Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgccttagtccatcttatggttgaatccaattgggccaaattagggactctgattctgatattttccagcccccactgattgcttttatttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT

Basic information

species Glycine max
transcript GLYMA20G31630.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31630.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G165176_T01 (Zea mays), 3'ss of exon 5
--ttgccttagtccatcttatggttgaatccaattgggccaaattagggactctgattctgatattttccagcccccactgattgcttttattt-ttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT
  | ||||   |   | |||      || |  ||    | |  |     ||  |||   || | ||||       | |   | |||   | ||  || |  ||| || || ||||| || ||||| || |||||||| |||||| | |||||||| || |||||||||||||||
gatagcctc--ttggtgttaaccaataaccacatcaaac-atgtagaatacggtgaccatgttcttttgtgtatgctaagaactgcacatgttcattctgcagGCACGTTTACTCTCTCGAATCTTGGTATGTTTGGAGTTGATAGGTTTGATGCAATACTGCCACCTGGAACT

upper sequence: GLYMA20G31630.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G34430.1 (Arabidopsis thaliana), 3'ss of exon 3
----ttgccttagtccatcttatggttgaatccaattgggccaaattagggactctgattctgatattttccagcccccactgattgcttttatttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT
    |     || |  |   |     ||| |  | || |   ||       |||    |  |    | ||   |     | |  |  |||     |  ||  |||||| |||||||| || || || |||||||||||||||||||| |||||||||||||| || |||||||| 
gtaatcctactactagaatattgaagtgatttgagtttgagtaatccttcaactagattgtttgagtcttgttgtttttatt--tcccttccgggtaattgcagGTACCTTCACTCTCTCTAACCTAGGAATGTTTGGCGTTGATCGGTTTGATGCTATTCTACCCCCTGGAACA

upper sequence: GLYMA20G31630.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 3
----ttgccttagtccatcttatggttgaatccaattgggccaaattagggactctgattctgatattttccagcccccactgattgcttttatttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT
    ||| | |       |   |  |||  ||| |    |  |  | |   | |||     || |   || |||       || ||| |  |  |  |||  ||||||||||||||| || || || ||||||||||| || ||||| ||||| || ||||||||||||||||||
aaaattggcatgccatgaccattccttggttcctaccttgttatttcatcaagtctatccatgtttaatttcagatgt--atgtttgat--tgctggtttgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT

upper sequence: GLYMA20G31630.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ37696 (Selaginella moellendorffii), 3'ss of exon 3
ttgccttagtccatcttatggttgaatccaattgggccaaattagggactctgattctgatattttccagcccccactgattgcttttatt--tttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT
                                                   || |  ||| |   |   | |       | |   |||  |  |||  | ||| ||||||||| |||| || ||||| ||||||||||||||| | ||||| || ||||| ||||| || || 
-------------------------------------------------gttggtgttgacaaactagtgactttgacaactttctttgatgatttcgacagGAACTTTCACTTTGTCAAACCTGGGGATGTTTGGCGTTGATAGGTTTGACGCGATTCTCCCACCCGGCACG

upper sequence: GLYMA20G31630.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ14990 (Selaginella moellendorffii), 3'ss of exon 3
ttgccttagtccatcttatggttgaatccaattgggccaaattagggactctgattctgatattttccagcccccactgattgcttttatttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT
                               |   | |||| ||| |||| |||    || ||||  || |   |  ||||          |||  | ||| ||||||||| |||| || ||||| ||||||||||||||| | ||||| || ||||| ||||| || || 
--------------------------gttggtgttgacaaagtagtgactttga----gacatttgacaactttctttgatga--------tttcgacagGAACTTTCACTTTGTCAAACCTGGGGATGTTTGGCGTTGATAGGTTTGACGCGATTCTCCCACCCGGCACG

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|208326317|gb|GE121483.1|GE121483
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCGTGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|208164905|gb|GD962879.1|GD962879
EST:     AGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: AGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|192313139|gb|FK003721.1|FK003721
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|193375685|gb|FK340482.1|FK340482
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTT
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTT
EST: gi|18039518|gb|BM307812.1|BM307812
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|208310067|gb|GE109795.1|GE109795
EST:     AACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAGTCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: AACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|7691381|gb|AW759439.1|AW759439
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCNACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTATGGCGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|208249676|gb|GE045439.1|GE045439
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|208158340|gb|GD956889.1|GD956889
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTT-CACTCTGTCCAATCTGGGAA
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAA
EST: gi|193609301|gb|FK562949.1|FK562949
EST:     GGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|208031676|gb|GD831212.1|GD831212
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAAT
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAAT
EST: gi|298180893|gb|HO022332.1|HO022332
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|192313138|gb|FK003720.1|FK003720
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|193555157|gb|FK515154.1|FK515154
EST:     CAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGGATGTTTGGCGTTGATCGCTTTGATG
genomic: CAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|208274109|gb|GE073285.1|GE073285
EST:     AGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: AGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|22929725|gb|BU546864.1|BU546864
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCANCNNCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTNNNGCGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|7591481|gb|AW707213.1|AW707213
EST:     GGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|207681905|gb|GD662470.1|GD662470
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|193545458|gb|FK503531.1|FK503531
EST:     GCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
genomic: GCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG
EST: gi|193523358|gb|FK482713.1|FK482713
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGC
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGC
EST: gi|193376952|gb|FK340587.1|FK340587
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCGACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGC
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGC
EST: gi|207753601|gb|GD725999.1|GD725999
EST:     GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGACGTTGATCGCTTTGATG
genomic: GGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtacagcaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggactctgattctgatattttccagcccccactgattgcttttatttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT
                             cactgat  putative branch site (score: 3)
                                   ttgcttttattttttt  CT-rich tract
                                tgattgcttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgccttagtccatcttatggttgaatccaattgggccaaattagggactctgattctgatattttccagcccccactgattgcttttatttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT

-tgcctta
- - - - - - - cttatgg
- - - - - - - - - - - - - - - - - -gccaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgc