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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttccttgtctttctttacgaatctgtgtgcaagccttttcttaatctgatgaaaaacaccagaagttgattatattgtgtggttaaaaccccctttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAGAATGTCCAGTGTGCTCACAGTATTTTAAG

Basic information

species Glycine max
transcript GLYMA15G01360.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01360.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g05080.1 (Oryza sativa), 3'ss of exon 4
-----------------gtaagtgttccttgtcttt----ctttacgaatct----gtgtgcaagccttttcttaatctg----atgaa------------aaacacca--gaagttga-ttatattgtgtggttaaaaccccctttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAGAATGTCCAGTGTGCTCACAGTATTTTAAG
                 |  | | |||||||| |||      | | ||| ||    |  || || | | | ||  ||||     || ||            || |||||  | | || | ||| | ||     ||  ||       | | | |||| || ||||||||||| || ||||||||| ||||||||||||||||  | ||||| || || ||| | ||||||||   |
gtatagtacctgtgcatgctaat-ttccttgtttttgacctataaagaagcttctaggatgaaatcttctcctgcatcttctctataaatattcatcgactaaccaccaatggaattaacttaaactgca-aattgcaatgattgatattttcagAGGACGAGCATGATGTCGTGTGGTTTTGGTTGGAGAAAGGCAAGCCACATGAATGCCCTGTCTGCACTCAGTATTTCTCG

upper sequence: GLYMA15G01360.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g06000.t01 (Vitis vinifera), 3'ss of exon 4
--------------------gtaagtgttccttgtctttc-tttacgaatctgtgtgcaagccttt--tcttaatctgatgaaaaacaccagaagtt-gattatattgtg--tggttaaaaccccctttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAGAATGTCCAGTGTGCTCACAGTATTTTAAG
                     |   |  |  || | || | ||||   || | | | |||    ||  | |  |||  || |||  |     || || | ||    |||   |  || |       ||  |||||||| |||||||||||||||||||||||||||||||||||||||||| |  | ||||| || ||||||||||||||||| | |
gtaagcctctgtcacttactctctttaattattattttccatttatttatttct-tacaattaattaatttgcatcccattaaattctttctaattttggttgctctgttatttatttatttgtttttcgtctgcagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCACATGAATGCCCTGTGTGCTCACAGTATTTCACG
















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|17400645|gb|BM177427.1|BM177427
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|254322314|gb|GR837728.1|GR837728
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|7589397|gb|AW705172.1|AW705172
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|10253522|gb|BE821288.1|BE821288
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|192320916|gb|FK013110.1|FK013110
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCGGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|192333618|gb|FK025435.1|FK025435
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGGTGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|6071202|gb|AW100589.1|AW100589
EST:     CAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: CAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|298195945|gb|HO044336.1|HO044336
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATAAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAA
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAA
EST: gi|21677694|gb|BQ630045.1|BQ630045
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|254322313|gb|GR837727.1|GR837727
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|33388406|gb|CA851613.1|CA851613
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|15814678|gb|BI786953.1|BI786953
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|192333647|gb|FK025436.1|FK025436
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGGTGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|14991330|gb|BI317003.1|BI317003
EST:     TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
EST: gi|5677887|gb|AI939017.1|AI939017
EST:     TAAATCTTACTTTGACAGAAGGATAGATGGATGCCCAGGAGATGAAGGCG                         AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: TAAATCTTACTTTGACAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaaacaccagaagttgattatattgtgtggttaaaaccccctttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAGAATGTCCAGTGTGCTCACAGTATTTTAAG
              agttgat  putative branch site (score: 5)
                                       ccccctttttctgc  putative PPT
             aagttgattatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttccttgtctttctttacgaatctgtgtgcaagccttttcttaatctgatgaaaaacaccagaagttgattatattgtgtggttaaaaccccctttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAGAATGTCCAGTGTGCTCACAGTATTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA