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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G08530.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattat---ctgttttctgt-----agAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
          |  || |||   || |    |  |   | | |||  |  || | |  ||     |  |   | ||| |  ||||  | |   || ||||         |||| | |||| |||| || ||||||||||| ||||| ||||||||||| || || |||||||| ||||| || ||||| ||||| |||||    ||||||
---------atatgctacac-ctatgctggagcagttcttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattat---ctgttttctgt-----agAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
          |  || |||   || |    || |     | |||  |  || | |  ||     |  |   | ||| |  ||||  | |   || ||||         |||| | |||| |||| || ||||||||||| ||||| ||||||||||| || || |||||||| ||||| || ||||| ||||| |||||    ||||||
---------atatgctacac-ctatgctggaacagtttttaaaagtttattacgtaatgctttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 4
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatct-tgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG-
      | |  |       | | | ||||  ||     |   | ||     |  |||||||  | |||  |  || | | |        | ||        |||||| |||| |||| || ||||||||||| ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||||| |||||    |||||| 
-cggactaaaagaaatttctgt-aagtcagtaattagtaattacacaatactt-tgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAGG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatct-tgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
      | |  |       | | | ||||  ||     |   | ||     |  |||||||  | |||  |  || | | |        | ||        |||||| |||| |||| || ||||||||||| ||||| ||||| ||||||||||| || ||||| ||||| || ||||| ||||| |||||    ||||||
-cggactaaaagaaatttctgt-aagtcagtaattagtaattacacaatactt-tgttgtatgtgcttctcatatttgtatgccctccttttgacgcaaccagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 5
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
 |  | ||  ||  ||    |     |||          | |  |   ||   |       ||| || |  |  | || |   |||  | |||| ||| ||||| | ||||||||| |||||||| ||||| || ||||||||||||||||||||||| ||||| ||||| |||||||| ||||| ||||| || || || 
ttgggattgttgatccttgaaaacaatcatggtctttt-ttactataactcctacaagtctgat-ctaggttttttttttgggtatgttgtgttgtctatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGATCAACAGCGGAGCCAGGCTCTTGAAGCACATGCGGCATCATTTGCTCAATTCAAA

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 5
-gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
  |  | ||  ||  ||    |     |||          | |  |   ||   ||      |||   |   |  | || |   | || | |  | | | ||||| | ||||||||| |||||||| ||||| || ||||||||||| ||||||||||| ||||| ||||| |||||||||||||| ||||| || || || 
attgggattgttggtccttgaaaacaatcatggtctttt-ttactataactcctataagtctgatc--tagtttcttttttgtatgttgtgttgtctatatagAGGCCACAATTGGTTAAAGGAAACATGCAACTCTTCTCTGTGGAACAACAGCGGAGCCAGGCTCTTGAAGCACATGCTGCATCATTTGCTCAATTCAAA

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
 ||  | |          |||  |  |   |      || |   | |      |   ||     | |||  | || ||  ||| ||||| | |    |||||||   |||||||||||| ||||| ||||| |||||||| ||||||||||| || |||||||| ||||| || ||||||||||| ||||| || ||||| 
ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccat-attattt-tgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 5
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
 ||  | |          | |  |  |   |       | ||  | |      |   ||     | |||  | || |   ||| ||||| | |    ||||||| |  ||||||||||| ||||| ||||| |||||||||||||||||||| || |||||||| ||||| || ||||| ||||| ||||| || ||||| 
ttatctgtgtataattgtacaagaattgtgatctttttaccatgaatttaacaagcctgatctattttggtttatttctccat-attattt-tgcattgtagAGGCCGCAATTGGTAAAGGGAAACATGCAACTTTTCTCTGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCCGCATCATTTGCCCAATTTAAA

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttca----tgttgtagattcttgactgatcttgtcat-tattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
      ||  ||    || |  | | |   |||      ||   | |  |||||    | |  | |  |  ||| |    ||  ||  |  ||| | |  | |  |||| | |||  | || ||||| |||||||||||||||||||| || || || || ||||| || ||||| || ||||||||||| || ||   |||||| 
------ttgttgttttacttggttgttgggaaatctttctcctcagttttttcagagatttcctggtgttctgattttaatttccacatcctatttatgct-tacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S270_53V6.1 (Physcomitrella patens), 3'ss of exon 5
-----gtaagtttactgcgccacatatt-aggtcaaaa---aaagacatca----------aaactgcttt---catgttgtagat----------tcttgactga--tcttgtcattattat-ctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
          || ||||||    | | | ||| || ||    || | || |          | | |  |||   ||  |  || |           || |  ||||  | |||  || | ||| | |   || | || | |    | |||| || || || |||||||| ||||| ||||| || ||||||||||||||||| || || ||||| |||   || |||  | || ||
gtaaaactgattgactgcggagtaaaatgaggacagaatttgaaaatataatcctactcatagatttttttgttcaattcataaacatgttctccctcgtttctgaatttttgaaataagtatgcgggcgtccgcagCGTCCGGCACTGGTTAAGGGCAACATGCAGCTGTTCTCCGTGGACCAGCAGCGGAGTCAGGCCCTGGAAGCTCATGCAGCAGTCTTCGCGTCGATTGAG

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|116431736|gb|EG474328.1|EG474328
EST:     CTAATGAGAAGTGGTTGGTTTTAATTGGAATTGCTCCTGGCTCTCCTGAG                         AGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAG
genomic: CTAATGAGAAGTGGTTGGTTTTAATTGGAATTGCTCCTGGCTCTCCTGAGgtaagtttac ... ttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAG
EST: gi|116430170|gb|EG472762.1|EG472762
EST:     CTAATGAGAAGTGGTTGGTTTTAATTGGAATTGCTCCTGGCTCTCCTGAG                         AGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACA
genomic: CTAATGAGAAGTGGTTGGTTTTAATTGGAATTGCTCCTGGCTCTCCTGAGgtaagtttac ... ttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACA
EST: gi|116430172|gb|EG472764.1|EG472764
EST:     CTAATGAGAAGTGGTTGGTTTTAATTGGAATTGCTCCTGGCTCTCCTGAG                         AGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGG
genomic: CTAATGAGAAGTGGTTGGTTTTAATTGGAATTGCTCCTGGCTCTCCTGAGgtaagtttac ... ttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
                     gactgat  putative branch site (score: 3)
                                         tctgttttct  putative PPT
                                  attattatctgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC