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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttatttgtgtacttgtatcatgtgtatgtatctttagtatcctctcatttccttatccatttatttgtatttcttttctgaccatgttctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAAGAAGCTACAAGAG

Basic information

species Glycine max
transcript GLYMA08G09640.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09640.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 7
atgttatttgtgtacttgtatcatgtgtatgtatctttagtatcctctcatttccttatccatttatttgtatttct--tttctgaccat-gttctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAAGAAGCTACAAGAG
 |||    | |     | |||||| | |    || | |  |||      | || || ||  | |    |  |||| |  | | |||  ||  ||   |   || || ||| ||||||||||||| ||||| || || || ||||| || ||||||||||||||||||
ttgtaccatatcaggatttatcatatat---catttctgttatgaaggaagtttctcatgaagtcgccttgatttatcgtctttgatgattatttctttgcagGCTTTTCCTGATGCTGCAACGATTTCCAGTAGAGTCTAAAGGGCGGCGCAAGAAGCTACAAGAG
















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|192314058|gb|FK008798.1|FK008798
EST:     GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAG                         ACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
genomic: GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAGgtgattgtct ... tctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
EST: gi|105633938|gb|DW247301.1|DW247301
EST:     GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGGAG                         ACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
genomic: GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAGgtgattgtct ... tctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
EST: gi|58024096|gb|CX710837.1|CX710837
EST:     GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAG                         ACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
genomic: GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAGgtgattgtct ... tctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
EST: gi|58023915|gb|CX710656.1|CX710656
EST:     GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAG                         ACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
genomic: GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAGgtgattgtct ... tctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
EST: gi|208285136|gb|GE082926.1|GE082926
EST:     GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAG                         ACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
genomic: GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAGgtgattgtct ... tctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
EST: gi|192314057|gb|FK008797.1|FK008797
EST:     GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACG-TGGAAG                         ACTATTCTTGATGCTGCAACGCTTTCCTGTTG
genomic: GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAGgtgattgtct ... tctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTG
EST: gi|57574634|gb|CX547609.1|CX547609
EST:     TACGGTGGAAG                         ACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
genomic: TACGGTGGAAGgtgattgtct ... tctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
EST: gi|15661719|gb|BI699090.1|BI699090
EST:     GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAG                         ACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA
genomic: GGGTTTCTTTGTTTGCAGCCCTTGGTTTTCTTCTTTACGGTGGAAGgtgattgtct ... tctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcatttccttatccatttatttgtatttcttttctgaccatgttctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAAGAAGCTACAAGAG
                                 ttctgac  putative branch site (score: 2)
                atttatttgtatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttatttgtgtacttgtatcatgtgtatgtatctttagtatcctctcatttccttatccatttatttgtatttcttttctgaccatgttctatgatagACTATTCTTGATGCTGCAACGCTTTCCTGTTGAATCCAAAGGTCGACGCAAGAAGCTACAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC