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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgttatatttcacatgtatatacagagttttttccctggttgtcacgttgaagcttagctaccttgagttgggtaacagcttttatatttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGCCCCACGGTGAAAACATTGAAGAGTATGGTAAATTGTGCCGAGAGAGGAC

Basic information

species Glycine max
transcript GLYMA06G03070.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G03070.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g13370.t01 (Vitis vinifera), 3'ss of exon 2
caatgttatatttcacatgtatatac-agagttttttccctggttgtcacgttgaagcttagctacct-tgagttgggtaacagcttttatatttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGCCCCACGGTGAAAACATTGAAGAGTATGGTAAATTGTGCCGAGAGAGGAC---
  |    |  | ||| ||| |      ||  |    |    |     | | | |    |||  |  |  | | || || |  |  ||  ||  || ||| ||||   |  ||||||||||||||||||||||| ||||| ||||| |||||||| |||  |||||| ||||| |||||||| ||||||||||| || |||||   
-gagtccaactgtcaaatggaggccttagtctaaaattaaagaacacctcatggttttttaattgtcaataactttggaaggaaattgcattctt-tttcagGT---AGAGTTGCAATGGAAGGGAAAGTAGAGCATAAATTTGACATGAAGCCTCACAATGAAAATATTGAGGAGTATGGCAAATTGTGCCGTGAAAGGACAAA
















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|19935508|gb|BQ080469.1|BQ080469
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|9898659|gb|BE607627.1|BE607627
EST:     CATGTTTAAAGACTACGTTCCTATGTGTGTCTTCTCTGAGACTATCCAAG                         GTGTGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAG
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTG-GCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAG
EST: gi|58023918|gb|CX710659.1|CX710659
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|19935238|gb|BQ080268.1|BQ080268
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|192294408|gb|FG987337.1|FG987337
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|298182572|gb|HO031307.1|HO031307
EST:     CATGTTTGAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|19348661|gb|BM893193.1|BM893193
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|151398032|gb|EV267910.1|EV267910
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|298193573|gb|HO040221.1|HO040221
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|213601504|gb|DB970420.1|DB970420
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|209722481|gb|BW668756.1|BW668756
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|58024109|gb|CX710850.1|CX710850
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|298191952|gb|HO036034.1|HO036034
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|7147539|gb|AW509461.1|AW509461
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|192300028|gb|FG991846.1|FG991846
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|298170674|gb|HO019298.1|HO019298
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|209702688|gb|BW675663.1|BW675663
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
EST: gi|9564300|gb|BE473809.1|BE473809
EST:     CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAG                         GTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC
genomic: CATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGACTAGCCAAGgtgagaatcg ... tttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacgttgaagcttagctaccttgagttgggtaacagcttttatatttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGCCCCACGGTGAAAACATTGAAGAGTATGGTAAATTGTGCCGAGAGAGGAC
                            gggtaac  putative branch site (score: 3)
                                             tttatttt  putative PPT
                               taacagcttttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgttatatttcacatgtatatacagagttttttccctggttgtcacgttgaagcttagctaccttgagttgggtaacagcttttatatttattttagGTGGCAAGGTTGCAATGGAAGGGAAAGTAGAACATAAGTTTGATATGAAGCCCCACGGTGAAAACATTGAAGAGTATGGTAAATTGTGCCGAGAGAGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
caatgtt
- - - - - - - -catgtat
- - - - - - - - - - - - - - - - - ttccctg
- - - - - - - - - - - - - - - - - - - - - -tgtcacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgggt