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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggccgtgatgggaataagtgattattgagaaaaaatattctctgtactcaaattacttattgtgcttgacaactacaaaccatgcatatcatttttgcagGTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAAATGTTGGTAGTGATAAAATAAGGGAACAAAAGAAAGCCAATCCAGTGGC

Basic information

species Glycine max
transcript GLYMA16G22640.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 3
---ggccgtgatgggaataagtgattattgagaaaaaat-attctctgtactcaaattacttattgtgcttgacaactacaaaccatgcatatcatttttgcagGTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAAATGTTGGTAGTGATAAAATAAGGGAACAAAAGAAAGCCAATCCAGTGGC
   | |    |   ||     |  ||    | |  |||| | | | | |  | ||||| | | |||   ||  ||||    |||| ||    |  | |||||||| || ||||||||||| || ||||| ||||| |||||||| |||||||| ||||| ||   | | ||| ||   |||||||||||||| |||||||||||
ctggtctagaaccagagcttcttgttccatacattaaatgaattttttttttaaaatttcatgttggcattttcaac----aaccttggtactggtgtttgcagGCAATGTTGGGGCTGATCATGCTGTTTTTGAACAAGGTGCTTCAGCAGGGAATGTGGGACATCAGAAACTAGTAGAACAAAAGAAAGCGAATCCAGTGGC
















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|6482120|gb|AW201391.1|AW201391
EST:     GCAAATACTGCAGCAGGCATTGCTGGAGGCACTG-AGTCATGCCCAGAAG                         GTA-CGTTGGGG
genomic: GCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCC-AGGAGgtacggttgt ... atttttgcagGTAACGTTGGGG
EST: gi|20814576|gb|BQ299054.1|BQ299054
EST:     CATGCCAGGAG                         GTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAA
genomic: CATGCCAGGAGgtacggttgt ... atttttgcagGTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAA
EST: gi|14259681|gb|BG882589.1|BG882589
EST:     TGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAG                         GTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAA
genomic: TGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAGgtacggttgt ... atttttgcagGTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAA
EST: gi|19348912|gb|BM893444.1|BM893444
EST:     TGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAG                         GTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAA
genomic: TGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAGgtacggttgt ... atttttgcagGTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAA
EST: gi|7639494|gb|AW733816.1|AW733816
EST:     TGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAG                         GTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAA
genomic: TGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAGgtacggttgt ... atttttgcagGTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAA
EST: gi|21994066|gb|BQ785594.1|BQ785594
EST:     TGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAG                         GTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAA
genomic: TGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAGgtacggttgt ... atttttgcagGTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcaaattacttattgtgcttgacaactacaaaccatgcatatcatttttgcagGTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAAATGTTGGTAGTGATAAAATAAGGGAACAAAAGAAAGCCAATCCAGTGGC
                  gcttgac  putative branch site (score: 4)
                                           tcattttt  putative PPT
     aattacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggccgtgatgggaataagtgattattgagaaaaaatattctctgtactcaaattacttattgtgcttgacaactacaaaccatgcatatcatttttgcagGTAACGTTGGGGCTGAGCACGCTGTGTTTGAGCAAGGTGCGTCAGCAGGAAATGTTGGTAGTGATAAAATAAGGGAACAAAAGAAAGCCAATCCAGTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - gtgatgg
- - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - -ctctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatat