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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtaacattgatcttgcagtgctgtgaagcccttgagaactgaattgcagctgttattgtaactctggattttctctcttactctctttgtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATGATATTGGCAAGGTTGCACATGTATGACTGGATAATACTTCTCCTCCTTG

Basic information

species Zea mays
transcript GRMZM2G050658_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050658_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g13870.4 (Oryza sativa), 3'ss of exon 1
tagtaacattgatcttgcagt-gctgtgaagcccttgagaactgaattgcagctgttattgtaact-ctggattttctctcttactctctttgtt-tttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATGATATTGGCAAGGTTGCACATGTATGACTGGATAATACTTCTCCTCCTTG
   |   |||  | ||  ||| ||  || | ||       |  || |||    | | | | ||  | ||   ||| || ||||  | | |||||| |||| |||| |||||||||||    ||||| | ||||||||| |  ||||||||||  | | |||| ||  | |||||||| ||||||||||||||||| |||||||
---ttttatttttattatagttgcattgtatccacattacatggagttgttattataactctagttactcactttgctttcttgttatgtttgttatttgaagGACACAATGGCAGATGTCTTAGGATGTTACACTATAAAGTCCCATGGAACCAAAGTGGCGAGACTTCACATGTACGACTGGATAATACTTCTACTCCTTG
















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|93013961|gb|EB639481.1|EB639481
EST:     CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
genomic: CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
EST: gi|148968163|gb|EE019452.2|EE019452
EST:     CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
genomic: CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
EST: gi|149072274|gb|EE160530.2|EE160530
EST:     CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
genomic: CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
EST: gi|211132095|gb|FL293579.1|FL293579
EST:     CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
genomic: CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
EST: gi|149074580|gb|EE162983.2|EE162983
EST:     CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
genomic: CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
EST: gi|211132097|gb|FL293581.1|FL293581
EST:     CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
genomic: CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
EST: gi|76923126|gb|DV169343.1|DV169343
EST:     CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
genomic: CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
EST: gi|148997626|gb|EE035845.2|EE035845
EST:     CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACC                         GAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG
genomic: CACCGATCCGTAGCGGCGATATCGTAGAGCCGCTGGTCTCACGCCGCACCgtgagttctt ... gtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcagctgttattgtaactctggattttctctcttactctctttgtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATGATATTGGCAAGGTTGCACATGTATGACTGGATAATACTTCTCCTCCTTG
                         ttttctctcttactct  CT-rich tract
         ttattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtaacattgatcttgcagtgctgtgaagcccttgagaactgaattgcagctgttattgtaactctggattttctctcttactctctttgtttttgtagGAGACAATGGCAGACCAGTTAGGGTCTTACACTATTAGATCCCATGGAATGATATTGGCAAGGTTGCACATGTATGACTGGATAATACTTCTCCTCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC