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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcatgcatactacccaaactctccaccactagctgaccctagtgattctagtttatcatcatttgtaacacccttatgctgaatctttccaacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGTTAATTCTGAGGATCTATGGGTACTCACTTGTGATGAAGATGTTGTTGAT

Basic information

species Glycine max
transcript GLYMA05G27640.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G27640.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0010g02200.t01 (Vitis vinifera), 3'ss of exon 4
--------------------ctcatgcatactacccaaactctccaccactagctgacccta-----gtgattctagtttatcatcatttgtaacacccttatgctgaatctttccaacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGTTAATTCTGAGGATCTATGGGTACTCACTTGTGATGAAGATGTTGTTGAT
                     |  |   | ||        |||| | ||||  |  ||   |     | ||||||||  |   ||  ||  | |||| |||   ||   | | |||||  | |||||||||  | |||||||| ||||| ||||| ||||| ||| ||| |||||||||||| || ||  ||||||| |||||||||| ||| ||||| ||  | 
gtaagttggtaactacaaggattgtattttctttattctgtctctaacactttccaactgcatacatgagattctagactgctatttttctttacactcttcctcttc-tttatccaaattacagGAACACAAGATCAGAGTCCTGCCCCTTTTGTCGTGGCAGCATAAAGAGAGTTAATTCAGAAGACTTATGGGTTCTCACTTGTGGTGACGATGTGGTCAAC
















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|254347421|gb|GR853670.1|GR853670
EST:     GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTG                         GAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
genomic: GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTGgtatgtattc ... caacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
EST: gi|22522945|gb|BU081756.1|BU081756
EST:     GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTG                         GAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
genomic: GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTGgtatgtattc ... caacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
EST: gi|15201711|gb|BI425017.1|BI425017
EST:     GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTG                         GAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
genomic: GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTGgtatgtattc ... caacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
EST: gi|254347420|gb|GR853669.1|GR853669
EST:     GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTG                         GAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
genomic: GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTGgtatgtattc ... caacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
EST: gi|20812773|gb|BQ297251.1|BQ297251
EST:     GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTG                         GAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
genomic: GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTGgtatgtattc ... caacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
EST: gi|31307506|gb|CD392709.1|CD392709
EST:     GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTG                         GAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
genomic: GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTGgtatgtattc ... caacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
EST: gi|192304134|gb|FG995350.1|FG995350
EST:     GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTG                         GAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
genomic: GTTTTGCCTAATTGCTGTCATGCCATGTGTATCAAATGCTACCGCAAGTGgtatgtattc ... caacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
EST: gi|7233514|gb|AW568859.1|AW568859
EST:     TGTATCAAATGCTACCGCAAGTG                         GAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT
genomic: TGTATCAAATGCTACCGCAAGTGgtatgtattc ... caacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctagtttatcatcatttgtaacacccttatgctgaatctttccaacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGTTAATTCTGAGGATCTATGGGTACTCACTTGTGATGAAGATGTTGTTGAT
                  ttgtaac  putative branch site (score: 2)
                                       tctttcc  putative PPT
       tttatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcatgcatactacccaaactctccaccactagctgaccctagtgattctagtttatcatcatttgtaacacccttatgctgaatctttccaacctgcagGAACACCCGGTCAGAGTCATGCCCTTTTTGCCGTGGTAGCTTAAGGAGAGTTAATTCTGAGGATCTATGGGTACTCACTTGTGATGAAGATGTTGTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-tcatgca
- - - - - - - ccaaact
- - - - - - - - - - -ctccacc
- - - - - - - - - - - - - - - - -ctgaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa