Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatacaaggaaaaccatttttctggagcctattatatatgtattcatttatgtgatttgttttgcggtaaactcacagaatattaccttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

Basic information

species Glycine max
transcript GLYMA08G20830.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
-------------------------------------------ttgcatacaaggaa-aaccat-----ttttctggagcctattatata----tgtattcatttatgtgatttgt-tttgcggtaaactcacagaatattacc----------------ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
                                            ||  |||  |    |  | |     | || ||  |  |   |  |     || ||    || | |  | | |  | |   || | |  || ||||| | |                 |||  |||||||||||||||| ||||| ||||| || ||||| || || |||||||| ||||| ||||| || || |||||||||   | |||||||||||| || |||
gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggctgcataagattctctattctatactagtaatagaatgtcacaatatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 8
-----------ttgcatacaaggaaaaccatttttctggagcctattatatatgtatt--------catttatgtgatttgttttgcggta--aactcacagaatattaccttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
           || || || |  | |  | | |   |||||  ||| |  |   || |        || ||||   ||  |||| |  |||  |  ||      | ||  ||| | |  || |||||| | || || ||||| || || |||||||||||||| |||||||| |||||||| || ||||||||||||  ||||||||| ||  |||| || 
gtgagcttttatttcacactaacatatac-tctacttggagaatatcaagtgaatactgcccttctcaattatcctataagtttcgttgtactatttctatacctgttgtcttct-tgtagCTTTGAGCAGCATGAGGCCCCAGGTTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTC

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
------------------------------------ttgcatacaaggaaaaccat---ttttctggagccta----ttatatatgtattcatttatgtgatttgttttgcggtaaactcacagaa-tattaccttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
                                    |||  || |||| ||  | |   |||| |     |||     || | |  | || | ||   | ||| ||  ||   | | ||     || |    | | |||| |||||||||||| || ||||| ||||| || ||||| ||||| |||||||| || || ||| | ||||| ||||||||||  | |||||||||| | || |||
gttagtaaccccccttgaacttcagtaacattattgttgattagaaggcaatgcttagattttatcatttctaatggctacaaacattttaagtttatttattggtcatggtcttatctggtttaactggggcatcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 8
-------------------------ttgcatacaagg-----aaaaccatttttctggagcctattatatatgtattcatttatgtgatttgttttgcggtaaactcacagaatattacct---------tttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
                         || | |||||       |  |   | |   |||||  ||||   |   || | |  |     |||    |    ||   ||   |   |  |||||         ||  |  || |||||| | || || ||||| || || |||||||||||||| |||||||| || ||||| || |||||||| |||  ||||||||| ||  || | || 
gtgagcttttagtttacactttttatttcctacaatatgttcagtatactctacttggagaatattgggtggatactgaccttatcaattatcctaaaagtttccttgtatttttatacctgttcatgtcttcttgtagCTTTGAGCAGCATGAGGCCCCAGGCTCAAGATCATTTTTCACTGAGATTATAGCCTCAATTTCGGACATAAAGTTTTCGAAGGATGGGAGGCATCTTCTC

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 8
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------------------------------------------ttgcatacaaggaaaaccatttt---tctggagcctattatatatgtattcattt--atgtgatttgttttgcggtaaactcacagaatattaccttttgt-----------acagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
                                                                       |    | | |      |||||    | |    | | |  | |  | | | | ||  |  |||    |  |  | |||| |  | ||  | |  |  ||||           |||||||||| ||||  ||||| ||||| || |||||||||||||||||||| || || ||||| ||||| || |||||    |||||||| ||||| ||||||
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT

upper sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
ttgcat--acaaggaaaaccatttttctggagcctattatatatgtattcatttatgtgat-ttgttttgcggtaaactcacagaatattaccttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
 |||||  |  ||| |||            | | | ||  |  |  |    ||||| |  |  | |||   ||   | |||  || || ||| ||   | ||| |||||||||||||| || ||||| || |||||||||||||||||||| || || ||||| |||||||| ||||||   ||||||||||||| |||||| 
-tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttagtgctctttcctggatcagtcagtga-tagtac-ttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC

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|193650550|gb|FK599845.1|FK599845
EST:     CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|207794480|gb|GD764791.1|GD764791
EST:     GTCTTAGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: GTCTT-GTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|208290901|gb|GE086773.1|GE086773
EST:     CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|14990248|gb|BI315921.1|BI315921
EST:     CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|208198530|gb|GD995551.1|GD995551
EST:     CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|208255790|gb|GE052769.1|GE052769
EST:     CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|193488304|gb|FK456127.1|FK456127
EST:     CTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|208216614|gb|GE012546.1|GE012546
EST:     CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|207767896|gb|GD740308.1|GD740308
EST:     CTTGTTTGACTTTGTCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CTTG-TTGAC-TTG-CGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|208333147|gb|GE128194.1|GE128194
EST:     CATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|207823418|gb|GD795745.1|GD795745
EST:     CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|208073582|gb|GD869431.1|GD869431
EST:     GTCTTGTTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: GTCTTG-TTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|193687174|gb|FK630415.1|FK630415
EST:     CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttac ... ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTAT
EST: gi|207842807|gb|GD817319.1|GD817319
EST:     TCATGCCAAACTT                         ATTTTGTAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGAT
genomic: TCATGCCAAAC-Tgtaagcttac ... ttttgtacagA-TTTG-AGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttatgtgatttgttttgcggtaaactcacagaatattaccttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
                           aactcac  putative branch site (score: 2)
                                        ttacctttt  putative PPT
            atttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatacaaggaaaaccatttttctggagcctattatatatgtattcatttatgtgatttgttttgcggtaaactcacagaatattaccttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA