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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaattttcctgatatgtgataaaattattccccacttttatagttacaaccagctttatgatcctgatatgactattaatttcttgtcgtgcagACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG

Basic information

species Glycine max
transcript GLYMA10G34820.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G34820.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0106g00610.t01 (Vitis vinifera), 3'ss of exon 10
---------------------------------gtgagtaattt-tcctgatatgtgataa-aattattccccacttttatagttacaaccagctttatgatcctgat-----atgactattaatttcttgtcgtgcagACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG
                                    || | | | |  ||| ||   || |   |||||| |    | |  | ||      |  | | |  ||||  |      ||  |  |   || ||      ||||||||||||||||||||||| || ||||||||| ||||||||
gtaagtactatttctattgaatctgttttctttcctagaattctgtaatgacattcaattatggttattcactttatattcaattttttttaaatattttttcctcttttcctgtgggttctttctttttacttgacagACTTATGCTATTATTTCAAAAGCATCAAGCTCATCCAATCAG
















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|51338462|gb|CO982328.1|CO982328
EST:     CATACTTAAGTGCCTCTTTTGGTATCATCTATGTCCTTGTGAAACCTGCC                         ACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG
genomic: CATACTTAAGTGCCTCTTTTGGTATCATCTATGTCCTTGTGAAACCTGCCgtgagtaatt ... tgtcgtgcagACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG
EST: gi|51344538|gb|CO985271.1|CO985271
EST:     CATACTTAAGTGCCTCTTTTGGTATCATCTATGTCCTTGTGAAACCTGCC                         ACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG
genomic: CATACTTAAGTGCCTCTTTTGGTATCATCTATGTCCTTGTGAAACCTGCCgtgagtaatt ... tgtcgtgcagACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG
EST: gi|151406306|gb|EV276121.1|EV276121
EST:     CATACTTAAGTGCCTCTTTTGGTATCATCTATGTCCTTGTGAAACCTGCC                         ACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG
genomic: CATACTTAAGTGCCTCTTTTGGTATCATCTATGTCCTTGTGAAACCTGCCgtgagtaatt ... tgtcgtgcagACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG
EST: gi|18726842|gb|BM523788.1|BM523788
EST:     CATACTTAAGTGCCTCTTTTGGTATCATCTATGTCCTTGTGAAACCTGCC                         ACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG
genomic: CATACTTAAGTGCCTCTTTTGGTATCATCTATGTCCTTGTGAAACCTGCCgtgagtaatt ... tgtcgtgcagACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttacaaccagctttatgatcctgatatgactattaatttcttgtcgtgcagACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG
                                  tattaat  putative branch site (score: 2)
                                        tttcttgtc  CT-rich tract
                           atatgactattaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaattttcctgatatgtgataaaattattccccacttttatagttacaaccagctttatgatcctgatatgactattaatttcttgtcgtgcagACTTATGCTATTATTTCAAATGCGTCAAGCTCAACCAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA