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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcacattaattgctcaatgatttttgtcaaatgaaatccattgtgttaatttgtaaaccattggggctttggctgacattatatctatttgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCGGGGAGCTGCACTACCACTACTACCCGGTTCAGAAAACTCCGGTTGAACA

Basic information

species Zea mays
transcript GRMZM2G102596_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102596_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 3'ss of exon 6
ggcacattaattgctcaatgatt-tttgtcaaatgaaatcca-ttgtgttaatttgtaaaccatt---ggggctttg-----gctgacattata--tctatttgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCGGGGAGCTGCACTACCACTACTACCCGGTTCAGAAAACTCCGGTTGAACA
             |  | ||||| | ||   | || |  ||  || ||||| ||   | |  | |   |||  | ||      ||||| ||||   | | |||||||| |||||||||| ||||||||  | || ||||||||||||||||| |||||||| ||||||||||||||| | |||||||||||| ||   ||||| || || ||
------------tcctattgattatctgctgactgcaccccgcttttgttagttcaaacatgaattgtgggattgtgccagaactgacgttatccttttgtttgaatttcagTTTACCATGTTGGCCCGAACGGCTGGACGAAGCTTTCTGGAGATGATGTTGGGGAGCTGCACTACAAGTACTACCCGGTTGAGGCCACTCCTGTCGAGCA

upper sequence: GRMZM2G102596_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G13060.2 (Arabidopsis thaliana), 3'ss of exon 8
ggcacattaattgctcaatgatttttgtcaaatgaaatccattgtgttaatttgtaaaccattggggctttggctgaca---ttatatctatttgaattg--cagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCGGGGAGCTGCACTACCACTACTACCCGGTTCAGAAAACTCCGGTTGAACA
      ||| |      |     | |||    | ||||  | | | |||| ||  ||     ||    ||| ||| | |   || |     | | |  ||  |||| ||||||||||| || || || |||||||| || || || |||||||| |||||||| |||||||| |||||||| ||      | || | |  |||||
-----gttagtaatctgaatgcatctgt-ggttcaaatgtaatat-ttaactttcaagattctga---tttagctcataagtttgttctcttctcatatgaccagTGTACCACGTTGGTCCCGAAGGATGGACGAAACTATCAGGAGATGATGTTGGGGAGCTACACTACCATTACTACCCCGTGGCACCAGCTACCGCAGAACA

upper sequence: GRMZM2G102596_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 3'ss of exon 7
ggcacattaattgctcaatgatttt-tgtcaaatgaaatccattgtgttaatttgtaaaccattggggctttggctgacatt-atatctatttgaattgc-agTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCGGGGAGCTGCACTACCACTACTACCCGGTTCAGAAAACTCCGGTTGAACA
 | || ||| |  |||  |   | | | ||        |||  ||||   |  |  |||    ||  | | ||  |    || | |  | | |   |||  ||||||  | || || ||  |||| |||| |||||| ||||| ||||||||||| || || |||||| | ||||||||||||  |  ||   | || |||||
-gtac-ttactctctctctctctctctctctctctctctcccatgtggatacatacaaatgtatgtagttgtgtttacggtttaaacatgtattttttgttagTTTATTATGTGGGGCCAAATGGGTGGAAGAAGCTGTCTGGTGATGATGTCGGAGAACTCCACTACAAATACTACCCGGTTATGCCAAGCACAGTGGAACA

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|93283423|gb|EB675687.1|EB675687
EST:     TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTG                         TTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
genomic: TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTGgtatgtttca ... tgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
EST: gi|18383461|gb|BM416661.1|BM416661
EST:     TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTG                         TTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
genomic: TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTGgtatgtttca ... tgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
EST: gi|166526830|gb|EG149948.1|EG149948
EST:     TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTG                         TTTACCACGTTGGCCCTGATGGTTGGACG
genomic: TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTGgtatgtttca ... tgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACG
EST: gi|22542995|gb|BU093433.1|BU093433
EST:     AAGTGGTGGTTGTGTTAGTG                         TTTACCCCGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
genomic: AAGTGGTGGTTGTGTTAGTGgtatgtttca ... tgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
EST: gi|74233649|gb|DT641563.1|DT641563
EST:     GGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTG                         TTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
genomic: GGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTGgtatgtttca ... tgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
EST: gi|33103207|gb|CF063167.1|CF063167
EST:     TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTG                         TTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
genomic: TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTGgtatgtttca ... tgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
EST: gi|32851166|gb|CD990847.1|CD990847
EST:     GCAAGTGGTGGTTGTGTTAGTG                         TTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTAGGGATGATGTCG
genomic: GCAAGTGGTGGTTGTGTTAGTGgtatgtttca ... tgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
EST: gi|166577222|gb|EG146441.1|EG146441
EST:     TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTG                         TTTACCACGTTGGCCCTAGATGGTTGGACGAAGCTTTCT
genomic: TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTGgtatgtttca ... tgaattgcagTTTACCACGTTGGCCCT-GATGGTTGGACGAAGCTTTCT
EST: gi|32936164|gb|CF040976.1|CF040976
EST:     TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTG                         TTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
genomic: TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTGgtatgtttca ... tgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
EST: gi|14621502|gb|BI142263.1|BI142263
EST:     TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTG                         TTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG
genomic: TATTTATGGGGCAACATTCCGTGATGCAGCAAGTGGTGGTTGTGTTAGTGgtatgtttca ... tgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaatttgtaaaccattggggctttggctgacattatatctatttgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCGGGGAGCTGCACTACCACTACTACCCGGTTCAGAAAACTCCGGTTGAACA
                          ggctgac  putative branch site (score: 3)
                                       tctattt  putative PPT
                                 attatatctatttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcacattaattgctcaatgatttttgtcaaatgaaatccattgtgttaatttgtaaaccattggggctttggctgacattatatctatttgaattgcagTTTACCACGTTGGCCCTGATGGTTGGACGAAGCTTTCTGGGGATGATGTCGGGGAGCTGCACTACCACTACTACCCGGTTCAGAAAACTCCGGTTGAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC