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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaacagatacttgaaaacatagtatcatgtggtgaatgctttggctttacttgttgcattgctctcacataatcttgtggatttgatattctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGTGGAACAGTAAACAGAATCACCATTCGAACTGATAAGTTTGGCCAACCCA

Basic information

species Glycine max
transcript GLYMA08G18970.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18970.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
--gttaacagatacttgaaaaca-tagtatcatgtggtgaatgctttggctttacttgttgcattgctctcacataatctt-gtggatttgatattctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGTGGAACAGTAAACAGAATCACCATTCGAACTGATAAGTTTGGCCAACCCA
       ||  ||  |  |  ||  ||| | | ||  ||  | |||||  |  |    ||  |  ||   ||| || |||  ||  |||   | | || | ||||| || ||| | |||||||| || ||||| ||||||||||||||||| ||||| ||||| ||  |  |||| |||   ||||| ||||||||   |||||
gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttg--tgaaggaatttta--gcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
















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|192331322|gb|FK021019.1|FK021019
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|298176392|gb|HO023093.1|HO023093
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|192331321|gb|FK021018.1|FK021018
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|9986244|gb|BE660352.1|BE660352
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|192293827|gb|FG986036.1|FG986036
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|151400813|gb|EV270627.1|EV270627
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|298164876|gb|HO010873.1|HO010873
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|151395650|gb|EV265527.1|EV265527
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|209716504|gb|BW653892.1|BW653892
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|207773491|gb|GD744531.1|GD744531
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAAGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|18039322|gb|BM307616.1|BM307616
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|192295486|gb|FG987100.1|FG987100
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|192310468|gb|FG999183.1|FG999183
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|192310467|gb|FG999182.1|FG999182
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
EST: gi|213593154|gb|DB969896.1|DB969896
EST:     GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAAT                         GTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT
genomic: GTCAGGCCAATAAAGAGGAAATAGATTCTCGATCAGTCTTTGTAGGCAATgtgagctctc ... ttctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttacttgttgcattgctctcacataatcttgtggatttgatattctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGTGGAACAGTAAACAGAATCACCATTCGAACTGATAAGTTTGGCCAACCCA
                                           tattctcc  CT-rich tract
                                     atttgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaacagatacttgaaaacatagtatcatgtggtgaatgctttggctttacttgttgcattgctctcacataatcttgtggatttgatattctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGTGGAACAGTAAACAGAATCACCATTCGAACTGATAAGTTTGGCCAACCCA

- - - - - - - -aaaacata
- - - - - - - - - - - - - tcatgtg
- - - - - - - - - - - - - - - - - -gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttgtg