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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacttttgtatgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG

Basic information

species Arabidopsis thaliana
transcript AT1G73670.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 3
-----ccacttttgtatgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttgat-tacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
        || ||| |  |  |     | |  |||||    ||| | | ||   |||||  |   ||  ||       || ||||    |  | ||     | ||||| || ||||| ||||||||||||||||| ||||| |||||||||||||||||  | || ||||| || |||||||| || |||||||| || |||||||
atgccatgctcttgaactatcgatacatatgcttagca---taccaatttg---gataatttcaaatgcacttgcaccatactaaactcaaatgtgttttttgcagTACACTCCTGCAATTGATATTTGGAGCGTCGGTTGTATATTTGCTGAAATGCTTATGGGAAAGCCACTTTTTCCTGGAAAGAATGTGGTACATCAATTGG

upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G375975_T01 (Zea mays), 3'ss of exon 3
-----------------------ccacttttgtatgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
                       | |||| |    |     |    |||  | | | | |||   |    || | |    || |||   | |    |   ||||  ||  ||      | |||||||| |||||||||||||| |||||| | ||||| |||||||||||||||||  |||||||||| || ||||||||||| |||||||| || ||| |||
gtcggatagttttcacccggacacaacttctactagctcttcattgctatatggttttttactgtttaagagtacaccacttcatttt-gctgaatttacaacttaacactta-attttgcagTATACTCCTGCGATTGATATCTGGAGCCTAGGTTGTATATTTGCTGAAATGCTTATAGGGAAGCCTCTCTTTCCTGGCAAGAATGTGGTACATCAACTGG

upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
ccacttttgta-tgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
  ||||    | ||    | |  | | |      || ||  ||  ||    | ||  |||    |   |   | | || | |||    ||      | ||||| || ||||| ||||||||||||||||| || || |||||||||||| ||||   ||||||||| || ||||| || || ||||| || || || ||||
-tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttttacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG

upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
ccacttttgtatgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttgattacagatctgatgc-taactcta--cttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
   || ||  ||      || |     ||   |||     |    |  | |||   ||| | ||  |  ||  ||  ||| |  |     |||     | |||||||| ||||| ||||||||||||||| |||| ||||||||||| ||||||||    ||||||||  | |||||||| |||||||| || ||||||||||
--cctcttcaatcctcctctaccgggattgtgtatgatttatgaagttgaatata-tttaagtattgcactagtgtgtaatttcaaatccttgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG

upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
-----ccacttttgtatgaaggcctgctctagttagctatcta-------caagtgtgcaggataag---gtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
     |  ||||| | | ||    |  ||| |    |||| ||       ||| ||  || | |       ||  ||||   ||   ||  ||| | || ||        | ||||| |||||||| ||||||||||||||| |||| ||||||||||| ||||||||    ||||||||  | |||||||| |||||||| || ||||||||||
gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaattgaacatgcttgatatattgaattatgcatgcaattttaaatttatttcctttt--tgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG

upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
ccacttttgtatgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttg--attacagatctgatgctaactcta-cttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
   || ||  ||      || |     ||   |||     |    |  | |||   ||    ||| |||  |   | | |  || |    |||     | ||||||||||| || ||||| ||||||||| |||| ||||||||||| ||||||||    ||||||||  | |||||||| |||||||| || ||||||||||
---ctcttcaatcctcctctaccaggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttcaaatccttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG

upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 4
-------ccacttttgtatgaaggcctgctct--agttagcta---tcta--caagtgtgcaggataag---gtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
        |   ||| | | ||   ||  |||   |||   ||   | ||  ||| ||  ||   |  |    ||  | ||   || | ||  ||| | || ||        | ||||| || || || ||||||||||||||| |||| ||||||||||| ||||||||    ||||||||  | |||||||| |||||||| || ||||||||||
gtaagtttcttcttttttttaacatcttttcttgggttgaatataatttaagcaattgaacatacttggtgtattgaaatatgcatgtaattttaaatttatttcctttt--tgcagTACACTCCAGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG

upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0011g04920.t01 (Vitis vinifera), 3'ss of exon 4
ccacttttgtatgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttgattacagatctgatgctaactcta----cttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
    |||| ||  ||   |||   || |||  |   |  || ||  ||  | |   |       | ||  || | |    ||||     |||       | ||||| |||||||| ||||||||||||||| | || || |||||||| ||||||||    || |||||  | |||||||| ||||||||||| || |||||||
---gttttatactaatatctgtgttatttatttcgattgaactgatcat-acaccataatccctctgaaatggtacagtttctaaagcttttcatcttttgcagTACACCCCTGCTATTGATATTTGGAGCATAGGATGTATATTTGCGGAAATGCTTACTGGAAAGCCCTTGTTTCCTGGTAAAAATGTGGTCCAGCAATTGG

upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
ccacttttgtatgaaggcctgctctagttagctatctacaagtgt-gcaggataaggtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
|   |  || |  | | ||| || | |||    |  |  |||||  |     |    ||  | || | |||  ||          ||| | |    | ||||| || ||||||||||||||||||||| | || ||||||||||| ||||||||   ||| || ||||| ||||| || |||||||| || ||||| ||||
cttttgatgaaatatgacct-ctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG

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|86072907|gb|DR368664.1|DR368664
EST:     CTACTCGGTGGTACCGTGCCCCTGAACTCTGTGGATCATTTTTCTCAAAA                         TATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATG
genomic: CTACTCGGTGGTACCGTGCCCCTGAACTCTGTGGATCATTTTTCTCAAAAgtaagcttat ... cgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATG
EST: gi|86072909|gb|DR368666.1|DR368666
EST:     CTACTCGGTGGTACCGTGCCCCTGAACTCTGTGGATCATTTTTCTCAAAA                         TATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATG
genomic: CTACTCGGTGGTACCGTGCCCCTGAACTCTGTGGATCATTTTTCTCAAAAgtaagcttat ... cgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaggataaggtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
                            tgctaac  putative branch site (score: 1)
                                       cttttgc  putative PPT
           tttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacttttgtatgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG

- - - - - - - - - ctgctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgc