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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgctcatcaggattttcaatttggtcttttacttgataaattttatttagaagaattcttaaaactgtttgttttattttcttagGCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCCAGGTTGGATGCTCAACAGAAGAAATTGAATCTTTCTGTTCTTCCAACAA

Basic information

species Glycine max
transcript GLYMA04G30350.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G30350.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0009g01080.t01 (Vitis vinifera), 3'ss of exon 7
gtgagt-gctcatcaggattttcaatttggtcttttacttgat--aaattttatttagaaga---------att--cttaaaactgtttgttttattttcttagGCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCCAGGTTGGATGCTCAACAGAAGAAATTGAATCTTTCTGTTCTTCCAACAA
|| |||   |  | |      |||||||  |||  ||  || |    | |  | |   | ||         |||  | | | |||| |    || |||   ||||||||| || ||||||| |||||||| ||  | |||||| |||| ||||||||||| |||||||| ||||||||  ||   ||| | || ||||| || |
gtaagtcattttttaatgaaatcaatttt-tctcctatatggtttggaatggactgcaatgatcctcttgtatttaccttagactgatgtccttttttgtatagGCTGCTTCTTTGAAGGGTTCTGATCACCGCCGAGCCACAGATGTCAGTGCCAGGTTAGATGCTCAGCAGAAGAAGCTGGGCCTTCCAGTCCTTCCCACTA
















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|151395301|gb|EV265172.1|EV265172
EST:     CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCC                         GCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
genomic: CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCCgtgagtgctc ... attttcttagGCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
EST: gi|207730170|gb|GD705014.1|GD705014
EST:     CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCC                         GCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
genomic: CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCCgtgagtgctc ... attttcttagGCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
EST: gi|208080756|gb|GD873290.1|GD873290
EST:     CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCC                         GCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
genomic: CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCCgtgagtgctc ... attttcttagGCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
EST: gi|14990789|gb|BI316462.1|BI316462
EST:     CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCC                         GCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
genomic: CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCCgtgagtgctc ... attttcttagGCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
EST: gi|208150386|gb|GD946959.1|GD946959
EST:     CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCC                         GCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
genomic: CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCCgtgagtgctc ... attttcttagGCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
EST: gi|208059894|gb|GD857406.1|GD857406
EST:     CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGCCCAAAAAGCC                         GCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC
genomic: CTTCAAGGAAGTCCTCCCCAAGGGTGATAAATGAGGCTGTCCAAAAAGCCgtgagtgctc ... attttcttagGCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgataaattttatttagaagaattcttaaaactgtttgttttattttcttagGCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCCAGGTTGGATGCTCAACAGAAGAAATTGAATCTTTCTGTTCTTCCAACAA
 acttgat  putative branch site (score: 5)
                                     tttgttttattttctt  putative PPT
     ataaattttatttaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgctcatcaggattttcaatttggtcttttacttgataaattttatttagaagaattcttaaaactgtttgttttattttcttagGCTGCTGCTCTGAAGGGCTCTGATCATCGGAGGGCCACAAATGTTAGTGCCAGGTTGGATGCTCAACAGAAGAAATTGAATCTTTCTGTTCTTCCAACAA

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