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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtacctaaaagtgtcaattttcttgcatcagaatagaggaaaaagttttgtttttgggtcatgaaagttaagtaattctgattagaatttgtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACCACGGGTTCAGGGATGGAAGGCCCCTCTGTTCCTGCAGTTGGTAGGGATA

Basic information

species Glycine max
transcript GLYMA20G23970.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23970.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g50870.1 (Oryza sativa), 3'ss of exon 2
gtacctaaaagt-gtcaattttcttgcatcagaatagaggaaaaagttttgtttttgggtcatga-aagttaagtaattctg-----attagaatttgtggggt-cagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACCACGGGTTCAGGGATGGAAGGCCCCTCTGTTCCTGCAGTTGGTAGGGATA
 |   |  || | || |||    |||       ||   | ||| || | | | ||| || ||    | ||| | | || |||      ||   || | |    | |||||||| || |||||||||||| |||| || || ||||| || || ||||| ||||| || |||||||| |||||  |     | || | |||  | ||  
-tctttgcaatttgtgaatgactttg-------atgatgaaaatagctgtttgttttggccagatcaggttgatttatgctgctgacgttgtcatctctcatctgcagGATGCGGCCATGGGGCTGGTGGTGAGCGCCGCCACGGGGAGGGGCTGGACGACGGGGTCGGGGATGGAGGGCCCGCCCAAGGCCGCCGGTGGGGGAGACC
















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|120532027|gb|EH260160.1|EH260160
EST:     ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAA                         GATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
genomic: ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAAgtacgtcgtt ... gtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
EST: gi|193654616|gb|FK599144.1|FK599144
EST:     CTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAA                         GATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
genomic: CTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAAgtacgtcgtt ... gtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
EST: gi|193706237|gb|FK645777.1|FK645777
EST:     CTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAA                         GATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
genomic: CTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAAgtacgtcgtt ... gtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
EST: gi|151406646|gb|EV276461.1|EV276461
EST:     ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAA                         GATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
genomic: ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAAgtacgtcgtt ... gtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
EST: gi|193560073|gb|FK518834.1|FK518834
EST:     TTCCTTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAA                         GATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
genomic: TTCC-TATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAAgtacgtcgtt ... gtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
EST: gi|254328089|gb|GR835054.1|GR835054
EST:     ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAA                         GATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
genomic: ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAAgtacgtcgtt ... gtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
EST: gi|193313543|gb|FK278742.1|FK278742
EST:     ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAA                         GATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
genomic: ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAAgtacgtcgtt ... gtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
EST: gi|7796356|gb|AW781753.1|AW781753
EST:     ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAA                         GATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
genomic: ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAAgtacgtcgtt ... gtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
EST: gi|9563944|gb|BE473453.1|BE473453
EST:     ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAA                         GATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC
genomic: ATCTTCCTATTCTCAGTGATCGCTGCCTCTCCCTTTCCCCTCTTTCCAAAgtacgtcgtt ... gtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtttttgggtcatgaaagttaagtaattctgattagaatttgtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACCACGGGTTCAGGGATGGAAGGCCCCTCTGTTCCTGCAGTTGGTAGGGATA
                              ttctgat  putative branch site (score: 3)
                  aaagttaagtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctaaaagtgtcaattttcttgcatcagaatagaggaaaaagttttgtttttgggtcatgaaagttaagtaattctgattagaatttgtggggtcagGATGCTGCGATGGGGCTGGTGCTGAGTGCTGCAACGGGCAGAGGATGGACCACGGGTTCAGGGATGGAAGGCCCCTCTGTTCCTGCAGTTGGTAGGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - -cttgcat
- - - - - - - - - - - - - - - - - - - gaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaaa