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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaacctgtaaaatagatcttggtttgtcacttgttcaaagaggcacttccttcttccccagttttgcaaaatgatgaatcagatttttcttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTGTACAGAATTAAGGTTC

Basic information

species Glycine max
transcript GLYMA11G14530.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G14530.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g62650.1 (Oryza sativa), 3'ss of exon 8
--------acaacctgtaaaatagatcttggtttgtcacttgttcaaagaggcacttccttcttccccagttttgcaaaatgatgaatcagatttttcttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTGTACAGAATTAAGGTTC
        | ||  || |    | ||  || | | ||  || ||       |   ||  || |       |||||     |  |   |  ||    |   |  | ||||| |||||||| ||||| ||||  || ||||||||||| || || ||||| |||||||||||||| || |||||| |||| ||||   || | |||||||
ccccccggaaaagttgcattcaacattctgatctctctgttttttt-----gtttttgtttttgttttgtttttgtgttttttt---tttgaaaaataacacttgcagGCCATGATGAAGGATCAGTTTGGTAACTATGTTGTACAGAAAGTACTGGAGACTTGTGATGATCAGCAGCGTGAGTTGATCCTGTCACGAGTAAAGGTTC

upper sequence: GLYMA11G14530.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g05100.t01 (Vitis vinifera), 3'ss of exon 7
acaacctgtaa--aatagatcttggtttgtcacttgttcaaagaggcacttccttcttccccagttttgcaaaatgatgaatcagatttttcttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTGTACAGAATTAAGGTTC
  |  |||     | || |  || | || |  |||| |   |  |  || ||    |       |||  ||   || ||  ||   ||  |  |  ||  |||| |||||||||||||| |||||||| ||||||||||||||||||||||| ||||||||||| || || |||||||||||  ||| | ||||||||||||
-gattctgatgctattaaaattttgcttattgcttgatttcatggttacgtcaacatatagttatttcccactttgttgt-tcttgttgcttgtgcatctagGCTATGATGAAAGATCAGTTTGCAAACTATGTTGTACAAAAGGTGCTGGAGACTTGTGATGACCAGCAGCGTGAGCTGATCTTGTCCCGAATTAAGGTTC

upper sequence: GLYMA11G14530.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------acaacctgtaaa-atagatcttggtttgtcact-tgttcaaagaggcacttccttcttcc----ccagttttgcaaa-----------------------atgatgaat-cagattt---------ttcttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTGTACAGAATTAAGGTTC
                                         ||     ||   || || |||| | |   | |  |||    |||  |  | ||||   |     | || ||| ||                        ||| ||||| ||  | |         ||||  ||| |||||||||||||| || || ||||||||||| ||||| || |||||  ||||||| ||||||||    ||||| |||||| | ||   | |||||   || |
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC

upper sequence: GLYMA11G14530.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S35_216V6.1 (Physcomitrella patens), 3'ss of exon 9
-----acaacctgtaaaatagatcttggtttgtcacttgttcaaagaggcacttccttcttccccagttttgcaaaatgatgaatcagatttttcttat----atacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTGTACAGAATTAAGGTTC
        ||||||  |  |     || |||||    || | || |   || ||  |||       | | |||  | |||  |  | ||| ||   |      || ||||||||||||||||| || |||||||| || || || || |||||| ||||||| ||||||||    ||||| |||||| | |||    | |||  |||||
ggatttgtacctgtggaggaagc--tgatttgtgttatggtgaatgcctcaattgtttcc------ggtatgcgta-tgagtagcctgatgttcggtgatgtgatgcagGCAATGATGAAAGACCAGTTTGCAAACTACGTGGTCCAGAAGGTGTTGGAAACCTGTGATGAATCTCAACGCGAGCTGTTGCTGGGTCGTATTCGGGTTC

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|15200699|gb|BI424484.1|BI424484
EST:     TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAG                         GCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
genomic: TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAGgtgtgttgaa ... ttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
EST: gi|151393232|gb|EV263107.1|EV263107
EST:     TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAG                         GCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
genomic: TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAGgtgtgttgaa ... ttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
EST: gi|254341616|gb|GR852753.1|GR852753
EST:     TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAG                         GCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
genomic: TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAGgtgtgttgaa ... ttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
EST: gi|15201417|gb|BI424860.1|BI424860
EST:     TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAG                         GCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
genomic: TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAGgtgtgttgaa ... ttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
EST: gi|254341617|gb|GR852754.1|GR852754
EST:     TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAG                         GCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
genomic: TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAGgtgtgttgaa ... ttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
EST: gi|120492720|gb|EH220887.1|EH220887
EST:     TACTAGTGAGTGAGATGCTNGGCTCCACAGATGAAAATGAACCTCTTCAG                         GCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA
genomic: TACTAGTGAGTGAGATGCTTGGCTCCACAGATGAAAATGAACCTCTTCAGgtgtgttgaa ... ttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttccttcttccccagttttgcaaaatgatgaatcagatttttcttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTGTACAGAATTAAGGTTC
                                       tttttcttat  CT-rich tract
                                    agatttttcttatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaacctgtaaaatagatcttggtttgtcacttgttcaaagaggcacttccttcttccccagttttgcaaaatgatgaatcagatttttcttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTGTACAGAATTAAGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- -acctgta
- - - - - - - - - - - - -tgtcact