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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttatttcagcgaatcctttgtttcatagtcatcaatatgggccattactcttgactttgttggttgctatgtgggattgtttttctggaaccagTTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGATGGAATCTTCGGGTTTGGGCAGCAAGGAATGTCTGTCATTTCTCAGCTT

Basic information

species Arabidopsis thaliana
transcript AT5G22850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G22850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G30430.1 (Glycine max), 3'ss of exon 3
gtgagtttatttcagc--gaatcctttgtttcatagtcatcaatatgggccattactcttgactttgttggttgctatgtgggattgtttttctggaaccagTTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGATGGAATCTTCGGGTTTGGGCAGCAAGGAATGTCTGTCATTTCTCAGCTT
||||||||   | |||  |||    ||| ||| |  || |   | |      ||| | |||  ||  |   |||  | |      | |||   |||| | || || ||||     || || || || ||    |||||||||||||| |||||||| || || || |||||||| || | ||||||||||||||||||||| 
gtgagttttcatgagcctgaaatggttgattc-tgttcctgttttttcatgtttattgttgttttaatc--ttggaaagcattggtttttgaatggagc-agATGTAGCAATCAGCAAACTGGGGACTTGACAAAGTCTGATAGAGCAGTTGATGGGATATTTGGATTTGGGCAACAGGAAATGTCTGTCATTTCTCAGCTC

upper sequence: AT5G22850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G05490.1 (Glycine max), 3'ss of exon 3
gtgagtttatttcagc--gaatcctttgtttcatagtcatcaatatgggccattactcttgactttgttggttgctatgtgggattgtttttctggaaccagTTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGATGGAATCTTCGGGTTTGGGCAGCAAGGAATGTCTGTCATTTCTCAGCTT
||||||||   | |||  |||    |||  |   | || |   | |      ||  | |||  ||  |   |||  | |      | |||   |||| | ||||| |||| |   || || || || ||    |||||||||||||| |||||||| || || || |||||||| || | |||||||||||||||||| |||
gtgagttttcatgagcctgaaatggttgaatttcattcctgttttttcatgtttgttgttggtttaatc--ttggaaagcattggtttttgaatggagc-agTTGTAGCAACCAGCAAACTGGGGACTTGACAAAGTCTGATAGAGCAGTTGATGGGATATTTGGATTTGGGCAACAGGAAATGTCTGTCATTTCTCAACTT

upper sequence: AT5G22850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G08870.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------gtgagtttatttcagcgaatcctt--tgtttcatagt--catcaatatgggccattactcttgactttgttggttgctatgtgggattgtttttctg-gaaccagTTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGATGGAATCTTCGGGTTTGGGCAGCAAGGAATGTCTGTCATTTCTCAGCTT
                                                         ||   | |  |   | || ||     |  |||| | |  |||    |||      |    || |  |||        |   |   | |||| | ||| | | |||||| |||| |   ||||| || || |||   |||||||| ||||| |||||||| || ||||| |||||||| || || |||||||||||||| || || 
gtgagctatcatgagtttgaaataactgacctcatcaagtaggataagacttttgttgttgttgttgtgtcgtgagtctgaaatagttcaaaatagcattcccatgtatttgttagtttaaacttggaaagcattgccttataatgttgtgctgtggaacagTTGTAGCATCCTGCAGACTGGGGACTTAACAAAGTCTGAGAGAGCAGTTGATGGGATATTCGGATTTGGGCAACAGGGCATGTCTGTCATTTCCCAACTC

upper sequence: AT5G22850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G19640.2 (Glycine max), 3'ss of exon 3
------------------------------------------------------gtgagtttatttcagcgaatcctt--tgtttcatagt--catcaatatgggc-cattactcttgactttgttgg--ttgctatgtgggattgtttttctggaaccagTTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGATGGAATCTTCGGGTTTGGGCAGCAAGGAATGTCTGTCATTTCTCAGCTT
                                                      ||   | |  |   | || ||     || |||| | |  |||    |||      ||| | |  | || |   |  ||||  | |    ||||  |  |||||| ||||| |||| |   ||||| || || |||   |||||||| ||||| |||||||| || || || ||||| || ||||| |||||||||||||| || || 
gtgagctatcatgagttagaaataaccgacctcgtcaagtaggataaggcttttgttgttgttgtattgtgagtctgaaatggttcaaaatagcattcccatgtatatgttagtttaaaattggaaagcattgccttataattttgtgctg-tggaac-agTTGTAGCATCCTGCAGACTGGGGACTTAACAAAGTCTGAGAGAGCAGTTGATGGGATATTTGGATTTGGACAACAAGGCATGTCTGTCATTTCGCAACTC

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|164060341|gb|ES199724.1|ES199724
EST:     CCGGTTGTGTTTGG                         TTGCAGTCACCTCTCAGACGGGTAGATTTAGTGAAGTCTGATAGAGCGGTT
genomic: CCGGTTGTGTTTGGgtgagtttat ... ctggaaccagTTGCAG-CACCTCTCAGACGGG-AGATTTAGTGAAGTCTGATAGAGCGGTT
EST: gi|86063836|gb|DR359593.1|DR359593
EST:     ATTGTGGGAAGCTCTCTGGTCCCAAACTCAACGGCTCCGGTTGTGTTTGG                         TTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGA
genomic: ATTGTGGGAAGCTCTCTGGTCCCAAACTCAACGGCTCCGGTTGTGTTTGGgtgagtttat ... ctggaaccagTTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGA
EST: gi|164218357|gb|ES147341.1|ES147341
EST:     CCGGTTGTGTTTGG                         TTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGA
genomic: CCGGTTGTGTTTGGgtgagtttat ... ctggaaccagTTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGA
EST: gi|86063835|gb|DR359592.1|DR359592
EST:     ATTGTGGGAAGCTCTCTGGTCCCAAACTCAACGGCTCCGGTTGTGTTTGG                         TTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGA
genomic: ATTGTGGGAAGCTCTCTGGTCCCAAACTCAACGGCTCCGGTTGTGTTTGGgtgagtttat ... ctggaaccagTTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggccattactcttgactttgttggttgctatgtgggattgtttttctggaaccagTTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGATGGAATCTTCGGGTTTGGGCAGCAAGGAATGTCTGTCATTTCTCAGCTT
         tcttgac  putative branch site (score: 3)
                                     ttgtttttct  putative PPT
                                    attgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttatttcagcgaatcctttgtttcatagtcatcaatatgggccattactcttgactttgttggttgctatgtgggattgtttttctggaaccagTTGCAGCACCTCTCAGACGGGAGATTTAGTGAAGTCTGATAGAGCGGTTGATGGAATCTTCGGGTTTGGGCAGCAAGGAATGTCTGTCATTTCTCAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT