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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactctggacttaaatgttagagtggtagtaggatctgtaatatgtattgagacatctctcctgagtcctgactacttgaacacag

Basic information

species Zea mays
transcript GRMZM2G020002_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020002_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 5'ss of exon 12
CTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactctggact-taaatgttagagt-ggtagtaggatctgtaatatgtattgagacatctctcctgagtcctgacta-cttgaacacag--------------------------------------
|||||||| |||||||| ||||| ||||||||||||||||||||||| || |||||||||||  | |||||||| |||||||| |||||||     | |||  | | ||| | |  || |  |      | | ||| |    ||  ||  |        | || ||  |   ||||| | |                                       
CTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATGgtaatccttgtgggttgtgaatttcaacgttgacaaataagtatataaaagaacttttgattttataaggaattcgtgtttggtttgaataaacccagctaaggcatctctctcttaaacgcttgaccccag

upper sequence: GRMZM2G020002_T03 (Zea mays), 5'ss of exon 9
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 5'ss of exon 9
CTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactctggacttaaatgttagagtggtagtaggatctgtaatatgtattgagacat---ctctcctgagtcctgactacttgaacacag
|||||||| |||||||||||||| ||||| || ||||| |||||| | ||   ||||||||| || |  || || |||||||| |||||||    ||   ||||| | || |    || |                  |  | |    |     ||  |||  | || | |  ||   |   
CTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATGgtaatagct---gacttgactggtttcttgctttctctgctcactgcccctgctaacctgtaaatacttttgaa-cttgtccatatgtttag--

upper sequence: GRMZM2G020002_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 5'ss of exon 9
CTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtaggg------actctggacttaaatgttagagtggt-agtaggatctgtaatatgtattgagaca---tctctcctgagtcctgactacttgaacacag---------------------
|||||||| |||||||| ||  | ||||| ||||||||||||||||||||   ||||||||| || || ||||| |||||||| |||||||         |   |   |    || || | |  || | |      |    ||  |||  ||      ||  |  |  || || | | |||  |                          
CTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATGgtaatacaagttatcatcaccactgatatttgggaagtcaattattatttccctagttatcaagttggtctcatttttccgttctaatt-cttatatttgttgcaatcctgggaacaattag

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|74240936|gb|DT648850.1|DT648850
EST:     GATGATTTTCGGAAGATTCCCAATGGTGTAAATG                         GTC-TGAGGGAACGGATGCATATACTTTGGGACAGCATGGTG
genomic: GATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGA-GGAACGGATGCATATACTTTGGGACAGCATGGTG
EST: gi|28187829|gb|CB179439.1|CB179439
EST:     GAAGATTCCCAATGGTGTAAATG                         GTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG
genomic: GAAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG
EST: gi|78079711|gb|DV508123.1|DV508123
EST:     AAGATTCCCAATGGTGTAAATG                         GTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG
genomic: AAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG
EST: gi|113703820|gb|EE681324.1|EE681324
EST:     GAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATG                         GTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG
genomic: GAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG
EST: gi|148929734|gb|EC876616.2|EC876616
EST:     TCCCAATGGTGTAAATG                         GTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG
genomic: TCCCAATGGTGTAAATGgtagggactc ... ttgaacacagGTCTTGAGGAACGGATGCATATACTTTGGGACAGCATGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactctggacttaaatgttagagtggtagtaggatctgtaatatgtattgagacatctctcctgagtcctgactacttgaacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA