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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccattccatgattgcagttgttcttcaattaattagaattgttcatgttctgattacttgtaagctattcccattgtag

Basic information

species Glycine max
transcript GLYMA17G34690.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os01g51410.2 (Oryza sativa), 5'ss of exon 10
AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccattccatg-attgcagttgttcttcaattaattagaattgttcatgttctgattacttgtaagctattcccattgtag
||  | || || |||||||||||||||||||||||||| ||||| |||||||||||||||||  | ||||| |||||||||  ||||    | | |||   |   ||   || | | |||    | | |||  | || | | | |  |      |   ||| ||
AAACACTACCCAGTTCTTTTCCGTGGAGTCAATGGAACTGTTGCCCATGAATTCATCATTGATTTAAGAGGATTTAAGgta--tccaacataggtattttggcatttggacattgagttatgcatttccat--tttgttaattggatattggaactttttgcag

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os06g40940.1 (Oryza sativa), 5'ss of exon 11
AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccattcca-tgattgcagttgttcttcaattaattagaattgttcatgttctgattacttgtaagctattcccattgtag
||  | || || |||||||||||||||||||||||||| ||||| ||||| ||||| |||||  | ||||| |||||||||  || ||   | | |||   |   ||   |  | | |||    | |  || |||| |  | | |  | |    ||  ||| ||
AAACACTACCCAGTTCTTTTCCGTGGAGTCAATGGAACTGTTGCCCATGAGTTCATTATTGATTTAAGAGGATTTAAGgta--tctatcatagttattttggcatttggaccttgagttatgcatttcaattttctta--attggatatcgcaaccttttgcag

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G104310_T02 (Zea mays), 5'ss of exon 9
AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccattccatgattgcagttgttcttcaattaattagaattgttcatgttctgattacttgtaagctattcccattgtag
||  | || || ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| || || |  |||||||||  |  ||   |   |     | |   || ||  |   |     ||   |   ||| |  | |||||  |  ||         
AAACACTACCCAGTTCTGTTCCGTGGAGTCAACGGAACTGTTGCCCATGAATTCATCATTGATCTAAGGGCATTTAAGgtacttttatctgac--tcatgttagcaattgaaccatgcattgcggtctctaacctgctc-cctgtaactttgtcag-------

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 11
lower sequence: AT4G33010.2 (Arabidopsis thaliana), 5'ss of exon 10
AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccattccatga-ttgcagttgttcttcaattaattagaattgttcatgtt-ctgattacttgtaagctattcccattgtag
||  | || || |||||||||||||| || || |||||||| || || ||||||||||| ||| |||||||||| |||||| |   ||    |||  || | ||    |  | ||  || |  |  | ||| |  ||||    ||  ||  |       | |   
AAACACTACCCAGTTCTTTTCCGTGGTGTTAACGGAACAGTAGCACACGAATTCATCATAGACTTGAGAGGCTTCAAGgtatgaaaatgttgtgaactgaaattaaagt--agttgttttgggt-atgcatatcactgaccgattcaaatatgaatttgtag---

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 11
lower sequence: AT2G26080.1 (Arabidopsis thaliana), 5'ss of exon 11
AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccattc-catgattgcagttgttcttcaattaattagaattgttcatgtt---ctgattacttgtaagctattcccattgtag
|   | || || |||||||||||||| |||||||||||||| ||||| ||||||||||||||| ||||||| || |||||| ||   ||    |  ||  |||   |  ||  ||  || |  |||| |||| |      ||  |||||    | | | ||      
AGCCACTACCCAGTTCTTTTCCGTGGTGTCAATGGAACAGTCGCTCACGAATTCATCATTGACTTGAGAGGATTCAAGgtatgtttctttatctcgtttgagtaaatgctctgttttttgg--ttgtacatgctaaatcaatgtcttgttcaatgtcctcag-----

upper sequence: GLYMA17G34690.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 5'ss of exon 11
AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtcc-attccatgattgc---agttgttcttcaattaattagaattgttcatgttctgattacttgtaagctattcccattgtag
||  | |||||| ||||||||||||| ||||||||||||||||| |||||||||||  ||||| |||||||||| ||||||  |   | |  ||  | ||   | ||  || |  |||  | | | |||||  |  | ||| ||     |||  | |     || ||
AAGCACTATCCCATTCTTTTCCGTGGCGTCAATGGAACAGTTGCCCATGAATTCATTGTTGACTTGAGAGGCTTCAAGgtagtttttactaaatattcgctataattcatcctttatttgtcatatttgttatttatttgactaaccacaagtcaatattgctgcag

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|20448765|gb|BQ252889.1|BQ252889
EST:     TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAG                         AATACTGCTGGAATTGAGCCTGAAGAT
genomic: TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccat ... cccattgtagAATACTGCTGGAATTGAGCCTGAAGAT
EST: gi|26058323|gb|CA801237.1|CA801237
EST:     TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAG                         AATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
genomic: TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccat ... cccattgtagAATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
EST: gi|209717715|gb|BW671533.1|BW671533
EST:     TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAG                         AATACTGCTGGAATTGAGCCTGA
genomic: TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccat ... cccattgtagAATACTGCTGGAATTGAGCCTGA
EST: gi|20075344|gb|BQ094127.1|BQ094127
EST:     TCAATGGAACAGTTGCTCATGAATTCATCATTGACTTGAGAGGCTTTAAG                         AATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
genomic: TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccat ... cccattgtagAATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
EST: gi|120493515|gb|EH221682.1|EH221682
EST:     TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAG                         AATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
genomic: TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccat ... cccattgtagAATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
EST: gi|13480387|gb|BG509730.1|BG509730
EST:     TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAG                         AATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
genomic: TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccat ... cccattgtagAATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
EST: gi|20812005|gb|BQ296483.1|BQ296483
EST:     TCAATGGAACAGTTGCTCATGAATTCATCATTGACTTGAGAGGCTTTAAG                         AATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
genomic: TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccat ... cccattgtagAATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
EST: gi|192315105|gb|FK009929.1|FK009929
EST:     TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAG                         AATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC
genomic: TCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccat ... cccattgtagAATACTGCTGGAATTGAGCCTGAAGATGTTGCAAAGCGCCTCATGGACTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTATTATCCCGTTCTTTTCCGTGGAGTCAATGGAACAGTTGCTCATGAATTCATCATTGACCTGAGAGGCTTTAAGgtaagtccattccatgattgcagttgttcttcaattaattagaattgttcatgttctgattacttgtaagctattcccattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG