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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggttattggtattgtacaatatgatttatacttagtctctttgtgtggttaattgattaaagttgtgtgttttgtattgttacgatttgggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGAATTTACCAGCTGAAGAAGTGCCTCCTGAGTTACCAGAGCCAGCTCTTGG

Basic information

species Arabidopsis thaliana
transcript AT3G42790.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G42790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S97_167V6.1 (Physcomitrella patens), 3'ss of exon 2
gtggttattggtattgtacaatatgatt-tatacttagtctctttgtgtggttaattgattaaagttgtgtgttttgtattgttacgatttgggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGAATTTACCAGCTGAAGAAGTGCCTCCTGAGTTACCAGAGCCAGCTCTTGG
 |  | |   | |     | ||  ||   | |  |     |  |  |    |  | || ||   |  |||  |  |  ||||    | ||     || |||||||||||||  | || |||||||| || ||| ||||||  ||||||||||||||||| || ||||| || || || ||  | || || || || |||||
attctcaaaaggaggaatccatgagacggtgtcgtcgcattggtcataatatgcagtggttcgcgaagtgactccttaattggc-tgcttcttaattgcagAGAAGGAGAACTTGTGTTTGTATGGTTTCCCGGATGAAGCTTGGGAAGTGAATTTACCGGCGGAAGAGGTTCCACCAGAACTTCCTGAACCTGCACTTGG

upper sequence: AT3G42790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S38_137V6.1 (Physcomitrella patens), 3'ss of exon 3
gtggttattggtattgtacaatatgatttatactt--agtctctttgtgtggttaattgattaaagttgtgtgttttgtattgttacgatttgggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGAATTTACCAGCTGAAGAAGTGCCTCCTGAGTTACCAGAGCCAGCTCTTGG
    |    ||||    |  ||    ||| || |   ||     ||  | ||    | |      ||      |   |||  | |    |   |  || |||||||||||||| | ||  |||| || || ||| |||| | ||||||||| ||||||||||| ||||| || ||||||||  | ||||| || || |||||
--attggagggtacataaggatccagtttgtattggaagagagattcggaggcatgtcgtagcgtgtatcacatcacgtagcggtggtctgctgaattgcagAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG

upper sequence: AT3G42790.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
gtggttattggtattgtacaatatgatttatacttagtctctttgtgtggttaattgattaaagttgtgtgttttgtattgttacgatttg---ggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGAATTTACCAGCTGAAGAAGTGCCTCCTGAGTTACCAGAGCCAGCTCTTGG
||  |  | ||     |   |  |  ||  | |   || |   |   |   | |  | ||     |||| |||||  ||  ||   ||||       || |||||||||||||| | ||||| ||||| || ||  | |||| ||||||||| ||| ||||||||||||| || ||||||||  | ||||| || ||||||||
gttttcgtagggcaattttgaggtagttggtgccatgtgt---tacatcacttagcgctttgttatgtgagttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG

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|86069053|gb|DR364810.1|DR364810
EST:     ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|86069050|gb|DR364807.1|DR364807
EST:     ATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|86069049|gb|DR364806.1|DR364806
EST:     ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|164105669|gb|ES025254.1|ES025254
EST:     TTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: TTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|86069051|gb|DR364808.1|DR364808
EST:     ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|86069052|gb|DR364809.1|DR364809
EST:     ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|86069048|gb|DR364805.1|DR364805
EST:     ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|86069046|gb|DR364803.1|DR364803
EST:     ATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|124905636|gb|EH979716.1|EH979716
EST:     ATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTG
genomic: ATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTG
EST: gi|86069047|gb|DR364804.1|DR364804
EST:     ATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|86069054|gb|DR364811.1|DR364811
EST:     ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ACCACCGATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|125043921|gb|EL116190.1|EL116190
EST:     ATGTTCAAGAGTTTTACCTAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ATGTTCAAGAGTTTTACC-AACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
EST: gi|116471935|gb|EG514527.1|EG514527
EST:     ATGTTCAAGAGTTTTACCAACAATGTGACCCTG                         AGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA
genomic: ATGTTCAAGAGTTTTACCAACAATGTGACCCTGgttagggttt ... gggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggttaattgattaaagttgtgtgttttgtattgttacgatttgggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGAATTTACCAGCTGAAGAAGTGCCTCCTGAGTTACCAGAGCCAGCTCTTGG
       aattgat  putative branch site (score: 4)
                                                ttttc  putative PPT
     ttaattgattaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggttattggtattgtacaatatgatttatacttagtctctttgtgtggttaattgattaaagttgtgtgttttgtattgttacgatttgggttttcagAGAAGGAGAATCTTTGCTTGTATGGGTTACCGAATGAAGAATGGGAAGTGAATTTACCAGCTGAAGAAGTGCCTCCTGAGTTACCAGAGCCAGCTCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - ctctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg