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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctaaaacctaaaacacgacaatggacttggcattttttactttgattctaataatgttttattttccattgtttgccacagGGGTCTCAAGTCACTGACAGATAGAGAAGTCTGTTGCTTCATGATATCTTGCAAGAACTCTACCAACATCGATCAAGTCATTGATTGGCTTGTAAAGCAC

Basic information

species Arabidopsis thaliana
transcript AT5G67560.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 4
gtaagcctaaaacctaaaacacgacaatggacttgg-cattttttactttga--ttctaata----atgttttattt-tccattgtttg----------ccacagGGGTCTCAAGTCACTGACAGATAGAGAAGTCTGTTGCTTCATGATATCTTGCAAGAACTCTACCAACATCGATCAAGTCATTGATTGGCTTGTAAAGCAC
|||||   |    ||||   || ||| |    | ||  ||||||| | | ||  | | | |     |  ||||| |  || | ||  ||             |||||| || ||| || | || ||  |||||||    || ||||||| |||||||||||||||||||||||| |||   |||||||| ||||| || ||||||
gtaagaacatg--ctaatctactacactctgttaggatatttttttcctagaaataccagttcgatacattttactcatctactgcctggtgaatggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTGCAAGAACTCTACCAACATTGATTCTGTCATTGAATGGCTGGTGAAGCAC

upper sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G27070.1 (Glycine max), 3'ss of exon 2
----gtaagcctaaaacctaaaacacgacaatggacttggcattttttactttgattctaataatgt--tttattttccat---tgtttgcca----cagGGGTCTCAAGTCACTGACAGATAGAGAAGTCTGTTGCTTCATGATATCTTGCAAGAACTCTACCAACATCGATCAAGTCATTGATTGGCTTGTAAAGCAC
     |  | ||  ||| |  ||   |       | ||    ||    | ||| | | | | |||||  |||| |||| ||   |||||   |    |||||| || || |   | |  | |||||| || |||||||||||||| || || || ||||| | |||||| |||  ||| ||||||||||||||||| || 
tttattctgtctgcaacttctaatgtggtttaataatttcatttaaacaatttaactttcagaatgtgctttactttcaatatttgtttcatatgtgcagGGGACTGAAATGCATCAATGGTAGAGACGTTTGTTGCTTCATGATCTCCTGTAAAAACTCCATCAACATTGATACAGTTATTGATTGGCTTGTAAAACAT

upper sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 5
gtaagcctaaaacc-----taaaacacgacaatg--gacttggcattttttactttgattctaataatgttttattttc----cattgtttgcc--acagGGGTCTCAAGTCACTGACAGATAGAGAAGTCTGTTGCTTCATGATATCTTGCAAGAACTCTACCAACATCGATCAAGTCATTGATTGGCTTGTAAAGCAC
|| |  | ||  ||     |    |  |    ||  |  ||    ||  |  || |  |  | ||  |||||  | ||        || ||||    |||||  || |  ||  | ||  |||||||||| ||||| | |||||| || ||||||||||| ||||||||||||   || ||||| |||||||||||||| 
gtgaatccaatccccttccttttgcttggttgtgatggtttaaggttcatggctattttatttatggtgtttagtgttgagaatggtgcttgctttgcagGGAGCTTAGATCCATTACCAATAGAGAAGTATGTTGTTACATGATTTCATGCAAGAACTCAACCAACATCGATACGGTTATTGACTGGCTTGTAAAGCAT

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|124993338|gb|EL065607.1|EL065607
EST:     AAAATCGACAAGCCTGGAGCTTTGTCCAAAGAAGCCCTAACCGATGAAAT                         GGGTCTCAAGT
genomic: AAAATCGACAAGCCTGGAGCTTTGTCCAAAGAAGCCCTAACCGATGAAATgtaagcctaa ... tttgccacagGGGTCTCAAGT
EST: gi|86079865|gb|DR375622.1|DR375622
EST:     AAAATCGACAAGCCTGGAGCTTTGTCCAAAGAAGCCCTAACCGATGAAAT                         GGGTCTCAAGTCACTGACAGATAGAGAAGTCTGTTGCTTCATGATATCTTG
genomic: AAAATCGACAAGCCTGGAGCTTTGTCCAAAGAAGCCCTAACCGATGAAATgtaagcctaa ... tttgccacagGGGTCTCAAGTCACTGACAGATAGAGAAGTCTGTTGCTTCATGATATCTTG
EST: gi|163992848|gb|ES053427.1|ES053427
EST:     CGACAAGCCTGGAGCTTTGTCCAAAGAAGCCCTAACCGATGAAAT                         GGGTCTCAAGTCACTGACAGATAGAGAAGTCT
genomic: CGACAAGCCTGGAGCTTTGTCCAAAGAAGCCCTAACCGATGAAATgtaagcctaa ... tttgccacagGGGTCTCAAGTCACTGACAGATAGAGAAGTCT
EST: gi|125003035|gb|EL075304.1|EL075304
EST:     AAAATCGACAAGCCTGGAGCTTTGTCCAAAGAAGCCCTAACCGATGAAAT                         GGGTCTCAAGTCACT
genomic: AAAATCGACAAGCCTGGAGCTTTGTCCAAAGAAGCCCTAACCGATGAAATgtaagcctaa ... tttgccacagGGGTCTCAAGTCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcattttttactttgattctaataatgttttattttccattgtttgccacagGGGTCTCAAGTCACTGACAGATAGAGAAGTCTGTTGCTTCATGATATCTTGCAAGAACTCTACCAACATCGATCAAGTCATTGATTGGCTTGTAAAGCAC
                   ttctaat  putative branch site (score: 2)
     attttttactttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcctaaaacctaaaacacgacaatggacttggcattttttactttgattctaataatgttttattttccattgtttgccacagGGGTCTCAAGTCACTGACAGATAGAGAAGTCTGTTGCTTCATGATATCTTGCAAGAACTCTACCAACATCGATCAAGTCATTGATTGGCTTGTAAAGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC