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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctcttattacagttctaacctaactgatttcagattcgggttatagtgttggaggtttgattattgcgtttatgtgaaatgatgtttcag

Basic information

species Arabidopsis thaliana
transcript AT3G06700.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06700.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os05g28750.1 (Oryza sativa), 5'ss of exon 1
GGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctcttattacagttctaacctaactgatttcagattcgggt----tatagtgttggaggtttgattattgcgtttatgtgaaatgatgtttcag--
||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| ||||||||||| | | | ||||| || ||| | ||||  || ||  |||||||    |  | |    ||  |   | |||||| | | |    |  | |  || ||  |||  | | |  | |     |||||||||||     
GGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGCCAGACCTCCACCAAGGGGgtgcgtctctttgctccttccctctctctc-actctcagatccagattccctgcaatcctgtagccttgcct-tggtttcttgcaaaaatgatgttttcttc

upper sequence: AT3G06700.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 5'ss of exon 2
GGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtc--tcttattacagttctaaccta-actgatttcagattcgggttatagtgttggaggtttgattattgcgtttatgtgaaatgatgtttcag--
||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| ||||||||||| | | | ||||| || ||| | ||||  || ||||| |  ||      |  ||||| | |   |   | |  |      | | |  |     ||  | |   |  |  | || ||  | | |||| |||   
GGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGACCTCCACCAAGGGGgtaagccaatccacgccctcttctagcttccgcgcgtgtgcgccatctgctttgatagcccagagtcgccaaaagtctcta-gtagattcatgtatcatgt

upper sequence: AT3G06700.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G009894_T01 (Zea mays), 5'ss of exon 2
GGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaag-tctcttattacagttctaacctaactgatttcagattcgggttatagtgttggaggtt-----tgattattgcgtttatgt-gaaatgatgtttcag
||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| ||||||||||| | | | ||||| || ||| | ||||  || ||||| |   ||| |  |  ||   | |  | |   ||   ||||| | || |||  |  |  |     || | |||| ||| ||   | ||| ||||  | |
GGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAGACCTCCACCAAGGGGgtaagatgatttacttgatgtccctctt--ccgtcgtcccgttcggttgattgtgcagatgcgtcagagtggtcattg-gttgataccggaatcatgtagctg

upper sequence: AT3G06700.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G147791_T03 (Zea mays), 5'ss of exon 2
GGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaag-tctcttattacagttctaacctaactgatttcagattcgggttatagtgttggaggttt------gattattgcgtttatgtga-aatgatgtttcag
||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| || ||||| || | | | ||||| || ||| | ||||  || ||||| |   ||  | | |   |  |  | | |   ||  |||||  | || |||  |  |  |       | | |||| ||| ||| || ||| ||||     
GGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAGACCTCCACCAAGGGGgtaagataatttgctcctgacgttcctcacccgtcgtcccattcgattgattgtgcagctgcgtcactggcggtcattg-gttcatgcgagaatcatgtaa---

upper sequence: AT3G06700.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0077g01220.t01 (Vitis vinifera), 5'ss of exon 1
GGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctcttattacagttctaacctaactgatttcagattcgggttatagtgttggaggtttgattattgcgt-ttatgtgaaatgatgttt-cag
||| ||||||||||| ||||| || || ||||| |||   || |||||||||||||| |||||||||||  | | |||||| ||| |  | |||| ||| |||| | ||| |     | | ||  ||             ||| |   |   |||    | |  ||| | |  || || ||  |  |||  |   |||
GGCGAAGTCGAAGAACCACACAGCTCACAACCAATCGTACAAGGCCCACAAGAACGGCATCAAGAAGCCCCGCAAACACCGCCACGCTTCCACCAAAGGGgtaa-tttctcaactttgatttactcttttccccccttttttctgaagaatatgtgattgatgcgatgaatttgtgttttgaaatctgaaatgaacag

upper sequence: AT3G06700.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv07s0005g01340.t01 (Vitis vinifera), 5'ss of exon 2
GGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaag---tctct-tattacagt----tctaacc--taactgatttcagattcgggttatagtgttggaggtttgattattgcgtttatgtgaaatgatgtttcag-----------------------
||| ||||||||||| ||||| || || ||||||||    |||||||||||||| ||||||||||| ||  | |  ||||| |||||| | |||| ||| ||  |   ||||| | ||  | |    || || |  |   |  ||||   ||    || |  | |    |||  | ||  || ||||  |||  ||| ||||| |                        
GGCGAAGTCGAAGAACCACACTGCCCACAACCAGTCCTACAAAGCCCACAAGAATGGAATCAAGAAACCCCGAAAGCACCGCCACACCTCCACCAAAGGGgtttgatttctctctgttttaatctcttccaatcgtttgtttttttccttttacttttgtgatctccttggtgggttttctg-gtttgagtgctatggtgtttgatttcttttatttgcattggcgtag

