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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgattttggaataggctattgtgtttatgtgactttggtctttctttgttttcattaagaaattattggctgactttttgtatgttattggtgcttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATGCAAGGAAGCAATGCCCGTTTCTTGGCTTGTGAAGTGTAACAGAACTGCA

Basic information

species Glycine max
transcript GLYMA10G28530.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G28530.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 12
gttgattttggaataggctattgtgtttatgtgactttggtctttctttgttttcattaagaaattattggctgactttttgtatgttattggtgct-tgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATGCAAGGAAGCAATGCCCGTTTCTTGGCTTGTGAAGTGTAACAGAACTGCA-
     | |   |  |  ||       || | | |        | ||||  ||| |  |   || || ||  |||| || || | || |  || | || |  | ||||| |||| || || |||| ||||||||||||||||||| | || || |||||||| ||||||||||| || |||||  | |||  |  | | ||| ||   
----gtatgcaatcatcctgaaacaattttatcagcaccag-tgtcttgttttcccatgcaaagttgtta-ctga-ttgttat-tgctgctgcttctgtcaatcagAATTGAAGGGAGTACCAGTTGAGATTTTGGTGAAATTGATCCCGGAACATGCAAGAAAGCAATGCCCCTTCCTTGGGCTATGAT-TCCATCTGAAATGTGA
















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|23729240|gb|BU762707.1|BU762707
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATG--A-                         A-CTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|19453358|gb|BM954768.1|BM954768
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATG--A-                         A-CTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|254331482|gb|GR843439.1|GR843439
EST:     TTTAATTTCAAATCCCAT-G---                         AACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: TTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|214005861|gb|DB988702.1|DB988702
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCAT-G---                         AACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|31307101|gb|CD392304.1|CD392304
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATG--A-                         A-CTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|151395928|gb|EV265805.1|EV265805
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATG--A-                         A-CTGAAAGGTGTTCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|21677182|gb|BQ629533.1|BQ629533
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATG--A-                         A-CTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|254344096|gb|GR851006.1|GR851006
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCAT-G---                         AACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|9983502|gb|BE657610.1|BE657610
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCAT-G---                         AACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|16342133|gb|BI967728.1|BI967728
EST:     TTCCTTCCACCACTATTTAATTTCAAATCCCAT-G---                         AACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: TTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|27426035|gb|CA937555.1|CA937555
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATG--A-                         A-CTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|16104780|gb|BI892520.1|BI892520
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATG--A-                         A-CTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|7029921|gb|AW459704.1|AW459704
EST:     GATTCCTTCCACCACTATTTAATTTCAAATCCCAT-G---                         AACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: GATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|18039146|gb|BM307440.1|BM307440
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCAT-G---                         AACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|10253276|gb|BE821042.1|BE821042
EST:     GATTCCTTCCACCACTATTTAATTTCAAATCCCAT-G---                         AACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: GATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|214004064|gb|DB984970.1|DB984970
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCAT-G---                         AACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|207786927|gb|GD755386.1|GD755386
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATG--A-                         A-CTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTT
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTT
EST: gi|22929643|gb|BU546782.1|BU546782
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCAT-G---                         AACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
EST: gi|24206278|gb|BU965531.1|BU965531
EST:     CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATG--A-                         A-CTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG
genomic: CCAAATGGCCGATTCCTTCCACCACTATTTAATTTCAAATCCCATGGTATgttgattttg ... cttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcattaagaaattattggctgactttttgtatgttattggtgcttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATGCAAGGAAGCAATGCCCGTTTCTTGGCTTGTGAAGTGTAACAGAACTGCA
                   ggctgac  putative branch site (score: 3)
     attaagaaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgattttggaataggctattgtgtttatgtgactttggtctttctttgttttcattaagaaattattggctgactttttgtatgttattggtgcttgtaccagAACTGAAAGGTGTCCCAGCTGAGATTTTGGTGAAATTGGTTCCAGAGCATGCAAGGAAGCAATGCCCGTTTCTTGGCTTGTGAAGTGTAACAGAACTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA