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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttttgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtccttttacag

Basic information

species Arabidopsis thaliana
transcript AT5G06360.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 5
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctc--tctgcttttgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtccttttacag
||||| |||||||| ||||| ||||||||||  || || ||||||||||||||||| ||| | ||||||||||  |    | |   ||| || |     |   || |   ||   | |   |  | | | ||||       |||      |||||| |   
GTTCTCAGCAACACAATTAAGCAAAAGAGGATGGAAAAGGCTGGCAAATGGGAGGTTCCTTTGCCAAAGgtgattttcaacacaaactgtttctagtacctggcaatcaatgg-ttttcctaccttgactaagcactgtcacaattttcttcctttcag--

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 5
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttttgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtccttttacag
||||| |||||||| || || ||||||||||| || || |||||||||||||| || ||||| ||||||||||        ||||  |      |   |  |  | | ||    ||    ||||||  |   || | |   ||   | |||||| |   
GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtga-------ttctcaac----acagcacgcccatttctggttgct--tcaatgggttagtttttactcacagttttatcctttcag--

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G174204_T02 (Zea mays), 5'ss of exon 1
-------------------------------GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttttgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtccttttacag
                               || || |||||||| || || ||||||||||| || || |||||||||||||| || || || |||||||||         |||   |      |  |  |   || ||||  |  ||  | |           | |||     | |||||||| |   
GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtcaaatctgaacacagcaaacctatttctggttga--ttcaatgagtta--------catattt----cttgtcctttcag--

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G174204_T01 (Zea mays), 5'ss of exon 5
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttttgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtccttttacag
|| || |||||||| || || ||||||||||| || || |||||||||||||| || || || |||||||||         |||   |      |  |  |   || ||||  |  ||  | |           | |||     | |||||||| |   
GTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtcaaatctgaacacagcaaacctatttctggttga--ttcaatgagtta--------catattt----cttgtcctttcag--

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 5
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgctttt-gtattccttcagt---gtttgaactctaacaaatggg-caaagcttaaattcaagccctgtcct----tttacag-----------------------------------------------------------
|||||||||||||||||||| ||||||||||| ||||| || || |||||||| || ||||| || ||||||||||  |  ||  | ||||| | |    ||  ||        | ||||  ||| | |  |   | ||  |||  |    |||  |    ||  | |                                                           
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaaacgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G00490.1 (Glycine max), 5'ss of exon 5
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttt-tgtattccttcagt---gtttgaactctaacaaatgggcaaagcttaaattcaagccctgt-ccttttacag-----------------------------------------------------------------
|||||||||||||||||||| ||||||||||| ||||| || || |||||||| || ||||| || ||||||||||  |  ||  | |||| || |||  ||  ||    |   |  |||  ||| | |    | ||||     | | | |||   |||||                                                                    
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttgtgcattgattatgttaaatgatatgtcttgcaatttgt---atcttattgctatgtcatgtgtgttttatgtttccctgtgaatggaagggagtgaacttggtaattaaatgaatgtatgctttctcatttcttcag

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 5
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttt-tgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtcct----tttacag----------------------------------------------------------
|||||||||||||| ||||| ||||||||||| ||||| || || |||||||| || ||||| || ||||||||||  |  ||  | |||| || |||   | |     |    | |   |  ||        |   |||  |    |||  |    ||  | |                                                          
GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 5'ss of exon 5
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttttgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtccttttacag---------------
||||||||||| || || || ||||| ||||||||||||||||| |||||||| |||||||| || || || | ||| |    | ||   |||| ||  |||||  ||  | || |     ||   |  |  | |  |||  || || |  | | |  |               
GTTCTTAGCAATACTATAAAGCAAAAAAGGAAAGAGAAAGCTGGGAAATGGGAAGTCCCTCTACCCAAAgtaagatcaca---tttgacattgtgttatttcagcatt-aaccttttcagtattttctgatttgagtttcctgcact-ttttctaatggtacttttcccttttt

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S136_220V6.1 (Physcomitrella patens), 5'ss of exon 5
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaa---atctc-------tctctctgcttttgtattccttcagtgtttgaactc-taac---aaatgggcaaagcttaaattcaagccctgtccttttacag
||||| ||||||||||| || || ||  | || ||||| ||||| ||||||||||| |||||||| |||||||    || ||       |      |||| || |   ||| | |  |  | | | | ||   || || | |   | | ||   | ||  |||  |||     
GTTCTCAGCAACACCATCAAGCAGAAACGTAAGGAGAAGGCTGGTAAATGGGAGGTGCCTCTTCCTAAGgtgagccgatatcgtacgaatgctgtagcttgtgaaactcttgaataatccaccacatcacttaaattgtgaagtacgtgaacggaggcgatgtggtttc----

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|86050590|gb|DR346345.1|DR346345
EST:     AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG                         GTCCGTCCAGTTGCTGAAAGATGAAATGTTTAGAGTGATACGATCTGGAAA
genomic: AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctc ... ccttttacagGTCCGTCCAGTTGCTGAA-GATGAAATGTTTAGAGTGATCCGATCTGGAAA
EST: gi|86050587|gb|DR346342.1|DR346342
EST:     AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG                         GTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATACGATCTGG
genomic: AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctc ... ccttttacagGTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGG
EST: gi|164175091|gb|ES188430.1|ES188430
EST:     AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG                         GTCCGTCCAGTTGCTGAAGATGAAAT
genomic: AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctc ... ccttttacagGTCCGTCCAGTTGCTGAAGATGAAAT
EST: gi|86050595|gb|DR346350.1|DR346350
EST:     AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG                         GTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATACGATCTGGAAAA
genomic: AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctc ... ccttttacagGTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAA
EST: gi|86050588|gb|DR346343.1|DR346343
EST:     AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG                         GTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATACGATCTGGAAAA
genomic: AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctc ... ccttttacagGTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAA
EST: gi|163988744|gb|ES117307.1|ES117307
EST:     TGGGAGGTCCCTCTTCCAAAG                         GTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAA
genomic: TGGGAGGTCCCTCTTCCAAAGgtgaaatctc ... ccttttacagGTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAA
EST: gi|86050593|gb|DR346348.1|DR346348
EST:     AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAG                         GTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATACGATCTGGAAAA
genomic: AACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctc ... ccttttacagGTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAAA
EST: gi|86072911|gb|DR368668.1|DR368668
EST:     ACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAANNN                         NTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATACGATCTGGAAA
genomic: ACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAA-AGgtgaaatctc ... ccttttacagGTCCGTCCAGTTGCTGAAGATGAAATGTTTAGAGTGATCCGATCTGGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttttgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtccttttacag

- - - - - - - - - - - - AAGAGG
- - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - -  AAGCTG