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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcatggcaaagaacttggccttttccttaattgtttctatctataaaattttagagattcacagaccaaacgttcgggctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTC

Basic information

species Arabidopsis thaliana
transcript AT1G09430.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 8
gtgagtcatggcaaagaacttggccttttccttaattgtttctatctataaaattttagagattcacagaccaaacgttcgggctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTC
|| ||   |    | |||| |    |||    | |  ||||      || |  |||  |    | ||| |   |   || |    ||   ||||||||||| |||||||||| || |||||  |||||||||| |||||||| || || || || ||||||||||| || ||||| ||||  || |||||||
gtaagggctccagaggaacct----tttcggctgacagttt--gatcattatgtttccgct-ctgacaaaatga-tatttgaatctttgtagTGTGCCACTGCTGATCCTGATGGCCGTAAGAGAGCTCTTCTCATTGGAGGTGGTATAGCGAACTTCACTGATGTCGCTGCTACATTCAGTGGCATCATTC

upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 9
----------gtgagtcatggcaaa------gaacttggccttttccttaattgtttctatctataaaattttagagattcacagaccaaacgttcgggctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTC
           |||    ||||| |      |  |||   || ||  ||||   || ||   || || | |||  |  ||    |    |||  |      ||  |||||||| ||| |||| ||||| || |||||  |||| ||||| |||||||| || ||||| || ||||||||||| || || |||||||| || ||  | |
gtaagaaattatgaactttggcataccttttgggcttcagctctttgttaaaatttgctgcttaaaataattttca--tttgttg-tggaacaatatactctttacagTGTGCTACTGCTGACCCTGATGGCCGTAAGAGAGCCCTTCTCATTGGAGGGGGTATTGCTAACTTCACTGATGTTGCTGCCACTTTCAATGGGATTGTCC

upper sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 11
----gtgagt-catg-gcaaagaacttggccttt--tccttaattgtttctat--ctataaaattttagagattcacagaccaaacgttcgggctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTC
     ||| | ||   | |  ||| |||   |||  |||||   || |  ||      | | |||| ||    |||    |  ||| |    | | |  ||||||   ||  |  ||||||| || || ||  ||||| |  |  | || ||||||||||| || ||||||||||| ||||| ||||||||||| |||||||
tctaatgatttcacaagtatcgaagttgctttttagtccttgggtgctattacaatagttagatttcagttgctcattatc--aacctctttgttatgccagTGTTGTACAGCAAATCCTGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTC

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|301502490|gb|HO208030.1|HO208030
EST:     GAGCACCTAATGAGGAAGAGGTGTTACAATATGCAAGAGTTGTCATTGAT                         TGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGA
genomic: GAGCACCTAATGAGGAAGAGGTGTTACAATATGCAAGAGTTGTCATTGATgtgagtcatg ... gctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGA
EST: gi|116442520|gb|EG485112.1|EG485112
EST:     GAGCACCTAATGAGGAAGAGGTATTACAATATGCAAGAGTTGTCATTGAT                         TGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGA
genomic: GAGCACCTAATGAGGAAGAGGTGTTACAATATGCAAGAGTTGTCATTGATgtgagtcatg ... gctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGA
EST: gi|116442521|gb|EG485113.1|EG485113
EST:     GAGCACCTAATGAGGAAGAGGTATTACAATATGCAAGAGTTGTCATTGAT                         TGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGA
genomic: GAGCACCTAATGAGGAAGAGGTGTTACAATATGCAAGAGTTGTCATTGATgtgagtcatg ... gctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctatctataaaattttagagattcacagaccaaacgttcgggctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTC
                                              ctttctc  CT-rich tract
     tatctataaaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcatggcaaagaacttggccttttccttaattgtttctatctataaaattttagagattcacagaccaaacgttcgggctttctcagTGTGCCACTACTGATCCTGACGGGCGTAAACGAGCTCTTCTAATTGGAGGAGGCATTGCCAATTTCACTGATGTGGCAGCTACTTTCAACGGTATCATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT