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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcactttacattcattcacattggggattatgaagtgtatgttacttgatatattataatcagtctaaatgataaaccaaatcatatcatggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG

Basic information

species Glycine max
transcript GLYMA08G26180.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 6
gcactttacattcattcacattggggattatgaagtgtatgttacttgatatattataatcagtctaaatgataaaccaaatcatatcatggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG
| |      |   ||  ||  |     | || |     || |   ||   || ||   |      |||| |   ||  ||    | || |  ||| |||||||||||||||||| || || |||||  | || |||||||||||||| || ||  |  | ||||| ||  | ||| | |  || ||||| 
gtaagcctaacgtatctactcttattttcattagagaaatctctattcccatttttcga------taaaggcgtaa--aagcgctgtcttcattt-gtagATTGACGAGGAGATTCTCCAAGAAGTTATCAATATGGGATTTGACAGAAACCACCTCATCGAATCGCTCCGCAACCGAACCCAGAATGAT

upper sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 6
gcactttacattcattcacattggggattatgaagtgtatgttact-tgatatattataatcagtc-taaatgataaaccaaatcatatcatggttt--tgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG
      | | || |            ||| ||   | | | ||| | | |||   | | | |||    |    || ||   | ||||  | |    |  || ||||||| |||||||| |||||||||||||| || ||||||||||||||||||| | | |||||||||||| | |||||  |||||||||| 
----ggttcctttaagggttacatacattttgttctttgtattattattatactctgtgaacagctgcatgaaattaattcactcattgctttacctcatgcagATTGATGAGGAGATTCTTCAGGAAGTGGTTAAGATGGGATTTGACAGGAATCTACTTGTTGAATCTCTTCGCAACAGAGTACAAAATGAT
















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|9819566|gb|BE555079.1|BE555079
EST:     CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAG                         ATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
genomic: CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAGgtttattttt ... ggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
EST: gi|23734193|gb|BU765320.1|BU765320
EST:     CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAG                         ATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
genomic: CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAGgtttattttt ... ggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
EST: gi|308099103|gb|HO760944.1|HO760944
EST:     CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAG                         ATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
genomic: CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAGgtttattttt ... ggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
EST: gi|207745075|gb|GD714421.1|GD714421
EST:     CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAG                         ATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
genomic: CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAGgtttattttt ... ggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
EST: gi|193685389|gb|FK626605.1|FK626605
EST:     CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAG                         ATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
genomic: CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAGgtttattttt ... ggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
EST: gi|208265553|gb|GE063081.1|GE063081
EST:     CTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAG                         ATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
genomic: CTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAGgtttattttt ... ggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
EST: gi|17519479|gb|BM188521.1|BM188521
EST:     CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAG                         ATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT
genomic: CGCGTTATTTAGCTGTGCCACCACCAGATACAATGCAACAGGCCAAAAAGgtttattttt ... ggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatatattataatcagtctaaatgataaaccaaatcatatcatggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG
                 gtctaaa  putative branch site (score: 3)
     atattataatcagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcactttacattcattcacattggggattatgaagtgtatgttacttgatatattataatcagtctaaatgataaaccaaatcatatcatggttttgtagATTGACGAGGAGATCCTTCAGGAAGTGGTGAAAATGGGATTTGACAGGAATCAATTGGTTGAATCTCTTGGGAACAGGATACAAAATGAG

- - - - - - cattcac
- - - - - - - - - - ttgggga
- - - - - - - - - - - - - - tatgaag
- - - - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catatca