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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttaattcgtgttcacgacatacaaaagggtgcctgtccatctaaagggaaactaactgatgctgcaagcgatatttttcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTTCATCGGTTTGGAAGTTAATCACATCGATGAAAGGAACATGTGCTGTGGA

Basic information

species Zea mays
transcript GRMZM2G070708_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070708_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 9
gtatgtttaattcgtgttcacgacatacaaaagggtgcctgtccatctaaagggaaactaactgatgctgcaagcgatatttt-tcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTTCATCGGTTTGGAAGTTAATCACATCGATGAAAGGAACATGTGCTGTGGA
||||||||  |  |    || | ||| |||||         ||| | | |  | |||   ||| ||| | | |  ||| |||| ||||||||||||| |||||||  || |||||||| || || ||||| || ||||| || ||||| ||||| ||||| ||||||||||| ||||||||||| || 
gtatgtttcctatgc---catgccatgcaaaa---------tccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTTTATTGGTTTAGAAGTGAATCATATCGATGAAAGAAACATGTGCTGCGGG

upper sequence: GRMZM2G070708_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv18s0001g04150.t01 (Vitis vinifera), 3'ss of exon 9
----------gtatgtttaattcgtgttcacgacatacaaaagggtgcctgtccatctaaagggaaactaactgatgctgcaagcg-atattttt----cagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTTCATCGGTTTGGAAGTTAATCACATCGATGAAAGGAACATGTGCTGTGGA
          | | |  | ||   || | | | | | || |        | | | | |    |  |  |   | | |||    | |  |||| |     |||||| || ||||||||||| || || ||||| ||||| ||||| |||||||| |||||| | |||||| | ||||| |||||| | || ||||||||||| 
taacccggaggaaagcctgat--atggtgaagtcttccacattaaataatcttcttttttctgagacatggttaaagctctgggggtgtattgtgaatgcagGCCCATATTGCACAAATATGCCAATGAAGATGTGTCTCTTGGTTCGTGGTTTATCGGTCTTGAAGTTGAGCACATTGATGAACGCAATATGTGCTGTGGG
















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|32823095|gb|CD962817.1|CD962817
EST:     GATCTGGCGACTTATATCTCAATCAATCG                         GCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGACCGTGGTT
genomic: GATCTGGCGACTTATATCTCAATCAATCGgtatgtttaa ... tatttttcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTT
EST: gi|211239910|gb|FL238805.1|FL238805
EST:     CAGATATATGCCATTTCGAAAGATCTGGCGACTTATATCTCAATCAATCG                         GCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTGGCGACTTATATCTCAATCAATCGgtatgtttaa ... tatttttcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTT
EST: gi|32792940|gb|CD945176.1|CD945176
EST:     GATCTGGCGACTTATATCTCAATCAATCG                         GCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTT
genomic: GATCTGGCGACTTATATCTCAATCAATCGgtatgtttaa ... tatttttcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTT
EST: gi|32839092|gb|CD978773.1|CD978773
EST:     CAGATATATGCCATTTCGAAAGATCTGGCGACTTATATCTCAATCAATCG                         GCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTT
genomic: CAGATATATGCCATTTCGAAAGATCTGGCGACTTATATCTCAATCAATCGgtatgtttaa ... tatttttcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTT
EST: gi|211169871|gb|FL077600.1|FL077600
EST:     CAGATATATGCCATTTCGAAAGATCTGGCGACTTATATCTCAATCAATCG                         GCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGGATCGTGGT
genomic: CAGATATATGCCATTTCGAAAGATCTGGCGACTTATATCTCAATCAATCGgtatgtttaa ... tatttttcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGG-ATCGTGGT
EST: gi|32790616|gb|CD942852.1|CD942852
EST:     GATCCGGCGACTTATATCTCAATCAATCG                         GCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTT
genomic: GATCTGGCGACTTATATCTCAATCAATCGgtatgtttaa ... tatttttcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtgcctgtccatctaaagggaaactaactgatgctgcaagcgatatttttcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTTCATCGGTTTGGAAGTTAATCACATCGATGAAAGGAACATGTGCTGTGGA
                                             tatttttc  CT-rich tract
                                            atatttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttaattcgtgttcacgacatacaaaagggtgcctgtccatctaaagggaaactaactgatgctgcaagcgatatttttcagGCCTATCTTGCACAAATACGCAAACGAAGACGTGTCGCTTGGATCGTGGTTCATCGGTTTGGAAGTTAATCACATCGATGAAAGGAACATGTGCTGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA