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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_T07
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|211526997|gb|FL156384.1|FL156384
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523994|gb|FL156376.1|FL156376
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526993|gb|FL156380.1|FL156380
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523996|gb|FL156378.1|FL156378
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523991|gb|FL156373.1|FL156373
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523992|gb|FL156374.1|FL156374
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526998|gb|FL156385.1|FL156385
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|32808494|gb|CD960728.1|CD960728
EST:     GATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: GATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526996|gb|FL156383.1|FL156383
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526994|gb|FL156381.1|FL156381
EST:     CGGATCTGATCTCATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGARATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|33092405|gb|CF052399.1|CF052399
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|37395178|gb|CF634869.1|CF634869
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523997|gb|FL156379.1|FL156379
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|78026630|gb|DV495017.1|DV495017
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523990|gb|FL156372.1|FL156372
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGYCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|6671465|gb|AW282244.1|AW282244
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526995|gb|FL156382.1|FL156382
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211526999|gb|FL156386.1|FL156386
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGA-CGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
EST: gi|211523995|gb|FL156377.1|FL156377
EST:     CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCAT                         GGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA
genomic: CGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 2 RNA-Seq libraries.


Block sizes: 20 (upstream exon), 30 (downstream exon)
Score: 1

CCTGCCACGCTTGAACGGCTCTCAATCCCAACCCTAACAGCACCGTCTCTCGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG


Block sizes: 47 (upstream exon), 33 (downstream exon)
Score: 4

CCTGCCACGCTTGAACGGCTCTCAATCCCAACCCTAACAGCACCGTCTCTCGGATCTGATCTGATCTGATCCTCCAATTCGTTCGTCCACGTCTCGCCATgtgagtgatc ... tctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccctttttcctcctgtctcaagttccatgctttcctaatgttgctctatctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG
                                 tcctaat  putative branch site (score: 4)
                                            ctctatctc  putative PPT
                                    taatgtt  TA-rich tract