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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacttttgtttttgtttttctttctcccaccatatatctcctgtgtgaagggttatatttatcttatggatgagtaagtatttgatttgatattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCATAAACGACGAGTTGATGTTGGATGGGAACCCAAGGTTGAATTTGGCATCA

Basic information

species Glycine max
transcript GLYMA18G04940.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G04940.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0079g00600.t01 (Vitis vinifera), 3'ss of exon 1
--------taacttttgtttttgtttttctttctcccaccatatatct-------cctgtgtgaagggttatatttatcttatggatgagtaa-gtatttgatttgatattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCATAAACGACGAGTTGATGTTGGATGGGAACCCAAGGTTGAATTTGGCATCA
          || | | | ||| | | ||| ||||   | |||||| |        |   ||| |    || || ||| ||  | || |  ||  ||| |    || |  ||  |||||||||||  ||||| | |||||||||||||||||||| |||||||| |||||||||||| ||||| ||||||||||||| ||| ||||  |||| |||
gtcattatctacatctctctttctctctctctctctttctatatatatgtttggatccaggtggaaatatacatatatgttcggaattatgaacatatatagggtggtggtg-cagGTTCAAGATTCCGGAGAATTCGATACCGAAGGAGGCAGCGTACCAGATAATAAACGACGAGCTGATGCTGGATGGGAACCCGAGGCTGAACCTGGCTTCA

upper sequence: GLYMA18G04940.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g06600.t01 (Vitis vinifera), 3'ss of exon 1
taacttttgtttttgtttttctttc-tcccaccatatatctcctgtgtgaagggttatatttatcttatggatgagtaagtatttgatttgatattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCATAAACGACGAGTTGATGTTGGATGGGAACCCAAGGTTGAATTTGGCATCA
              ||    |  || |   |   |   | |   || |       | | ||| | ||| | | |     ||  || | || |  |    ||||||||| || ||||| | ||||| ||||||||||| || ||||||||||||||||||||  ||||| | ||||| || || ||| | ||  |||| || 
--------------gtaaacccgtcatagtattttgcttttttggtttcttcccctttctttgtttta-gcaggcaggggtgattaaattaacgt--gcagGTTCAAGTTGCCGGAGAACTCGATCCCGAAGGAGGCGGCGTACCAGATCATAAACGACGAACTGATGCTTGATGGCAATCCTAGGCTAAACCTGGCTTCG
















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|213595762|gb|DB966205.1|DB966205
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|9899411|gb|BE608379.1|BE608379
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|209718158|gb|BW677429.1|BW677429
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|209699991|gb|BW652592.1|BW652592
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|213606562|gb|DB959016.1|DB959016
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|213588693|gb|DB957578.1|DB957578
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|7588995|gb|AW704779.1|AW704779
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|209722811|gb|BW682884.1|BW682884
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|7588868|gb|AW704654.1|AW704654
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|213599238|gb|DB960006.1|DB960006
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|209703624|gb|BW656580.1|BW656580
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|9259742|gb|BE347889.1|BE347889
EST:     TGTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|213614307|gb|DB956835.1|DB956835
EST:     CCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|209727302|gb|BW663221.1|BW663221
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|209728381|gb|BW652038.1|BW652038
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|15203394|gb|BI426162.1|BI426162
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|213597758|gb|DB960315.1|DB960315
EST:     TC--TCCACTCAACCTTCGCTTCTCGCTGTGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|209702090|gb|BW652330.1|BW652330
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|209716269|gb|BW657572.1|BW657572
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCGGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|209704261|gb|BW683489.1|BW683489
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|5058355|gb|AI736831.1|AI736831
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|23732463|gb|BU764391.1|BU764391
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|213589811|gb|DB959422.1|DB959422
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
EST: gi|9820626|gb|BE556136.1|BE556136
EST:     TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAG                         GTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT
genomic: TCTGTCCACTCAACCTTCGCTTCTCGCTATGTCAGAACTTCGCTTCCCAGgtatgcatgg ... atattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaagggttatatttatcttatggatgagtaagtatttgatttgatattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCATAAACGACGAGTTGATGTTGGATGGGAACCCAAGGTTGAATTTGGCATCA
                                        atttgat  putative branch site (score: 5)
        ttatatttatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacttttgtttttgtttttctttctcccaccatatatctcctgtgtgaagggttatatttatcttatggatgagtaagtatttgatttgatattgatagGTTCAAGATGGCGGAGGAGTCGATACCGAAGGAGGCAGCATACCAGATCATAAACGACGAGTTGATGTTGGATGGGAACCCAAGGTTGAATTTGGCATCA

- - - - - - - - - - - - ctcccac
- - - - - - - - - - - - - - - - - - - ctcctgt
- - - - - - - - - - - - - - - - - - - - - - -gtgaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg