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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttactgtttgaagaaaattctttccattgacaccagctctctaaagactgtctttgactgtgtttttatcagGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAGCAAGCAAGCCAAATACACCCCA

Basic information

species Glycine max
transcript GLYMA20G34020.1
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 27
lower sequence: Vv13s0064g00180.t01 (Vitis vinifera), 3'ss of exon 26
gtgtgttactgtttgaagaaa--attctttc--cattg----acaccagct--ctctaaagactgtctttgactgtgtttttatc---agGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAGCAAGCAAGCCAAATACACCCCA
||| ||||   | | | |     |||  |||  |||||    | |    ||  || | |||| || |||| | | |||||||  |   ||| |||||||||||||||||||| ||||||||||||||| |||||||||| |||||| | || |||||||| ||
gtgagttaaaatataatggtgttattgcttcgtcattgcaaaatatatactgcctttcaaga-tgacttttattttgtttttccccctagGAATGGACCCAATAAATGAAAGAAAGATGTTCCAGCAACTAGTGAGAGCTGCAAGCCAACCTAATACACCACA

upper sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 27
lower sequence: EFJ13183 (Selaginella moellendorffii), 3'ss of exon 24
gtgtgttactgtttgaagaaaattctttccattgacaccagctctctaaagactg-tctttgactgtgtttttatcagGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAGCAAGCAAGCCAAATACACCCCA
                           |    || |   |||| |||     |   ||||| || |   ||| |||||| ||||| ||  | || ||| | |||||||| ||||||||||||||||| |||||  |||| || ||||||||
--------------------------gtatcctggc-tgagctttctggttgcgaatctttaacag--gtttgatcagGAATGGATCCCTTCAACGAACGTAAGATGTTTCAGCAATTAGTGAGAGCTGCAAGTCAGCCCAACACACCCCA

upper sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 27
lower sequence: EFJ24458 (Selaginella moellendorffii), 3'ss of exon 25
gtgtgttactgtttgaagaaaattctttccattgacaccagctctctaaagactg-tctttgactgtgtttttatcagGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAGCAAGCAAGCCAAATACACCCCA
                           |    ||||   || | |||     |   ||||| || |   ||| |||||| ||||| ||  | || ||| | |||||||| ||||||||||||||||| |||||  |||| || ||||||||
--------------------------gtatcctgac-tgagatttctggttgcgaatctttaacag--gtttgatcagGAATGGATCCCTTCAACGAACGTAAGATGTTTCAGCAATTAGTGAGAGCTGCAAGTCAGCCCAACACACCCCA

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|193670818|gb|FK609132.1|FK609132
EST:     TCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAG                         GGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAG
genomic: TCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAGgtgtgttact ... tttttatcagGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAG
EST: gi|6071342|gb|AW100729.1|AW100729
EST:     CAAGATCTTANCAA-CTGCCCATTTAGAGTCGNTGATGAGATCAACCAAG                         GGATGGNACCCA-TAAATGAAAGGAAGATGTTNCAGCNATTAGTGAGAGCA
genomic: CAAGATCTTA-CAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAGgtgtgttact ... tttttatcagGGATGG-ACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCA
EST: gi|22522297|gb|BU081099.1|BU081099
EST:     TCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAG                         GGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAG
genomic: TCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAGgtgtgttact ... tttttatcagGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAG
EST: gi|8402650|gb|BE058284.1|BE058284
EST:     AGATCAACCAAG                         GGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAG
genomic: AGATCAACCAAGgtgtgttact ... tttttatcagGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAG
EST: gi|193703777|gb|FK634735.1|FK634735
EST:     TCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAG                         GGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAG
genomic: TCAAGATCTTACAAACTGCCCATTTAGAGTCGTTGATGAGATCAACCAAGgtgtgttact ... tttttatcagGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttccattgacaccagctctctaaagactgtctttgactgtgtttttatcagGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAGCAAGCAAGCCAAATACACCCCA
                                             tttttatc  CT-rich tract
                                           tgtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttactgtttgaagaaaattctttccattgacaccagctctctaaagactgtctttgactgtgtttttatcagGGATGGACCCAATAAATGAAAGGAAGATGTTCCAGCAATTAGTGAGAGCAGCAAGCAAGCCAAATACACCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG