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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcactgcacaacggccggtcgtcactagaatgttttgaaccgctcccctttttcctcctgtctcaagttccatgctttcctaatgttgctctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG

Basic information

species Zea mays
transcript GRMZM2G122039_T05
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 1
-ttcactgcacaacggccggtcgtcactagaatgttttgaaccgctcccctttttcctcctgtctcaagttccatgctttcctaatgttgctct-atctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG
  |  ||||  |  |  |    |    |   || || |         |  | | ||||  |   |  | |||  |  | |    || |||   | ||   ||||  |||||||||| |||||||||||||| ||||||||| ||    ||||| ||  ||||||||||| || |    |||||  ||
gctgcctgctga--gttcttctgcttgtgttattttcttttttatggcattctctcctatttattgcatttcatttatgtttggattttgtcatgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG

upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------ttcactgcacaacggccggtcgtcactagaatgttttgaaccgctcccctttttcctcctgtctcaagttccatgctttcctaatgttgctctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG
                                                             | |  ||  |  | ||  || || | |  | | || |         |  | | ||||  | | |    || |||   ||   | | |  |   ||   ||||  |||||||||| |||||||||||||| ||||||||| ||    ||||| ||  ||||||||||| || |    |||||  ||
gttggtttaattttggtacttcaatgtaattgtggtgtcaccatcaatagcttccgccgactgctgtgttcttctgcttgt-gttattttacttttcttttttatggcattctctcctatt-tattgcatttcatttgtttggattttgtcatgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTAGAATACCAG
















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|211523990|gb|FL156372.1|FL156372
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGYCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526998|gb|FL156385.1|FL156385
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|6671465|gb|AW282244.1|AW282244
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523995|gb|FL156377.1|FL156377
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523997|gb|FL156379.1|FL156379
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526993|gb|FL156380.1|FL156380
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523991|gb|FL156373.1|FL156373
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523994|gb|FL156376.1|FL156376
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526996|gb|FL156383.1|FL156383
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526995|gb|FL156382.1|FL156382
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|33092405|gb|CF052399.1|CF052399
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|15499626|gb|BI596139.1|BI596139
EST:     CCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523996|gb|FL156378.1|FL156378
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526997|gb|FL156384.1|FL156384
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|37395178|gb|CF634869.1|CF634869
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526994|gb|FL156381.1|FL156381
EST:     CGGATCTGATCTCATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGARATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|32808494|gb|CD960728.1|CD960728
EST:     GATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: GATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|78026630|gb|DV495017.1|DV495017
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523992|gb|FL156374.1|FL156374
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccctttttcctcctgtctcaagttccatgctttcctaatgttgctctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG
                                 tcctaat  putative branch site (score: 2)
                                            ctctatctc  putative PPT
                                    taatgtt  TA-rich tract