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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttcttcttcccttagatccaggattttttgccttctatatctaattataagaacttgtacgtgatgttagaatacatggctaatgacgtcctactcttttatgtgttggcccaaattgatgtctagGTTGAACACGTCAGAGAATCTGCTCATTTCAATTCAAGACAAGATCAAATGGGCGGACAATATGAGTGAGATGGACAAAAAACATCGTAAGGAAGCAGAA

Basic information

species Arabidopsis thaliana
transcript AT1G02090.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G02090.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 6
gtagttttcttcttcccttagatccaggattttttgccttctatatctaattataagaacttgtacgtgatgttagaatacatggctaatgacgtcctactcttttatgtgttggccc-aaattgatgtctagGTTGAACACGTCAGAGAATCTGCTCATTTCAATTCAAGACAAGATCAAATGGGCGGACAATATGAGTGAGATGGACAAAAAACATCGTAAGGAAGCAGAA
                            ||||||| |||||| |  || |||    ||  || |     |  | ||| |     ||||  |    | ||   |||| | | |   |    |||  |    |||||||   || ||||| ||||| ||| | ||||||||||| ||||| || ||||| || |  ||||||||| ||||||| ||||| || |||||||  |||
---------------------------tatttttt-ccttct-ttcctgatttatggagattattttgaagataagagt---ctgctag-gtttccttatgattttgtatatccactttgaatgaaaacttagGTTGGGTACATCAGATAATCTTCTCCTCTCAATTCAAGAGAAGATAAAGTGGGCAGATACCATGAGTGAGTTGGACAAGAAACACCGAAAGGAAGTCGAA

upper sequence: AT1G02090.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S271_80V6.1 (Physcomitrella patens), 3'ss of exon 6
gtagttttcttcttcccttagatccaggattttttgccttctatatctaattataagaacttgtacgtgatgttagaa------tacatggctaatgacgtcct------actctttt--------------atgtgttggcccaaattgatgtctagGTTGAACACGTCAGAGAATCTGCTCATTTCAATTCAAGACAAGATCAAATGGGCGGACAATATGAGTGAGATGGACAAAAAACATCGTAAGGAAGCAGAA
|||   |    |||  |     |  |    |        |||  ||||||||   ||   |  | |    || ||||       | |||  |||  | |           | | |||               |   ||| |      |||||||| ||||||||||  || || ||| ||||  || |||| ||||| |||||||||||||||||||  ||||| |||   |       |||    |||||||  |||
gtaaaatgtcacttttcaagagtgaacatatcacctagctctggatctaattgccagttttcatgcagcctggtagagcgattgtgcattcctagcggctcttcttgaggattttttctcactactcacaggacaagttcgattctcttgatgtccagGTTGAACAGTTCTGATAATTTGCTGCTTACAATACAAGAGAAGATCAAATGGGCGGACAGCATGAGCGAGCAAGTTCGGCGACACAAGAAGGAAGTCGAA
















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|164006620|gb|EL970637.1|EL970637
EST:     GATCTAAGGCCAGGTCAACTAGGGAATATGTTACACACATTGTCCAACTG                         GTTGAACACGTCAG
genomic: GATCTAAGGCCAGGTCAACTAGGGAATATGTTACACACATTGTCCAACTGgtagttttct ... tgatgtctagGTTGAACACGTCAG
EST: gi|86080813|gb|DR376570.1|DR376570
EST:     GATCTAAGGCCAGGTCAACTMGGGAATATGTTACACACATTGTCCAACTG                         GTTGAACACGTCAGAGAATCTGCTCATTTCAATTCAAGACAAGWTCAAATG
genomic: GATCTAAGGCCAGGTCAACTAGGGAATATGTTACACACATTGTCCAACTGgtagttttct ... tgatgtctagGTTGAACACGTCAGAGAATCTGCTCATTTCAATTCAAGACAAGATCAAATG
EST: gi|164205748|gb|ES045915.1|ES045915
EST:     GATCTAAGGCCAGGTCAACTAGGGAATATGTTACACACATTGTCCAACTG                         GTTGAACACGTCAGAGAA
genomic: GATCTAAGGCCAGGTCAACTAGGGAATATGTTACACACATTGTCCAACTGgtagttttct ... tgatgtctagGTTGAACACGTCAGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacatggctaatgacgtcctactcttttatgtgttggcccaaattgatgtctagGTTGAACACGTCAGAGAATCTGCTCATTTCAATTCAAGACAAGATCAAATGGGCGGACAATATGAGTGAGATGGACAAAAAACATCGTAAGGAAGCAGAA
                       tcttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttcttcttcccttagatccaggattttttgccttctatatctaattataagaacttgtacgtgatgttagaatacatggctaatgacgtcctactcttttatgtgttggcccaaattgatgtctagGTTGAACACGTCAGAGAATCTGCTCATTTCAATTCAAGACAAGATCAAATGGGCGGACAATATGAGTGAGATGGACAAAAAACATCGTAAGGAAGCAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA