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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaagatccctacacctgaacttatcatcagagtagaaggttagattgtgatggcgttaaaactaaaagaaacatgcatgttctctacttgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAGAAATTGAATCGGTTATAATAGAG

Basic information

species Glycine max
transcript GLYMA07G02180.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G02180.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 13
aaaaagatccctacacctgaacttatcatcagagtagaa--ggttagattgtgatggcgtta--aaactaaaagaaacatgcatgttctct---acttgt-ttatc------agGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAGAAATTGAATCGGTTATAATAGAG
  || || | || || |       |  |   | ||      | |||  ||||| ||    |    |  |  ||      ||  |  ||| |   | |||| |||||      ||| || |||||||| || || || | |||||| |||||||||||||||||||||||||| || ||  |  || ||
gtaaggaccacttcatcgttttccactagttgtgtttttttgtttaagttgtggtgctactgtctatttgtaatcgttttgggttatctgtctcatttgtattatcctgtgtagGCACAAATGCTGACATCATGAAAGTTGGTGGTTATAAGCTGTCTGCATTAGAAATTGAGTCAGTGCTGTTACAG

upper sequence: GLYMA07G02180.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0002g04170.t01 (Vitis vinifera), 3'ss of exon 13
aaaaagatccctacacctgaacttatcatcagagtagaaggttagattgtgatggcgttaaaactaaaagaaacatgcatgtt----ctctactt--gtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAGAAATTGAATCGGTTATAATAGAG
       | |||| |     |      ||   | || ||   || ||  | ||  | |  |||  |||| |   | || | ||    || |  ||   |||||||||||| | ||||||||| || |||| ||| || || ||| | |||||||||||||||||| | |   |  |||||
------tttcctagattcatagcatggatttaaatataatcatatatatttattacatataaataaaaaaagtgaagcttcttagacctttgatttaatttatcagGTACAAGTGCTGATATTATGAAGGTTGGCGGTTACAAGTTATCTGCATTAGAAATTGAAGCAGCGTTGTTAGAG
















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|19937440|gb|BQ081291.1|BQ081291
EST:     TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|254347505|gb|GR853754.1|GR853754
EST:     TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|254342855|gb|GR859017.1|GR859017
EST:     TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|254322526|gb|GR837940.1|GR837940
EST:     TGGAGATGCAG-TACTACAGATGAAGATGGATA-TTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|254317383|gb|GR826328.1|GR826328
EST:     TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|254342856|gb|GR859018.1|GR859018
EST:     TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|254348419|gb|GR852098.1|GR852098
EST:     TGGAGATGCAG-TACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|151393469|gb|EV263344.1|EV263344
EST:     TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|254347506|gb|GR853755.1|GR853755
EST:     TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|254321454|gb|GR824771.1|GR824771
EST:     TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|254348418|gb|GR852097.1|GR852097
EST:     TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG
EST: gi|9205100|gb|BE331324.1|BE331324
EST:     TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGAC                         GTACTAATGCTGATATAATCAATGCTGGTGGATATAAGCTGTCTGCATTAG
genomic: TGGAGATGCAGTTACTACAGATGAAGATGGATATTTCATCATTCTAGGACgtaaggaaat ... tgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtgatggcgttaaaactaaaagaaacatgcatgttctctacttgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAGAAATTGAATCGGTTATAATAGAG
                aactaaa  putative branch site (score: 2)
                                    ttctctacttgttt  putative PPT
            ttaaaactaaaagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaagatccctacacctgaacttatcatcagagtagaaggttagattgtgatggcgttaaaactaaaagaaacatgcatgttctctacttgtttatcagGTACTAATGCTGATATAATCAAGGCTGGTGGATATAAGCTGTCTGCATTAGAAATTGAATCGGTTATAATAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG