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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggtttccaattgtaaattgttgatttcctggttccattgattctcttgccatagttaatgaggttccatatttttttcttggctacatgaattttcagGCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACATAATTGCTACAAAGAATCGGTAGAATCATTCATTGCTTGCACGGGAGCAA

Basic information

species Glycine max
transcript GLYMA04G03080.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g13280.t01 (Vitis vinifera), 3'ss of exon 1
tgggtttccaattgtaaattgttgatttcctggttccattgattctcttgccatagttaatgaggttccatatttttttcttggctacatgaatttt---cagGCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACATAATTGCTACAAAGAATCGGTAGAATCATTCATTGCTTGCACGGGAGCAA
     ||   ||| ||| ||| ||  |   |  ||     | ||||||  ||||  || ||   |||   ||||||||      || |||  || ||   |||||| | ||||| | |||||||||||||||||| || ||||||||| | |||||||| |  |||||  | || |||||||| ||| |||| || ||    |
cacagttaagattttaa-ttgatgtataattctttatgaagtttctct-accatgcttgattttgtttt-tattttttataattcttcatacatctttaacagGCTATCAATGACAGTGACATCCACAACATTGTCCTATCATATCTTGTGCATAATTGTTTTAAAGAGACTGTGGAATCATTTATTTCTTGTACTGGGATGA
















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|192298544|gb|FG989220.1|FG989220
EST:     TCTCTCACTAAACAACCATGGACCTGGATCCTCGCCAATACGAAAACCTT                         GCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
genomic: TCTCCCACTAAACAACCATGGACCTGGATCCTCGCCAATACGAAAACCTTgtatgtttca ... gaattttcagGCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
EST: gi|19054068|gb|BM732735.1|BM732735
EST:     TCTCCCACTAAACAACCATGGACCTGGATCCTCGCCAATACGAAAACCTT                         GCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
genomic: TCTCCCACTAAACAACCATGGACCTGGATCCTCGCCAATACGAAAACCTTgtatgtttca ... gaattttcagGCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
EST: gi|9566116|gb|BE475554.1|BE475554
EST:     TCTCCCACTAAACAACCATGGACCTGGATCCTCGCCAATACGAAAACCTT                         GCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
genomic: TCTCCCACTAAACAACCATGGACCTGGATCCTCGCCAATACGAAAACCTTgtatgtttca ... gaattttcagGCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
EST: gi|298168072|gb|HO013335.1|HO013335
EST:     TCTCCCACTAAACAACCATGGACCTGGATCCTCGCCAATACGAAAACCTT                         GCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
genomic: TCTCCCACTAAACAACCATGGACCTGGATCCTCGCCAATACGAAAACCTTgtatgtttca ... gaattttcagGCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
EST: gi|207730605|gb|GD707492.1|GD707492
EST:     CGCCAATACGAAAACCTT                         GCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
genomic: CGCCAATACGAAAACCTTgtatgtttca ... gaattttcagGCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
EST: gi|254325123|gb|GR834548.1|GR834548
EST:     TCTCCCACTAAACAACCATGGACCTGGATCCTCGCCAATACGAAAACCTT                         GCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT
genomic: TCTCCCACTAAACAACCATGGACCTGGATCCTCGCCAATACGAAAACCTTgtatgtttca ... gaattttcagGCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgccatagttaatgaggttccatatttttttcttggctacatgaattttcagGCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACATAATTGCTACAAAGAATCGGTAGAATCATTCATTGCTTGCACGGGAGCAA
         agttaat  putative branch site (score: 4)
                                                ttttc  putative PPT
                        atatttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggtttccaattgtaaattgttgatttcctggttccattgattctcttgccatagttaatgaggttccatatttttttcttggctacatgaattttcagGCTGTAAATGATAATGACATCCACAACATTGTTCTGTCATATCTTATACATAATTGCTACAAAGAATCGGTAGAATCATTCATTGCTTGCACGGGAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA