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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtagtcacttttattttgcaaataaaagtggtctaaaacatcctgtttagtgactgggctggaaattaacatgttccattatggctgtgtacatgcagTGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGGTAGTCCAACCACTGAATCTTGGGCAGATGGACTCAAACTTGCCAGGGATATCAACTATCAG

Basic information

species Glycine max
transcript GLYMA16G08080.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G08080.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 8
----ttgtagtcacttttattttgcaaataaaagtggtctaaaacatcctgtttagtgactgggctggaaattaacatgttccattatggctgtgtacatgcagTGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGGTAGTCCAACCACTGAATCTTGGGCAGATGGACTCAAACTTGCCAGGGATATCAACTATCAG
    |   |   |     |      || ||  |    ||| |  |||  || |      ||    | | ||||||    || |  | |  || | |   ||||||||||||||||| ||||||||||||||||||||  | || ||||||||     | || ||||| || ||||| |||||||| |  | ||||||||| || 
tctatcaaaaaaaacaaaaaaaaaaaagtatgaaccttcttat-cattttgctattcacctactgttggaattaat---tttctctctttctttattggtgcagTGAAGCAGATGAAATTTACAAAATATGCAGTGTTATGGGCAGTCCAACTTGGAATTCATGGGCTGAGGGACTTAAACTTGCTAATGCTATCAACTACCAA
















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|207696428|gb|GD678217.1|GD678217
EST:     GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAG                         TGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGGTAGTCCAACCAC
genomic: GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAGgtattaactt ... gtacatgcagTGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGGTAGTCCAACCAC
EST: gi|208102908|gb|GD900898.1|GD900898
EST:     GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAG                         TGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGG
genomic: GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAGgtattaactt ... gtacatgcagTGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGG
EST: gi|10237923|gb|BE806811.1|BE806811
EST:     GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAG                         TGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTTAG-TAGTCCAACCA
genomic: GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAGgtattaactt ... gtacatgcagTGAAGCAGATGAGATTTACAAAATATGCAGTGTGCT-AGGTAGTCCAACCA
EST: gi|207754685|gb|GD729308.1|GD729308
EST:     GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAG                         TGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGGTAGTCCAA
genomic: GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAGgtattaactt ... gtacatgcagTGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGGTAGTCCAA
EST: gi|26056243|gb|CA799157.1|CA799157
EST:     GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAG                         TGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGGTAGTCCAACCAC
genomic: GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAGgtattaactt ... gtacatgcagTGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGGTAGTCCAACCAC
EST: gi|10237927|gb|BE806815.1|BE806815
EST:     GCTATAATGGCTGAGTTGGTCACTCTGCGTCCTCTATTCCGCGGGAACAG                         GGAAGCAGATGAGATGTACAAAATATG
genomic: GCTATAATGGCTGAGTTGTTCACTCTCCGTCCTCTATTCCCCGGTTCCAGgtattaactt ... gtacatgcagTGAAGCAGATGAGATTTACAAAATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttagtgactgggctggaaattaacatgttccattatggctgtgtacatgcagTGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGGTAGTCCAACCACTGAATCTTGGGCAGATGGACTCAAACTTGCCAGGGATATCAACTATCAG
                    aattaac  putative branch site (score: 2)
                   aaattaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtagtcacttttattttgcaaataaaagtggtctaaaacatcctgtttagtgactgggctggaaattaacatgttccattatggctgtgtacatgcagTGAAGCAGATGAGATTTACAAAATATGCAGTGTGCTAGGTAGTCCAACCACTGAATCTTGGGCAGATGGACTCAAACTTGCCAGGGATATCAACTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggctgt