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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaattttgagcctccatgccattattctttttcatagttccttggaagattttatttacaaagcacttaatatccttttcacctggatttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG

Basic information

species Glycine max
transcript GLYMA09G39150.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 11
----ccaaattttgagcctccatgccattattctttttcatagttccttggaagattttatttacaaagcacttaatatccttttcacctggatttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG
     |   |||   |     || | |  | |     |  | | |     ||| |  | |||| || |  |  |  | |   |   | ||  |  | ||||||||||||||| || || || |||||  | || ||||||||||| || || || |||||||| ||||||||||||
gccttctcttttaaggttgtaattctaagaattccagttctggataaaaagaacagat-atttccagaagagct--tttgagtaatatctcaacct-tttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTGAGCCGATCTTTTGAATTTCAG
















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|207818473|gb|GD790728.1|GD790728
EST:     GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAG                         CATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
genomic: GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAGgtacttttca ... ttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
EST: gi|192302659|gb|FG994897.1|FG994897
EST:     GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAG                         CATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
genomic: GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAGgtacttttca ... ttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
EST: gi|5175463|gb|AI759796.1|AI759796
EST:     CTTTGGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAG                         CATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
genomic: CTTTGGG-TTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAGgtacttttca ... ttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
EST: gi|7690863|gb|AW759000.1|AW759000
EST:     GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAG                         CATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
genomic: GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAGgtacttttca ... ttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
EST: gi|17519798|gb|BM188840.1|BM188840
EST:     GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAG                         CATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
genomic: GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAGgtacttttca ... ttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
EST: gi|19270564|gb|BM886820.1|BM886820
EST:     GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAG                         CATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
genomic: GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAGgtacttttca ... ttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
EST: gi|5175455|gb|AI759788.1|AI759788
EST:     GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAG                         CATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
genomic: GCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGCTCATCATATTTCAGgtacttttca ... ttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
EST: gi|22933929|gb|BU551068.1|BU551068
EST:     GTCCTCATTGGGCTCATCATATTTCAG                         CATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC
genomic: GTCCTCATTGGGCTCATCATATTTCAGgtacttttca ... ttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaagattttatttacaaagcacttaatatccttttcacctggatttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG
                     acttaat  putative branch site (score: 4)
                                            tttattt  putative PPT
     attttatttacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaattttgagcctccatgccattattctttttcatagttccttggaagattttatttacaaagcacttaatatccttttcacctggatttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
ccaaatt
- - - - - - - - catgcca
- - - - - - - - - - - - - - - - - - - - -ccttgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaagca