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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttgattttgcacagtacattacactgtgagcatgttcataagtgcgttgttgttacttgcacatcacttgtttgactttttgtttgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG

Basic information

species Arabidopsis thaliana
transcript AT3G11270.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 1
-catttgattttgcacagtacattacactgtgagcatgttcataagtgcgttgttgttact-tgcacatcacttgtttgactttttg-tttgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG
     ||| || ||   | ||  | |||  | || || |    |  |   ||   || ||  |  ||   | || |   |   | ||     ||||||| ||||||| ||||| ||||||||||| ||  | || || ||||| || ||||| || |||||||| |||||||||  |||||||||||| || || |
tggcgtgaatt-gcgttgaac-ctgcacaattag-atctgtggagttctattccagtgacgatttactgtatttatagcatgctatggcacttggttttgcagTGCCGTTTGAAGAGGATGACAAGGATCCGAGGATCTGGTTCCTCGATCATAATTACCACGAATCGATGTTTTCCATGTTCAAGAGGATCAACG

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 1
-catttgattttgcacagtacattacac-tgtgagcatgttcataagtgcgttgttgttacttgcacatcacttgtttgactttttgtttgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG
   || ||| |      ||  | | | | || |    || | | |  || |  |||||  |  |    | ||||| |  |     |  |||   |||| ||||||| ||||||||||||||||| ||  | || || ||||| ||||| ||||| ||||||||||| |||||   |||||||||||| |||||||
cagttagatctattgacgtggaatgcccgtgcggaattgattagatctgtgacgttgt--cccgggggtgacttgctaaatccgctacttgattttttgcagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCACGAGTCAATGTTCTCCATGTTCAAGAGGATTAATG

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G368908_T02 (Zea mays), 3'ss of exon 1
-catttgattttgcacagtacattacac-tgtgagcatgttcataagtgcg-ttgttgttacttgcacatcacttgtttgactttttgtttgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG
 |  ||||  | |      ||  | | | || | |  || | | |  || | | |||||  |  |    | ||||| |  |     |  ||||  ||||  |||||| ||||||||||||||||| ||  | || || ||||| ||||| ||||| ||||| || ||||||||   |||||||||||| ||||| |
tctattgacgtggattgccacgctgctcatgcgtgattgattagatctgtgatcgttgt--cccgggtgtgacttgctgaatccgctacttgtt-ttttgtagTGCCGTTTGAGGAGGATGACAAGGATCCTAGGATCTGGTTCCTTGACCACAATTACCATGAATCGATGTTCTCCATGTTCAAGAGGATTAACG

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 1
-catttgattttgcacagtacattacactgtgagcatgttcataagtgcgttgttgttacttgcacatcacttgtttgactttttgtt-tgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG
 |||  |||| |       | | |  | | |    |||||   | ||||  | |||  | |      ||  |   |      || ||| | |  ||| |||||||| ||||| || |||||||| ||  | ||||| ||||||||||| ||||| ||||| || |||||||||  |||||| || ||||| ||| 
gcataagattgttacttccaaaatgaatttttgagatgtttcaatgtgcaat-ttgacagtgaattgtctgtctctcactacttggttatctaatttgacaGTGCCCTTTGAAGAAGATGACAAGGATCCTAGCATCTGGTTTCTTGACCACAATTACCATGAATCGATGTTTTCCATGTTTAAAAGAATAAAT-

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 1
catttgattttgcacagtacattacactgtgagcatgttcataagtgcgt---tgttgttacttgcacatcacttgttt--gactttttgtttgtg-gttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG
   |  ||||||   |    || |  || || |||  ||   || |       | |||     ||   ||    ||| |   |||  ||| || |    || |||||||| ||||| || |||||||| ||  | ||||| ||||||||||| ||||| ||||| || || ||||||  |||||| || ||||| ||||
---tgaattttgttgaa---atgattctatgtgcaatttagaaaattaacacctattggggtgtgtgaattgtctgtctctcactacttggttatctaattgacagTGCCCTTTGAAGAAGATGACAAGGATCCTAGCATCTGGTTTCTTGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 3'ss of exon 1
---catttgattttgcacagtacattacactgtgagcatgttcataagtgcgttgttgttacttgcacatcacttgtttgactttttgtttgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG
   ||  | |   |  | | ||| |  || ||| |  | |     ||     ||||   | |||  |   |  ||| |  |   |    |  ||  ||| ||||||| ||||| || |||||||| ||| |||| ||||| |||||||| |||||||||||||| || ||||||  ||||||||||||||| ||||
aaacagattagggtttataatac-tggcattgttaagaggggacaaaaaaaattgtcaattctt--atggcttttgctaaatggtagagtgctgtgtttgcagTGCCCTTTGAAGAAGATGACAAGGACCCAAGTATATGTTTTCTTGACCACAACTACCACGAATCAATGTTTTCCATGTTCAAGAGAATAAATG

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 1
catttgattttgcacagtacattacactgtgagcatgttcataagtgcgttgttgttacttgcacatcacttgtt--tgactttttgtttgtggt-tttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG
           |         ||| | | |  ||||  | |  || |        || |      ||    ||||  | | |  | |  ||| || ||| ||||||| ||||| || |||||||| ||| ||||||||||||||||||| |||||||| || || || ||||||  ||||||||||||||| ||||
--ccaagcggagggttagggtttatagtattggcattgttaagagggtacaagaattgccaat-tattggctgttgctaaatagtagggtgttgtgtttgcagTGCCCTTTGAAGAAGATGACAAGGACCCAAGCATATGGTTTCTTGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 1
---catttgattttgcacagtacattacactgtgagcatgttcataagtgcgttgttgttacttgcacatcacttgtttgactttttgtttgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG
   |  |  | || | | |  | || | ||  |  |   | |   || | |  | |||  |||   | |  |      ||    |  |   ||| ||||  |||||| |||||||| |||||||| ||  | |||||||||||  | || |||||||| || ||| | |||||  ||||||||||||||||||| |
ggactataaaattggaagaaaaaataataccatagg-gcgatatgaaattctattttgggactgaaaaacgatcgcgatggggat--gggagtgattttttagTGCCCTTTGAGGAAGATGACAAGGATGCCAGCATATGGTTCTTGGACCACAACTATCATGAGACTATGTTCGACATGTTCAAGAGAATTAACG

upper sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ21414 (Selaginella moellendorffii), 3'ss of exon 1
catttgattttgcacagtacattacactgtgagcatgttcataagtgcgttgttgttacttgcacatcacttgtttgactttttgtttgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG
                |||      | |   || |  ||   | | | |   || |   || |     | | ||  || || || ||  |  | || |||| || ||||| ||||||||||  ||| ||||||| |||||| | ||||||||||| |||||  |||||||| | ||||||||| | || ||||
----------------gtatggccgatttgtaggagatttcgaggagagaatttctggtttcctggggagtcgtgagaattgttcttcct--tcttgcagTACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATG

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|164170594|gb|EL982405.1|EL982405
EST:     GCTCGGAAGTAGCTCTCGTGGTACTGTTGACGTCACCAACAGCTACGCAG                         TGCCTTTTGAGGAGGATGACAAAGACACAAGCAT
genomic: GCTCGGAAGTAGCTCTCGTGGTACTGTTGACGTCACCAACAGCTACGCAGgtgccttgat ... ggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCAT
EST: gi|19875108|gb|AU235939.1|AU235939
EST:     GCTCGGAAGTAGCTCTCGTGGTACTGTTGACGTCACCAACAGCTACGCAG                         TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACA
genomic: GCTCGGAAGTAGCTCTCGTGGTACTGTTGACGTCACCAACAGCTACGCAGgtgccttgat ... ggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACA
EST: gi|164146851|gb|EL996102.1|EL996102
EST:     GACGTCACCAACAGCTACGCAG                         TGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACA
genomic: GACGTCACCAACAGCTACGCAGgtgccttgat ... ggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgttgttgttacttgcacatcacttgtttgactttttgtttgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG
                           gtttgac  putative branch site (score: 4)
                                  tttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttgattttgcacagtacattacactgtgagcatgttcataagtgcgttgttgttacttgcacatcacttgtttgactttttgtttgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA