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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTGCAAGCACTTCTCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactctttctgttgtgtagttgtgtctctactcttaggaaaagtttcttcttatatcctttgcttatggaactgccaaagcacagtatattgaaga...

Basic information

species Glycine max
transcript GLYMA04G37620.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G37620.3 (Glycine max), 5'ss of exon 4
lower sequence: Vv17s0000g00610.t01 (Vitis vinifera), 5'ss of exon 3
GAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTGCAAGCACTTCTCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgact--ctttctgttgtgtagttgtgtctctactcttaggaaaagtttcttcttatatcctttgcttatggaactgccaaagcacagtatattgaaga
|||||| ||||| ||||||||||| ||||| |||||||| |||||  | |||||||| || || ||||||||||||||||| || |||||||| || |||||||   |  |||   ||  |       | ||||     |||    |   || || |  | |   ||   |  | | ||| | | |  || |  |||     
GAGCCCTGCACTTACTCTGAAGACAGCACTCCTTTCTGTACAAGCCTTGCTCTCTGCCCCTCAACCTGATGATCCTCAAGACGCTGTGGTGGCTCAACAGgtctagtttgcttctagtcttcctacattatctccttatttattttagtcttattttcttgttaattaaattagcagctgtctatggtcattccattatc--

upper sequence: GLYMA04G37620.3 (Glycine max), 5'ss of exon 4
lower sequence: PP1S16_326V6.2 (Physcomitrella patens), 5'ss of exon 6
GAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTGCAAGCACTTCTCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactctttctgttgtgtagttgtgtctctactcttaggaaaagtttcttc-------ttatatcctttgcttatggaactgccaaagcacagtatattgaaga------------------------------------------------------------------
||| ||||| || ||||| || ||||| || || ||  | || || ||| | ||  | ||| |||||||||||||||||||||| || ||||||||||||||   | ||      ||| ||     | |      ||||   | |   ||||||       || || | | |  || |     |  ||| |   | ||   | ||                                                                    
GAGTCCAGCTCTGACTCTCAAAACTGCCCTCCTCTCCCTTCAGGCTCTTTTATCAACACCAGAGCCTGATGATCCTCAAGATGCTGTTGTGGCACAGCAGgttgaattcccctcattgagtgtacattttgtctttcttgcaatacccttcttcgcaaaaattctaccatgtcattctcatcttatcaatgacaaatactctcaacctagacaagggctcttttgatctctacccttattcacatatgcgtggcatttctcttgtgtttgcag
















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|254321367|gb|GR824684.1|GR824684
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|192329042|gb|FK019713.1|FK019713
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|31466422|gb|CD408450.1|CD408450
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|214006685|gb|DB987567.1|DB987567
EST:     GCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: GCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|9440039|gb|BE440550.1|BE440550
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|9205392|gb|BE331616.1|BE331616
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGACAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAC
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|192334197|gb|FK026578.1|FK026578
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|209715403|gb|BW682121.1|BW682121
EST:     CTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: CTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|15204167|gb|BI426935.1|BI426935
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|23727022|gb|BU761524.1|BU761524
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|31467834|gb|CD409862.1|CD409862
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACCCTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|298172946|gb|HO019930.1|HO019930
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|10710312|gb|BF010036.1|BF010036
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|26268069|gb|CA819132.1|CA819132
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|10232663|gb|BE801551.1|BE801551
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAG
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|151410843|gb|EV280658.1|EV280658
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
EST: gi|192329717|gb|FK023291.1|FK023291
EST:     TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAG                         TATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA
genomic: TCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactct ... gataatgcagTATCTGAAAGACTATCAGACATTTGTTAACACTGCTCGCTACTGGACAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCCCAGCACTCACTCTGAAGACTGCACTTCTTTCTGTGCAAGCACTTCTCTCTGCTCCACAGCCTGATGATCCTCAAGATGCCGTGGTGGCACAGCAGgtctgactctttctgttgtgtagttgtgtctctactcttaggaaaagtttcttcttatatcctttgcttatggaactgccaaagcacagtatattgaaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG