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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctttgtcgctaatttttcattattgatatagatgtattacaggtgattttatgtaagattattttgcttatgtattgatgttctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTTGCTGCTTCTGAAAATGATGGTGCTATAT

Basic information

species Glycine max
transcript GLYMA04G14770.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G14770.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 14
gtattctttgtcgctaatttttcattattgatatagatgtattacaggtgattttatgtaagattattttgcttatgtattgatgttctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTTGCTGCTTCTGAAAATGATGGTGCTATAT
                  |  |  ||||| ||   | |   ||    | | ||  |  |     | | ||||   ||  ||  | || ||  |  || ||  ||||| || | ||| | |||||||||||||||||||| | || ||||||  | || || ||||||||||||||    ||||| |||||||||||||| || |
---------------gtatgcttgttattcat---ggttacttctgtgagcttccaccttcttgtttattgcacctgctttattcttttc--ttaaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTTGAAAAGGTTGAGCAAGAACTCATGGCTTCAGAAAATGATGGTGCAATTT

upper sequence: GLYMA04G14770.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 14
-----------------------------gtattctttgtcgctaatttttcattattgatatagatgtattacaggtgattttatgtaagattattttgcttatgtattgatgttctctgtccaat-atctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTTGCTGCTTCTGAAAATGATGGTGCTATAT
                                    |  | ||| | |||   | | |  ||   |  |   | || | || |  | |    |  | ||| || | |||  || ||   |  ||| | | | |||||||| | ||| | ||||| || |||||||||||||||||||||||| | || || ||||||||||||||  |||| || |  |||||||||||||| |
gtatgcttaacatgtcaaaagtattgtccccgcagctctttgcttagtttgtttaacttgtaacaacattccatagcttatct-gtatggtttcttgttggttct-tatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT

upper sequence: GLYMA04G14770.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S13_282V6.2 (Physcomitrella patens), 3'ss of exon 14
gtattctttgtcgctaatttttcattattgatatagatg-tattacaggtgattttatgtaagattat-tttgcttatgt-attgatgttctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTTGCTGCTTCTGAAAATGATGGTGCTATAT
        ||||      ||   ||| ||   | | ||| ||   ||     |    || | |||||   ||||  |    ||  |   | | ||    ||    |||||||||| ||  ||||||| || ||||||||||| ||||| || ||| |||||||||| || |||||  |||||   || || ||||||||| ||  ||
------actgtc-taggcttgcgattgttacaagatatgatacagcaaccattagcctgcatgattaaacttgccaactcgatctaacatatgtggtggattctcagATTCAACTGAAGTCATTGGCAGAGGAAATGCAAGCAGTGAGCAAGGGTCTAGAGAAAGTGGAACAAGAGATTGCTATGTCAGAGAATGATGGTCCTGCAT

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|7590237|gb|AW705994.1|AW705994
EST:     AATTGCTAGATTTTGATAAGGATCTTGTCCATTTGGAAGCAGCTTCTAAG                         ATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTA
genomic: AATTGCTAGATTTTGATAAGGATCTTGTCCATTTGGAAGCAGCTTCTAAGgtattctttg ... caatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttatgtaagattattttgcttatgtattgatgttctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTTGCTGCTTCTGAAAATGATGGTGCTATAT
                            tattgat  putative branch site (score: 3)
                                    ttctctgtcc  CT-rich tract
     tatgtaagattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctttgtcgctaatttttcattattgatatagatgtattacaggtgattttatgtaagattattttgcttatgtattgatgttctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTTGCTGCTTCTGAAAATGATGGTGCTATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT