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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagattttcttcctgcttctttcttgttcttacgatccttgttaggtcttttggtatttccatttgttcattacgtcctttactgcgatcgttcttta...

Basic information

species Glycine max
transcript GLYMA02G47210.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G47210.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagattttcttcctgcttctttcttgttcttacgatccttgttaggtctt--ttggtatttccatttgttcattacgtcctttactgcgatcgttcttta---
 || ||||| |||||||||||| | || ||| | || |||||||| ||||||||||||||||| || ||  |  | ||| | ||||| ||  | || |||||||  |||||||    ||| || |  ||||||       |   |   |||   ||| | | ||    |   |||| || | || | |  ||   |||   |   
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaa--ttttctttaaactt-ttgcaagttcttgaatatttgaatcattctcagttgatctatcagggt-cgcattgcg-ctttaagtctgagaattccagacat

upper sequence: GLYMA02G47210.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S258_52V6.1 (Physcomitrella patens), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagattttcttcctgcttctttcttgttcttacgatccttgttaggtcttt--tggtatttccatttgttcattacgtcctttactgcgatcgttcttta-----
 |||||||| || ||||| ||| | || ||| | |||||||||||||||||||||||||||||||| || || || || || ||||||||| | |||||||||||   |  | |   |     ||   | |   |  | |||||  ||  | |  |||    || || |||   | | || |   ||  ||||  ||  ||      
CTTTCAGGCGGAAATCAATCAGTTGCTGAGTTTGATCATCAACACCTTCTACAGCAACAAGGAGATTTTCCTGCGAGAACTTATCAGCAATTCTTCTGATgtaagtgctagtgctgacgaaagtcccatgcggtc--ttcttgtcgggattgtagtggccagtctatctgt--gtcatgtgc---acgccgattcttggttggtgca

upper sequence: GLYMA02G47210.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagattttcttcctgcttctttcttgttcttacgatccttgttaggtcttttggtatttccatttgttcattacgtcct--ttactgcgatcgttcttta--------
||| ||||| |||||||| ||  |  | ||| | ||||| ||||||||||| |||||||||||||| ||  | || || |||||||| ||| |||| ||||||||  ||| |||          |||| |  |    |  ||||   ||||  | || | || ||||||   || ||      ||   | |  ||   |||         
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttttttcac-------ccttgcttgtgtactgtttgt---gtctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag

upper sequence: GLYMA02G47210.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ25533 (Selaginella moellendorffii), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaag------attttcttcctgc-----ttctttcttgttctta-cgatccttgttaggtcttttggtatttccatttgttcattacgtcctttactgcgatcgttcttta
 || ||||| |||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||  | || |||||||||||||||||||| ||||| ||      ||  || | | ||     ||   |  | |||| | ||||| |||       || ||  |||||     | || || | | |||| |||||||         
CTTCCAGGCGGAGATCAACCAGCTTCTCAGTCTCATCATCAACACCTTCTACAGCAACAAGGAGATCTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtgttagatgctcgttcggcgatattttactgctattctcatcgatctttgcctt-ctttctgcgatttctcaccgatctttgcattcttt-ctgcgatttccag---

upper sequence: GLYMA02G47210.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ29061 (Selaginella moellendorffii), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagattttcttcctgcttctttcttgttcttacgatccttgttaggtcttttggtatttccatttgttcattacgtcctttactgcgatcgttcttta
 || ||||| |||||||||||||| |||||||| ||||||||||| |||||||||||||||||||| ||  | || |||||||||||||||||||| ||||| ||  ||||  |        | ||||||||| |  | ||||| |     |||     |||   |  | |    |  |  | ||| |            
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcc--------tccttgttcttccagttcttgtcaaactcttt----cttcttctcatgctgcgccgctgtgactccag----------

upper sequence: GLYMA02G47210.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ22362 (Selaginella moellendorffii), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaag------attttcttcctgc-----ttctttcttgttctta-cgatccttgttaggtcttttggtatttccatttgttcattacgtcctttactgcgatcgttcttta
 || ||||| |||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||  | || |||||||||||||||||||| ||||| ||      ||  || | | ||     |||  |    |||| | ||||| |||       || ||  |||||     | || || ||| |||| |||||||         
CTTCCAGGCGGAGATCAACCAGCTTCTCAGTCTCATCATCAACACCTTCTACAGCAACAAGGAGATCTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtgttagatgctcgttcggcgatatttcactgcgattctcatcgatctttgcctt-ctttctgcgatttctcaccgatctttgcgttcttt-ctgcgatttccag---

upper sequence: GLYMA02G47210.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagattttcttcctgcttctttcttgttcttacgatccttgttaggtcttttggtatttccatttgttcattacgtcctttactgcgatcgttcttta
 || ||||| |||||||||||||| |||||||| ||||||||||| |||||||||||||||||||| ||  | || |||||||||||||||||||| ||||| ||  ||||  |           | |||||| |  | ||||| |     |||  | ||  |||   | |  | |      | | |             
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcc-----------tcgttcttccagttcttgtcaaactctttcttcttctcatgc-tgcgctgctgtgactccag-------------

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|209706912|gb|BW653153.1|BW653153
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|208055391|gb|GD854570.1|GD854570
EST:     ACAGCAACAAGGAGACCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAA
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAA
EST: gi|209715369|gb|BW684678.1|BW684678
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|213608197|gb|DB963057.1|DB963057
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|213595973|gb|DB966276.1|DB966276
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|192324535|gb|FK016786.1|FK016786
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|11275146|gb|BF325469.1|BF325469
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|209722271|gb|BW651261.1|BW651261
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|192297661|gb|FG989580.1|FG989580
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATCCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|213616959|gb|DB959271.1|DB959271
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|4296389|gb|AI442468.1|AI442468
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|213589308|gb|DB961641.1|DB961641
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|213597221|gb|DB962067.1|DB962067
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|8826909|gb|BE210639.1|BE210639
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|6455834|gb|AW186517.1|AW186517
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|209696909|gb|BW660474.1|BW660474
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|18040372|gb|BM308666.1|BM308666
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|298182250|gb|HO026425.1|HO026425
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAGTGCCTCTGAT                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagatttt ... tacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagattttcttcctgcttctttcttgttcttacgatccttgttaggtcttttggtatttccatttgttcattacgtcctttactgcgatcgttcttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA