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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgggtttgggtggtgggtagcataataattttccaaattatctaaagtttagtttgtattaaagaactttctgaagtttttacttgtttttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAG

Basic information

species Glycine max
transcript GLYMA04G39690.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 3
ttgggtttgggtggtgggtagcataataattttccaaattat--ctaaagtttagtttgtattaaagaactttctgaagtttt-tact-tgtt------tttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAG
     |||    | | | |   |  |||| | |   |||||   ||  | ||| | |  || | ||    ||||||||| |   |||| || |      | | ||   |||||||||| |||||||| || || || || ||||| || ||||| |||||||||||||||||||||||||||
-----tttcctggatagatg--aacataaatcttggaattagaactgtattttggctgatactcaa---ttttctgaaggtacatactgtgatacacaatgttttctcagGTTGCTTCTTATGAGTTCACGACTTTGACATGCATTCCTGGTGTTATCACATATCGTGGAGCTAAAATCCAG

upper sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0031g01620.t01 (Vitis vinifera), 3'ss of exon 3
ttgggtttgggtggtgggtagcataataattttccaaattatctaaagtttagtttgtattaaagaactttctgaagtttttacttgtttttgt---ttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAG
                    |  | | |  ||||||       |    |||| | | | |||| ||| |||       | | |  | ||||| |   ||| |||||||||||||||| |||||||||||||||||||| || |||||||| || ||||| ||||||||||| |||
--------------------gtttgaaatctttcca------ttgtgattta-tatatcttaaggaatttttaagttgtctgatatttttttatgttttacagGTTGCTTCCTATGAATTTACTACCTTAACTTGCATTCCTGGTGTGATAACGTATCGAGGAGCTAAAATTCAG
















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|163920656|gb|EH039949.1|EH039949
EST:     CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAG                         GTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
genomic: CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAGgtatggaggt ... ttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
EST: gi|19269399|gb|BM885655.1|BM885655
EST:     CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAG                         GTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
genomic: CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAGgtatggaggt ... ttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
EST: gi|16996121|gb|BM085493.1|BM085493
EST:     GCAAAACTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAG                         GTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
genomic: GCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAGgtatggaggt ... ttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
EST: gi|18040270|gb|BM308564.1|BM308564
EST:     CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAG                         GTTGCTTCCTATGAGTT-ACTACCTTAACTTGCATCCCAGGTGTGATCACA
genomic: CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAGgtatggaggt ... ttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
EST: gi|7041848|gb|AW471742.1|AW471742
EST:     CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAG                         GTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
genomic: CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAGgtatggaggt ... ttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
EST: gi|151412834|gb|EV282646.1|EV282646
EST:     CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAG                         GTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
genomic: CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAGgtatggaggt ... ttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
EST: gi|254315459|gb|GR825268.1|GR825268
EST:     CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAG                         GTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
genomic: CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAGgtatggaggt ... ttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
EST: gi|11413788|gb|BF425799.1|BF425799
EST:     CAGTTGGCAAATCTACTCTTCTAAATAAGTTGACCGGGACATTTTCTGAG                         GTTGCTTCCTATGAGGTTACTACCTTAACTTGCATCCCAAGTGTGATCACA
genomic: CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAGgtatggaggt ... ttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
EST: gi|151406659|gb|EV276474.1|EV276474
EST:     CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAG                         GTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA
genomic: CAGTTGGCAAATCTACTCTACTAAATAAGTTGACCGGGACATTTTCTGAGgtatggaggt ... ttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttagtttgtattaaagaactttctgaagtttttacttgtttttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAG
 atctaaa  putative branch site (score: 3)
                                tttttacttgttttt  putative PPT
                                tttttacttgtttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgggtttgggtggtgggtagcataataattttccaaattatctaaagtttagtttgtattaaagaactttctgaagtttttacttgtttttgtttatagGTTGCTTCCTATGAGTTTACTACCTTAACTTGCATCCCAGGTGTGATCACATATCGTGGAGCTAAAATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- gggtttg
- - - - - -tggtggg
- - - - - - - - - - - - - - - - -ccaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctg