggagGA---CTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTAT
EST: gi|67041650|gb|CO467905.1|CO467905
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAA                         GAAGACTTTGGANGTGGTCATCCGGATCCTAAC-TTACCTATGCAAAAGAG
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... tttgcaggagGA---CTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAG
EST: gi|31354675|gb|CD439032.1|CD439032
EST:     GAATTGTGTCCCGAAAGA                        
genomic: GAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|31354675|gb|CD439032.1|CD439032
EST:     GAATTGTGTCCCGAAAGA                        
genomic: GAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|211541124|gb|FL006425.1|FL006425
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAGA                        
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga
EST: gi|211541124|gb|FL006425.1|FL006425
EST:     TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAGA                        
genomic: TGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCG-AA-Agtaatgagtt ... tttgcagga

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 9

TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagtt ... tttgcaggagGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGATGCACTCCATGGTGTTGCGGGAGCTTATGCCAAACACATCTTTGTGGAAGAGCTTGGTGCTGATGAAAGCTCACTGTTGAATTGTGTCCCGAAAgtaatgagttcttctattgtcacaaatatctacttataatgtggctaggtattaattcatcacttatatttttgcaggag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA