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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcaggctttcttaccttggtactgcacatcacgcgagtaccttcctccatgcatattcactcactcggatgtctatctgctgctggtttccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATTCAACAACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGCCATCGAAGG

Basic information

species Zea mays
transcript GRMZM2G168506_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168506_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g27340.2 (Oryza sativa), 3'ss of exon 6
--agcaggc--tttcttaccttggtactgcacatcacgcgagtaccttcctccatgcatattcactcactcggatgtctatctgctgctggtttccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATTCAACAACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGCCATCGAAGG
  ||||  |    | ||  ||| |   |||| ||        ||||||||   |||   ||| | | | || | ||| ||    ||| |||||  | ||| |||| ||||||||||||||||||||||| |||||||||||||||||||| ||| |||||||||||||||||||| ||||||| |||||||| | ||| |||||
ttagcactcagcatgttgtcttagccgtgcatatatgagttataccttccattatgatcatt-atttaatcagctgttta---actgttggttctcctcttcagTAAAACCGGTAAAGGGTGATGCCCTTCTGTTCTTCAGTCTCCACCCCGATGCAACAACAGACTCTGACAGCCTGCACGGGAGCTGCCCGGTCATTGAAGG

upper sequence: GRMZM2G168506_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv14s0066g02170.t01 (Vitis vinifera), 3'ss of exon 7
agcaggctttcttaccttggtactgca-catcacgcgagtaccttcctccatgcatattcactcactcggatgtctatc-tgctgctggtttcct---tctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATTCAACAACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGCCATCGAAGG
   |  |||  || | |||   |   |   |   | || |      |||| || || |||| |   || || |||| |  ||   |   ||| ||     |||||| || ||    || ||||||||| |||||||||||||||| || |||||| |||| |||||| |   |||||| || || || ||||| |  || |  ||
-atactcttcatttcattgtcgcccaagttttttgtgatttaaggtctccctgtat-ttcattt--tcaga-gtctgttatggctcacatttgctgtacttgcagTGAACCCCAAGAAAGGTGATGCCTTGCTGTTCTTCAGTCTGCATCCTGATGCAACCACAGACCCAAGCAGCTTACATGGAAGTTGCCCTGTTATTGCGGG
















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|74238562|gb|DT646476.1|DT646476
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|50334166|gb|CO529292.1|CO529292
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|61119514|gb|DN560475.1|DN560475
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|30088239|gb|CB886444.1|CB886444
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|32834904|gb|CD974582.1|CD974582
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|33103527|gb|CF063487.1|CF063487
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|148987376|gb|EE031220.2|EE031220
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|74239750|gb|DT647664.1|DT647664
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|71304282|gb|DR788255.1|DR788255
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|31998069|gb|CD661904.1|CD661904
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|166512308|gb|EG321376.1|EG321376
EST:     ACAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGC
genomic: -CAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGC
EST: gi|4647604|gb|AI622679.1|AI622679
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|12972561|gb|BG268043.1|BG268043
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|94475795|gb|EB704753.1|EB704753
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|211361742|gb|FL088467.1|FL088467
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|76913826|gb|DV165269.1|DV165269
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|83278553|gb|DV942561.1|DV942561
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
EST: gi|60398051|gb|DN230867.1|DN230867
EST:     GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG                         TTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT
genomic: GCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAGgtatagcagt ... ccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccatgcatattcactcactcggatgtctatctgctgctggtttccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATTCAACAACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGCCATCGAAGG
             cactcac  putative branch site (score: 2)
                                          tttccttctgc  putative PPT
        atattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcaggctttcttaccttggtactgcacatcacgcgagtaccttcctccatgcatattcactcactcggatgtctatctgctgctggtttccttctgcagTTAAACCGGTAAAGGGTGATGCCCTGCTGTTCTTCAGTCTCCACCCTGATTCAACAACAGACTCTGACAGCTTGCACGGTAGCTGCCCCGCCATCGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC