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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccatggggattgttgtgttgatatcatacttttgatgcttattaattgcttcttcgtgtgattatttttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAGGACCCGTGAACGTTCGCATGACCGGACTCGTGATAGAGATCTACGAGAT

Basic information

species Zea mays
transcript GRMZM2G113592_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113592_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g02630.1 (Oryza sativa), 3'ss of exon 9
gtaagccatggggattgttgtgttgatatcatacttttgatgcttattaattgcttcttcgtgtgattatttttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAGGACCCGTGAACGTTCGCATGACCGGACTCGTGATAGAGATCTACGAGAT
        |     || |    |  ||   || | |    |      ||||||          |  | ||  ||   || ||||| || || || ||||||||||||  |||||||||||| ||||| ||||| || |||||||| || |||||||| ||||| ||  | |||  |  ||| 
-------gtatatcttatcaaataaatggaattcctgcattaacatctaattgtggtgcttattactcatgatttgatgcagGGACCGCGAGAAGTCTCGTGAAAGGCCACGGGAAAGAGATCGTGATGAGAGAACTCGTGAACGATCCCATGACCGTACTCGCGAGCGTGATTCAAAAGAA
















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|16137393|gb|BI894258.1|BI894258
EST:     GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG                         GGATCGGGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
genomic: GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAGgtaagccatg ... ttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
EST: gi|20506948|gb|BQ279414.1|BQ279414
EST:     TCGTCGTGCCGATAG                         GGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
genomic: TCGTCGTGCCGATAGgtaagccatg ... ttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
EST: gi|60338720|gb|DN205693.1|DN205693
EST:     GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG                         GGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
genomic: GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAGgtaagccatg ... ttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
EST: gi|16137326|gb|BI894191.1|BI894191
EST:     GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG                         GGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
genomic: GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAGgtaagccatg ... ttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
EST: gi|15313685|gb|BI478905.1|BI478905
EST:     GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG                         GGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
genomic: GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAGgtaagccatg ... ttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
EST: gi|16137392|gb|BI894257.1|BI894257
EST:     GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG                         GGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
genomic: GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAGgtaagccatg ... ttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
EST: gi|15323613|gb|BI478906.1|BI478906
EST:     GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG                         GGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
genomic: GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAGgtaagccatg ... ttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
EST: gi|60342767|gb|DN209740.1|DN209740
EST:     GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG                         GGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
genomic: GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAGgtaagccatg ... ttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
EST: gi|16137327|gb|BI894192.1|BI894192
EST:     GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG                         GGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
genomic: GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAGgtaagccatg ... ttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
EST: gi|60342884|gb|DN209857.1|DN209857
EST:     GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAG                         GGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG
genomic: GGACGCCCTAGATCAGAAGAGCCTCGGAGGGATGATCGTCGTGCCGATAGgtaagccatg ... ttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatacttttgatgcttattaattgcttcttcgtgtgattatttttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAGGACCCGTGAACGTTCGCATGACCGGACTCGTGATAGAGATCTACGAGAT
                 tattaat  putative branch site (score: 2)
                                          tttttactt  putative PPT
                                      attatttttacttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccatggggattgttgtgttgatatcatacttttgatgcttattaattgcttcttcgtgtgattatttttacttgaagGGATCGTGAAAAATCTCGTGAAAGGGTACGGGAAAGAGACCGTGAGGAGAGGACCCGTGAACGTTCGCATGACCGGACTCGTGATAGAGATCTACGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC