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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttgtgaatgtattattagcagttaatgtgttcattgattcttttggaagtgatttggggattgatggattttgcttcttattatggtttatacacagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G17880.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0053g00620.t01 (Vitis vinifera), 3'ss of exon 1
tttttgtgaatgtattattagcagttaatgtgttcattgattcttttggaagtgatt--tggggattgatggattttgcttcttattatggtttatacacagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAG
 ||||         ||    | |  || |   ||    ||      | |   ||  |  | |  ||| ||   | |   | |   ||    | | |   |||||||||||||||||| | ||||||||||||  | | || ||||| || ||||||||||   | |||||
cttttacattcaatttgcctgta--tatttcattagaagacctggattgccttgtatagtagaaattcatttgtatccttacactttcctctctttgtgcagATGAATAGGGAGAAGCTTATGAAGATGGCTGGTGCAGTTCGCACCGGTGGAAAGGGTAGCATGAGAAG

upper sequence: AT1G17880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S28_196V6.1 (Physcomitrella patens), 3'ss of exon 1
tttttgtgaatgtattattagcagttaatgtgttcattgattct-tttggaagtgatttggggattgatggattttgcttcttatta-tggtttataca-cagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAG
       |  | |    |        |      ||||| |   |  | |  |   |  |    ||| |||   |    ||  | | |  |  |   | | |||||||| ||||||||| ||||||||||||||| | | || |||||||| |||||||| | |||||| ||
---agaagcgtttgacgtcgatttggaggaaactcattaagaatactcgtgatcaaagtattaattcatgatgtggaattactgtgaacgaatggcatatcagATGAACAGGGAGAAGCTGATGAAGATGGCTAGTGCAGTTCGCACTGGTGGAAAGGGCAGTGTCAGGAG
















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|125284828|gb|EL298913.1|EL298913
EST:     CACACTCTTCGAACAAGGAAGAACCCTAATCTCAAG                         ATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGAACACTGGCG
genomic: CACACTCTTCGAACAAGGAAGAACCCTAATCTCAAGgtaaattcat ... ttatacacagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCG--CACTGGCG
EST: gi|164101733|gb|ES050302.1|ES050302
EST:     TTATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAG                         ATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGA
genomic: TTATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAGgtaaattcat ... ttatacacagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGA
EST: gi|152035741|gb|BP855298.2|BP855298
EST:     TTTTCTTATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAG                         ATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGA
genomic: TTTTCTTATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAGgtaaattcat ... ttatacacagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGA
EST: gi|125103968|gb|EL158182.1|EL158182
EST:     TTTTCTTATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAG                         ATGAATAGGGAGAAG
genomic: TTTTCTTATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAGgtaaattcat ... ttatacacagATGAATAGGGAGAAG
EST: gi|47829080|gb|CK118764.1|CK118764
EST:     TTTTCTTATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAG                         ATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGA
genomic: TTTTCTTATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAGgtaaattcat ... ttatacacagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGA
EST: gi|125083094|gb|EL143780.1|EL143780
EST:     ATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAG                         ATGAATAGGGAGAAGTTGA
genomic: ATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAGgtaaattcat ... ttatacacagATGAATAGGGAGAAGTTGA
EST: gi|86074372|gb|DR370129.1|DR370129
EST:     TCTTCTTATCTCCTCACACTCTTCGAACAAGGAGGAACCCTAATCTCAAG                         ATGAATAGGGAAAAGTTGATGAAGATGGCTAACACCGTCCGCACTGGCGGA
genomic: T-TTCTTATCTCCTCACACTCTTCGAACAAGGAAGAACCCTAATCTCAAGgtaaattcat ... ttatacacagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaagtgatttggggattgatggattttgcttcttattatggtttatacacagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAG
                gattgat  putative branch site (score: 4)
                                   ttattatggtttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttgtgaatgtattattagcagttaatgtgttcattgattcttttggaagtgatttggggattgatggattttgcttcttattatggtttatacacagATGAATAGGGAGAAGTTGATGAAGATGGCTAATACCGTCCGCACTGGCGGAAAGGGTACTGTCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - -gatttgg