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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggacaaacccagaagtagctattattttgggatgtaggtagtacttgataatgtttgttgtgtatggaaaaaagttctaacatatccctgtgtgattagCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA

Basic information

species Zea mays
transcript GRMZM2G107101_T05
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 8
---aggacaaacccagaagtagctattat-tttgggatgtaggtagtacttgataatgtttgttgtgtatggaaaaaagttctaacatatccctgtgtgatt-agCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA
          |       |   |  |||| |||    || |  | | |  || ||||| || || |  |    | ||  | ||||||| | | || || ||| ||||| ||||||||||||||||||||||||||| |||||||| ||||| |||||||||||||||||||||||||||||||||||| ||||||||||||||||
gtttttctgcattggagtgggacctttatctttttcttgcaactcgga--tgctaatgcttattataaac---acaagttactaacatgtgcttgggtcattcagCTTACAGCCGAGGATCTGGGAAGCACCCACAACTTATGCCATCCACGCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATACTAAGTGTCTGTGATGA

upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 7
aggacaaacccagaagtagctattattttgggatgtaggtagtacttgataatgtttgttgtgtatggaaaaaagttctaaca---tatccctgtgtga------------ttagCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA
                |  | |||     |   | ||   ||   || || || ||  || |  |  || || | || ||| |   | | | |   |||            |||| ||     || || ||||||||||| || || ||  |||| || || || |||||||| ||||| ||||| ||||| |||||||||||||| ||||||||
---------------ttttccattgaacagcagtataaaaaggcattaatcattttgattctcgaaagacaagatttataataatcttttcttaactgaatttgtttttctttagTTTCTGCTCGCGGTTCTGGGAAGCATCCTCAACTCGTGCCATCAACTCCAAGATGGGCAGTTGCTAATGGTGCTGGTGTTATATTAAGTGTTTGTGATGA

upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 7
aggacaaacccagaagtagctattattttgggatgtaggtagtacttgataatgtttgttgtgt---atggaaaaaagttctaacatatccctgtgtgattagCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA
   |  || | ||||     | || |  |   || | |  | || | | | ||||| |   | |   | |||||  | || |    | |   | |    |||||||    ||| || ||||||||||| || || ||| ||||||| || || |||||||||||||||||||| ||||| |||||||||||||| ||||||||
--tattaaacaagaatatcattttttactatcatattgacactaat-gtttatgttcgaaatatgataaggaaatgacttttttttttttttttttaccttagCTTCTTCCCGTGGTTCTGGGAAGCATCCTCAACTTGTGCCTTCAACTCCAAGATGGGCTGTTGCCAATGGTGCTGGTGTTATATTAAGTGTTTGTGATGA

upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 8
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------------------------aggacaaacccaga-agtag--ctattattttg-------ggatgtaggtagtacttgataatgtttgttgtgtatggaaaaaagttctaacatatccctgtgtgattagCTTG-CAGC----CGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA---
                                                   |   |  | | | | ||| |  |||| | || |          ||||   |  || ||    | |    ||||| | ||      | |||  |  | | |||     ||  ||| ||||    ||||||||||| || || || || || |||||||| ||||| |||||||||||||| ||||||||||| || ||| | ||||| ||||||||   
gtgagttcaagaattccatgttaatatcccctggaactggattttgatgataattctgatcaatagagttgttctatcacttcgttcataaatgtgtatccatcacctgtggctatagaatgtgttttgagttgcttcctataactttcatgttgtcctactttggcagCTTCTCGAGGATCTGGTAAACATCCTCAACTGATGCCTTCAACCCCAAGATGGGCTGTTGCTAATGGAGCTGGTGTCATACTGAGTGTTTGTGATGATGA

upper sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 8
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 8
aggacaaacccagaagtagctattattttgggatgtaggtagtacttgataa---tgtttgttgtgtatggaaaaaagttc-----taacatatccctgtgtgatt--agCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA
          | |  ||  ||  |||||        |  ||||| ||  |||     ||| | ||   ||||| || || |     |||   |   ||   |  |   |||||  |  || |||||||| |||||||| ||||| || || || || || || ||||||||||| ||||| || || || ||||||||||| ||||||||
---------tctgttgtgtcttatatttgctttctaaactagtattttgtaaaagcatttctagt-cctggaacaaggtccatttttaatcaacttcttctttctccaagCTTCTACTCGTGGATCTGGAAAGCACCCCCAGCTCATTCCATCAACTCCAAGGTGGGCTGTTGCTAATGGTGCAGGTGTGATATTAAGTGTTTGTGATGA

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|19057921|gb|BM736588.1|BM736588
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgtcggtaaaa ... gtgtgattagCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCA
EST: gi|89106449|gb|DY576666.1|DY576666
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgtcggtaaaa ... gtgtgattagCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCA
EST: gi|18963999|gb|BM660750.1|BM660750
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgtcggtaaaa ... gtgtgattagCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCA
EST: gi|18963998|gb|BM660749.1|BM660749
EST:     TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTG                         CTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCA
genomic: TGTAATGGGAAAATATGCTGCTGGTGGAGAGTTGAAGCCTCCAACTACTGgtcggtaaaa ... gtgtgattagCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgataatgtttgttgtgtatggaaaaaagttctaacatatccctgtgtgattagCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA
                              ttctaac  putative branch site (score: 1)
                                        tccctgt  putative PPT
                       aaaaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggacaaacccagaagtagctattattttgggatgtaggtagtacttgataatgtttgttgtgtatggaaaaaagttctaacatatccctgtgtgattagCTTGCAGCCGAGGATCTGGGAAGCACCCACAGCTTATGCCTTCCACCCCCAGATGGGCTGTTGCCAATGGAGCTGGAGTTATATTAAGTGTCTGTGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA