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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtttacaattctgtttcgtaaactcaaagatgtatcggttagaagtctcttagtccaaactgtgttttcaacatag

Basic information

species Arabidopsis thaliana
transcript AT2G05990.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G125052_T01 (Zea mays), 5'ss of exon 8
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgag----tttacaattctgtttcgtaaactcaaagatgtatcggttagaagtctcttagtccaaactgtgttttcaacatag
||||||||| || ||||||||||| ||||| || || |||||||| ||||||||  |    |    |||| |||  | | || |  | | | | |   ||| |    |  ||  || | |  |||           
GTATGGTGGTGGCATGAGTTCTGCTAAAGCAGCTCTCGAGAGTGATACACGGgtatggtcttgcgtaattgtgtaccatgaattttatgttcttttttttaca---tttataaacctatcgatgtag---------

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G070422_T01 (Zea mays), 5'ss of exon 10
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtt----tacaattctgtttcgtaaactcaaagatgtatcggttagaagtctcttagtccaaact----gtgttttcaacatag
||||||||| || ||||||||||| ||||| || || |||||||| ||||||||  | |     | |||| |||    |||| ||     |    |    |    | |  |  |  |   |        |  | | ||||
GTATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgttgcataattgtgtgct-taaattcttcctttccccatgaattcattttctcttttacgtttataaacctgccgatatag

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 10
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtttacaattctgtttc-----gtaaactcaaagatgtatcggttagaagtctct-tagtccaaactgtgt----tttcaacatag-----
 |||||||| |||||||||||||||||||||||||| |||||||| ||||| || || ||  | | |     |     |   ||  | |  ||| ||  ||  |  ||||| |  |  ||| |   |    |||||   ||      
ATATGGTGGTGGTATGAGTTCTGCCAAAGCTGCACTGGAGAGTGATACACGAgtaagcttcaactcccccccccccccgctgacatagatgtgtttcatttttacttctctctcttttaaattacatcatatttcatgctatttcag

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 11
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtttacaattctgtttcgtaaactcaaagatgtatcggttagaagtctcttagtccaaactgtgttttcaacatag------------------------------------------
 |||||||| |||||||||||||| ||||||||||| |||||||| ||||| || || || ||| ||     |  |    |||| |   |      |||   |     | |  |   ||| ||      ||                                           
ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagctt-caactcctacccacaccaccaaaaaaaaactcaccagattacatactgacttagacgtgcttcatttttacttctctctcttttaaattacatcatatgtcatgccttttcag

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA18G31780.1 (Glycine max), 5'ss of exon 9
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtttacaat-tctgtttcgtaaact-------caaagatgtatcggttagaagtctcttagtccaaactgtgttttcaacatag------------------------------------------------
 |||||||| |||||||||||||| ||||||||  |||| ||||| ||| | |||||||| |  | ||| |||   |||||        | | |  ||    |  | | | |  |   |  || | |  ||||  |                                                    
-TATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGAGtgagttttctttctctttttttcaaactactatattatacacatagatatgtgcatttttctcaccttaattttcctttctccccttcccctttgaatatttgaaattatatctcaagttttctgcctcttcagg

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G45990.1 (Glycine max), 5'ss of exon 10
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtttacaat-tctgtttcgtaaactcaaagatgtatcggttagaa--gtctcttagtccaaactgtgttttcaacatag----------------------------------------------------
 |||||||| |||||||||||||| ||||||||  |||| ||||| ||| | |||||||| |  | ||| |||   |||||   | ||    ||  ||||   || | ||  |   | ||   |||||                                                           
ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGAgtgagttttctttctctttttttcaaactactatattacacgaatagatatgtttatttttgtcaccttcattttcctttctccccttcccctttgaatatttgaaattatatcccaagttttctgccttttcag

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S29_256V6.1 (Physcomitrella patens), 5'ss of exon 9
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagttt----acaattctgtttcgtaaactcaaagatgtatcggttagaagtctcttagtccaaactgtgttttcaacatag-------------------
 ||||||||||| ||||| |||||||| |||||||| |||||||||||||| || |||||    | ||   | | ||| |   |  | ||||| || ||  |   | ||   | |  || | |||    |   |||                   
ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagtttttgcataaggttatctcgcag--tggaggatgtctctgtaggtcatatcgaggacgtaatt-tgtcccaactgtagttgcacatctatcttttga

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S99_59V6.3 (Physcomitrella patens), 5'ss of exon 9
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtttacaattctgtttcgtaaactca---aagatgtatcggttagaagtctcttag-tccaaactgtgttttcaacatag-----------------
 ||||||||||| ||||| ||||||||||||||||| |||||||||||||| || ||||    || |||  |   || |||    |  |    ||  ||   | |  |  |  || |   | |     | || |                   
ATATGGTGGAGGGATGAGCTCTGCCAAAGCTGCACTTGAGAGTGACACACGTgtaagttccttat-ctgcgtaagaatctcttgtagtaatcgtcatttgcgaataacccatctctaggttattccgactacttgattagtagcaagtttggt

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|124940242|gb|EL016709.1|EL016709
EST:     AGAGTGACACACGG                         GTGCTTGCATTATGAAGCTGGAAGGAAATCAAACATTAGGGTCAACACCAT
genomic: AGAGTGACACACGGgtgagtttac ... ttcaacatagGTGCTTGCA-TATGAAGCTGGAAGGAAATCAAACATTAGGGTCAACACCAT
EST: gi|124791292|gb|EH880971.1|EH880971
EST:     TGCCAAAGCTGCACTAGAGAGTGACACACGG                         GTGCTTGCATATGAAGCTGGAAGGAAATCAAACATTAGGGTCAACACCATC
genomic: TGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtttac ... ttcaacatagGTGCTTGCATATGAAGCTGGAAGGAAATCAAACATTAGGGTCAACACCATC
EST: gi|47829300|gb|CK118984.1|CK118984
EST:     ATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGG                         GTGCTTGCATATGAAGCTGGAAGGAAATCAAACATTAGGGTCAACACCATC
genomic: ATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtttac ... ttcaacatagGTGCTTGCATATGAAGCTGGAAGGAAATCAAACATTAGGGTCAACACCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtttacaattctgtttcgtaaactcaaagatgtatcggttagaagtctcttagtccaaactgtgttttcaacatag

-  TGGTGG
- - GGTGGA
- -  GTGGAG
- - - TGGAGG
- - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - -  AGCTGC