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|163982276|gb|EL981103.1|EL981103
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|164230412|gb|ES134867.1|ES134867
EST:     GAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGT
genomic: GAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAA-CCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGT
EST: gi|124900521|gb|EH975139.1|EH975139
EST:     ACCCCAACCAGAGGA                         ATGGACCCTAAGGTTCCTGAGGAACCAGAGGTAACGCAAGGAAGCACAACG
genomic: ACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAA-GTTCCTGAGGAACCAGAGGT-ACGCAAGGAAGCACAACG
EST: gi|125237702|gb|EL251787.1|EL251787
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTG
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTG
EST: gi|125289066|gb|EL303151.1|EL303151
EST:     AGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: AGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|164071263|gb|ES182644.1|ES182644
EST:     AAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: AAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|125276559|gb|EL290644.1|EL290644
EST:     AACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: AACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|164149674|gb|ES106102.1|ES106102
EST:     AAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: AAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|125188171|gb|EL203125.1|EL203125
EST:     GAACGGAATCAAGAAGCCAAGGAGAACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAA
genomic: GAACGGAATCAAGAAGCCAAGGAG-ACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAA
EST: gi|125272765|gb|EL286850.1|EL286850
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCT
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCT
EST: gi|124984258|gb|EL056927.1|EL056927
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|125113367|gb|EL164208.1|EL164208
EST:     AGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: AGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|164153675|gb|ES060100.1|ES060100
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGC
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGC
EST: gi|124734557|gb|EH825959.1|EH825959
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGG
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGG
EST: gi|124922090|gb|EL000414.1|EL000414
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAAACCAGAGGTACGCAAGGAAGCACAACGT
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAA-CCAGAGGTACGCAAGGAAGCACAACGT
EST: gi|124821798|gb|EH906664.1|EH906664
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCATACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAA
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAA
EST: gi|124788516|gb|EH878195.1|EH878195
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|164034976|gb|ES143840.1|ES143840
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|164020812|gb|ES210166.1|ES210166
EST:     GACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: GACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|124753962|gb|EH844092.1|EH844092
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         AATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAA
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagA-TGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAA
EST: gi|125279536|gb|EL293621.1|EL293621
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAA
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAA
EST: gi|124962609|gb|EL037000.1|EL037000
EST:     ACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTTCCNGAGGAACCAGAGGTACGCAAGGAAGCACAACGT
genomic: ACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAG-TTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGT
EST: gi|164178724|gb|ES000887.1|ES000887
EST:     GACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: GACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|164164386|gb|ES060381.1|ES060381
EST:     CGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGC
genomic: CGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGC
EST: gi|125283807|gb|EL297892.1|EL297892
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACC-TAAGTTCCTGAGGAACCAGAGGTACGC
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGC
EST: gi|124751583|gb|EH841713.1|EH841713
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAACGTC
EST: gi|125206969|gb|EL221923.1|EL221923
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         -TGGACCCTAAGTTC
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTC
EST: gi|124889921|gb|EH968823.1|EH968823
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTAGAGGAACCAGAGGTACGCAAGGAA
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCT-GAGGAACCAGAGGTACGCAAGGAA
EST: gi|124974353|gb|EL047918.1|EL047918
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         ATGGACCCTAAGTTCCTGAGGAACCAGAGG
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGG
EST: gi|164071847|gb|ES038881.1|ES038881
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCC-AACCAGAGGA                         -TGGACCCTAAGTTCCTGAGGAACCAGAG
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAG
EST: gi|124890357|gb|EH969259.1|EH969259
EST:     AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGA                         AATGGACCCTAAGTTCCTAGAGGAACCAGAGGTACGCAAGGAA
genomic: AGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctct ... gatgtttcagA-TGGACCCTAAGTTCCT-GAGGAACCAGAGGTACGCAAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAGAGGAgtaagtctcttattacagttctaacctaactgatttcagattcgggttatagtgttggaggtttgattattgcgtttatgtgaaatgatgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA