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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattaccatctcatcttgagaatataacctgagaattaaaactttgcttttgaatttccttactcggggtttaattcaaatcattttgtttttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G16470.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g26970.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------------------------------aattaccatctcatcttgagaatataacctgaga--attaaaactttgcttttgaatttccttactcggggtttaattcaaatcattttgtttttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG
                                                              |  |   | || |  |     | |  | | |||  |||  |  |  |  |||| | ||  | |    |     | || | ||  |  |  ||||  | ||||| |||||||| || || || |||||||||||||| ||||| |||||||| || || || |||||||| || || |||||||||||
gtattgacaaataattatatacaacagagaaggttttgtgtaaatacaaagtgtcaaatgcgaacaatctttctttctttttttcttgcttcagaccattgcatttacgactttgtagttattaatattgcagacagttgacattgtcattgtttt--attagGTTGATCCATCAGGGTCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTGTCAAATGCAAAGACATTTCTTGAGAAAAG

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 6
--aattaccatctcatcttgagaatataacctgagaattaaaactttgcttttgaatttccttactcggggtttaat-tcaaat-cattttgtttttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG
    ||    |       ||| ||| | |||||  ||||     | |  | ||    |     | |   ||| ||||  || ||    | | || || |   |||| ||||| || || || || |||||||||||||| ||||| |||||||| || || || |||||||| || || ||||| |||||
agttttgttcttctggactga-aattttacctgtcaatttgtcatattttgttatggtgtaaaatt---ggtataatgccagatgtgctgtattatttctacagGTTGATCCCTCAGGATCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTCTCCAATGCAAAGACATTTCTTGAAAAAAG

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G41330.1 (Glycine max), 3'ss of exon 8
aattaccatctcatcttgagaatataacctg---agaattaaaactttg--cttttgaatttccttactcggggtt-taattcaaatcattttgtttttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG
     |  | |  | |||    ||  || ||   | | |||   ||||    |||  |        | |   |||| | |||  |     |||||||||    |||||||||||||| || || ||||| || ||||||||||| || |||||||| || |||||||||||||| || || |||||||| ||
-----ctctttgttgttgcatttaagacttgtttaaagttactgctttaaattttaaagagatggaattgaaggttgtgatttgatgtgatttgtttttttg-tagGTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAG

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G17810.3 (Glycine max), 3'ss of exon 8
aattaccatctcatcttgagaatataacctgagaattaaaactttg--cttttgaatttccttactcggggtt-taattcaaatcattttgtttttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG
   |||       ||||     |   |  ||| |  ||   |||||   |||  |        | |   |||| | |||  |  || |||| |||| |  |||||||||||||| || || ||||| || ||||||||||| || |||||||| || |||||||||||||| || || |||||||| ||
--ctactgggatctctttgttgttgcatttga-agctactgctttgaattttaaagagagggaattgaaggttgtgatttgatgcaatttgctttttctgtagGTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAG

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 8
------aattaccatctcatcttgagaatataacctgagaattaaaactttgcttttgaatttccttactcggggtttaattcaaatcattttgtttttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG
       |||     ||  | |  |     |    |||   |||||     |   |||||  |  | | | |  ||   |||    |  |||| ||||| |  |||||||||||||| || || ||||| || ||||||||||| || |||||||| || |||||||||||||| || || |||||||| ||
ttattgtatttaagacttgtttaaaattactgctttgaattttaaagagagggaattgaaggttgtgatttgatgt--gatt----ttttttttttttttctgtagGTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAG

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G17810.2 (Glycine max), 3'ss of exon 8
aattaccatctcatcttgagaatataacctgagaattaaaactttg--cttttgaatttccttactcggggtt-taattcaaatcattttgtttttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG--------------
   |||       ||||     |   |  ||| |  ||   |||||   |||  |        | |   |||| | |||  |  || |||| |||| |  |||||||||||||| || || ||||| || ||||||||||| || |||||||| || |||||||||||||| || || |||||||| ||              
--ctactgggatctctttgttgttgcatttga-agctactgctttgaattttaaagagagggaattgaaggttgtgatttgatgcaatttgctttttctgtagGTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAGGTAAGCTTTTCATC

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 8
--aattaccatctcatcttgagaatataacctgagaattaaaactttgcttttgaatttccttactcggggtt-taattcaaatcattttgtttttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG
  |  ||| || |     |    |||||   |    ||   |       || | |        |     |||| | |||  |     ||||||||| |  |||||||||||||| || || ||||| || ||||||||||| || |||||||| || ||||| |||||||| || || |||||||| ||
gcagatactatatatatatatatatata---tatatatatgagtaccatttgtaatagagggaatcgaaggttgtgatttgatgtgatttgttttttctgtagGTGGATCCATCGGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAG

upper sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 3'ss of exon 7
aattaccatctcatcttgagaatataacctgagaattaaaactttgct--tttgaatttccttactcggggtttaattcaaatcattttgtttttgca-ctagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG
    |  ||   |  ||  || | |    |   |    |  ||    |  | | |   | |  | |   | |   |||||  |  || | | | |||  ||||||||||||||| || || |||||||| |||||||| || || ||||||||||| || || |||||||| || || |||||||| ||
---cattattataagttttgagtctgtttttttaccctatcctgcattagtataatgctacaaatttctgctaatattcatttacttatttatatgcctctagGTGGATCCATCAGGTTCATATTTCTCATGGAAAGCCTCCGCAATGGGGAAGAATGTCTCAAATGCAAAGACATTTCTTGAGAAGAG

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|86030209|gb|DR325962.1|DR325962
EST:     TTTCCTTGCTGGTGGCTGGATATGATGACAAGGGTCCACAATTGTATCAG                         GTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGGAG
genomic: TTTCCTTGCTGGTGGCTGGATATGATGACAAGGGTCCACAATTGTATCAGgtttttcctc ... tttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAG
EST: gi|86075658|gb|DR371415.1|DR371415
EST:     TTTCCTTGCTGGTGGCTGGATATGATGACAAGGGTCCACAATTGTATCAG                         GTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAG
genomic: TTTCCTTGCTGGTGGCTGGATATGATGACAAGGGTCCACAATTGTATCAGgtttttcctc ... tttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAG
EST: gi|86082335|gb|DR378094.1|DR378094
EST:     TTTCCTTGCTGGTGGCTGGATATGATGACAAGGGTCCACAATTGTATCAG                         GTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAG
genomic: TTTCCTTGCTGGTGGCTGGATATGATGACAAGGGTCCACAATTGTATCAGgtttttcctc ... tttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAG
EST: gi|164158240|gb|ES029969.1|ES029969
EST:     TATGATGACAAGGGTCCACAATTGTATCAG                         GTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATTGGGAAG
genomic: TATGATGACAAGGGTCCACAATTGTATCAGgtttttcctc ... tttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttttgaatttccttactcggggtttaattcaaatcattttgtttttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG
                                      ttttgttttt  CT-rich tract
                        tttaattcaaatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattaccatctcatcttgagaatataacctgagaattaaaactttgcttttgaatttccttactcggggtttaattcaaatcattttgtttttgcactagGTGGATCCATCTGGCTCTTATTTCTCCTGGAAAGCTTCAGCCATGGGGAAGAACGTTTCTAATGCAAAAACCTTCCTTGAGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC