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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggattctctggcttctcaccacttgattcatcgaacgcaatctttgaataattttactttaacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT

Basic information

species Arabidopsis thaliana
transcript AT2G20140.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 4
---gtaagg-attctctggcttctcaccacttgattcatcgaac-gcaatctttgaataattttactttaacctttgtttggtcttctattggttt--agGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT--
    ||| |   || ||   |  | |   || ||   | | |   |||   |    |       | | | ||| | || || | || |||   ||   ||||||| ||||  |||||||||||||| ||||||||||| |||||||||||||| ||||| || || || |||||||||||||||    ||| ||  |     
tttataatgtgctcgctcattgattatgtctggaagaaacaatttgcatggtcctcacttccacattcttaccgtggtgtgctgttttatgatttcacagGTGACACATGCTGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAGGAAGGTGTGCCGGAGGGTCTTTACATGTGAT--GTGCTCACTGGTCGC

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------------------gtaaggattctctggcttctcaccacttgatt-catcgaacgcaa-tctttga-ataattttactttaacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT
                                                                                             |  |  ||         ||||  || |  || ||| ||| |||| ||||||    | || |  ||| || |||| | | |||||| ||| |||||||||| ||||  || ||||||||||| || |||||||| |||||||||||||| ||||| || || ||||| ||||| ||||||   || ||| ||   |
gtaactcagctttgttttctcaaccagactccttgctctctagtactgttaatgttaaaactttcgagcatactaagtgccaatcctttcagatctgagtttgagctgcgctcagaacatatttgcatggaatgcaagtctttgttgcacttctctttttacatttgct-gttcttctgttgctttagGTGACACATGCCGATTTCAAGAAGGCCAAAGAGAAGGTCATGTTCAAGAAGAAGGAAGGTGTACCGGAAGGGCTTTATATGTGAGACATCCACCACTCAT

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
----------gtaaggattctctggcttctcaccacttgattcatcgaacgcaatctttgaataattttactttaacctttgtttg-gtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAA--TGATGCACAACGACT
          || |   || | |     |   | |||||| |    |  | ||       ||||      | | |||   | |||   | |||| |||  |||||| |||||||  |||||||||||||| || || |||||||||||||||||||||||||| || || || || || || ||||||   | ||   || ||   
attcaccagagttaaccttttgtaatagcctgcaacttgaatacaaggtcacaga----aaatatccactcatgaactgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC--

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G095593_T02 (Zea mays), 3'ss of exon 1
gtaaggattctctggcttctcaccacttgattcatcgaacgcaatctttgaataattttactttaacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCA--CAACGACT----------------------------------
                        |  |    | |||| |  | |   |    |  ||| ||      ||||||| |  | |         ||||||| ||||  || ||||||||||| ||||||||||| |||| ||||||||| ||||| ||||| || ||||| |||||||     ||  |  || |                                      
------------------------atatagcacttcgatctgattaggttctgagatttgctgatgtttttgttttgggtac-----acccaggtgacccatgcagatttcaagaaggcaaaggagaagGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGCCAATCTATTCATCATGCCGAACAAGTTACCCGATTGTGTGTGTACTAGCAC

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 4
-------gtaaggattctctggcttctcaccacttgattcatcgaacg-caatctttgaataattttactttaacctttgtttg-gtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACA-ACGACT
       | |  |  |  ||| ||| ||   |||||    || | ||  | ||||    |   | | |  ||  |   |||||  || ||   |      ||||||| ||||  || ||||||||||| ||||||||||| |||| ||||||||| ||||| ||||| || ||||| |||||||     ||  |   |  |  
tccatttgcatagcataactgtcttgtc--tacttggaatatagcacttcgatctgattaggttctgagatttgctgatgtttttgttttgggtacacccagGTGACCCATGCAGATTTCAAGAAGGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGCCAATCTATTCATCAT-

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
-------gtaaggattctctggcttctcaccact-tgattcatcgaac-gcaatctttgaataattttactttaacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT
       ||  | |||  |    ||      ||| ||  | | |  |  | | | | ||  |   |||    |  |   ||||| || ||  ||      ||||||| ||||  || |||||||| || ||||||||||| |||| ||||||||| ||||| ||||| || ||||| |||||||    || |      | ||
ttttagtgtgtgtattacccaatttgctttaactatgtctgagcatatagtactttatggttccatttgacattgctgatgttttgttttggat--acccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 5
--gtaaggattctctggcttctcaccacttgattcatcgaacgcaatctttgaataattttact--ttaa---cctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT
  || |   |  | ||  ||||  |   ||        |   |     |||   | | | |  |    ||     ||| |||     |||     || ||||||||||||  |||||||||||||| ||||| ||||||||||| |||||||||||||| || || ||||| || || |||||||  ||   || |   |
aagtgatcctattttgttttctacctttttttggaggggtgtgtgtcttttcctttactctcatgaccaaatgttttttttttaaaatcttgctcttcagGTGACGCATGCCGACTTCAAGAAGGCAAAGGATAAGGTTATGTTTAAGAAGAAAGAAGGGGTGCCAGAAGGACTGTATATGTGAAGCATCTTCATCATTT

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 5
gtaaggattctctggcttctcaccacttgattc-atcgaacgcaatctttgaataattt-tacttt--------aacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT
      ||  ||    |||||   | || |||   |    | |  | ||||| |  | | |||  |        ||   || |||  |  |||     || ||||||||||||  ||||| |||||||| ||||| || |||||||| ||||||||||||||||| || ||||| || || |||||||  ||   || | | |
---tttatattcaattttctctgtattttattttgttttgcaccttttttgagtggtgtgtaccctcgtgaccaaatgcttttttttttatcttgctcttcagGTGACGCATGCCGACTTTAAGAAGGCAAAGGATAAAGTTATGTTTAAGAAGAAAGAAGGAGTGCCCGAAGGACTGTATATGTGAAGCATCTTCATCAATT

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 5
------gtaaggattctctggcttctcaccact-tgat-tcatcgaacgcaatctttgaataattttactttaacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT
       ||     ||| |||||| |      | | || | ||   | |   | ||      | ||||   || | | |   |  |  | | |||||  ||||||| ||||  ||||| |||||||| ||||| || || ||||| |||||||||||||| || |||||||| || || |||||||  |    |  | | |
taatgtttatcttctctttggcttgtattgtttataatataatttgaagtttttttctccccaatttatgatatcttcttactattactattttggtc-agGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 5
------gtaaggattctctggcttctcaccacttgattca--tcgaacgcaatctttgaataattttactttaacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT
       |  | ||  |  |  |       |  | ||  |  | |||     | ||      | ||||   || | | |   |  |  | | ||| || ||||||| ||||  ||||| |||||||| ||||| || || ||||| |||||||||||||| || |||||||| || || |||||||  |    |  | |  
tgtttaatgtgtatctttggtttgtattgtatataatataatttgaagttttttttctccccaatttatgatatcttcttactattacttttttg-ttcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAATACTATCCTCTATC

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
-gtaaggattctctggctt--ctcaccacttgattcatcgaacgcaatctttgaataattttactttaacc---tttgtttggtcttctattgg--tttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT
 | |    ||   ||  ||  || || || || ||    ||    | ||    |  |     |    ||     ||||  ||||    || ||   || ||||||| ||||| |||||||||||||| ||||||||||| |||||||||||||||||||| || || ||||| |||||||||||||       | ||   |
ggaagaagttgaatgcattacctgactacatg-tttgctgattttagtcacctaggaccaggatcccaattaaatttgactggttaaatactgtgcttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------gtaaggattctctggcttctcaccacttgattcatcgaacgcaatctttgaataattttactttaacctt---------tgtt-----tggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT-
                                                          || |   || | | | | |   || | ||  |     |  |||  ||||||||    ||  ||| |   |         | ||     |||  |  || ||    ||||||| || | ||||||||||||||| ||||| || || |||| ||||||||| ||||| || || || ||  | || ||||  |  |  ||   | | | 
gtgagcttgccatttctttgtattcttttatatgtatttttaatgcgtctcgtcagaggttacacttttttagttgc---cctcatggctgtataattgcaggctttgaattggcttgttttgattctgtgactaagtattgactgtggattcttaatgccacagGTGACTCAAGCGGACTTCAAGAAGGCTAAGGACAAAGTGATGTACAAGAAGAAGGAAGGTGTACCCGAGGGGTTATATATGTAGAATACTCA-GTCAAGTG

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 5
gtaaggattctctggcttctcaccacttgattcatcgaacgcaatctttgaataattttactttaacctttgtt-tggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT-
                                        | | | | |  ||  ||||          ||||   | | ||||  |  |  |||| || || |  || |||||||||||||| |||||||| |||| ||||||||||||||| || || || || || ||||||| |||    |    |  || 
----------------------------------------gtagtttctcgatgcttttcacaactttcttgtaacgattttcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTAAATAGC-CGTCCCAGCTT

upper sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 5
gtaaggattctctggcttctcaccacttgattcatcgaacgcaatctttgaataattttactttaacctttgtt-tggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT-
                                        | | | | | |||  ||||          ||||   | | ||||  |  |  |||| || || |  || |||||||||||||| |||||||| |||| ||||||||||||||| || || || || || ||||||| |||    ||   |  || 
----------------------------------------gtagtttctcaatgcttttcacaactttcttgtaacgattttcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTAAATAGC-CATCCCAGCTT

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|124971504|gb|EL045265.1|EL045265
EST:     CTGGTCTGCTTGCTCTTAGAGAGTCGTCGGATGAAA                         GTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAG
genomic: CTGGTCTGCTTGCTCTTAGAGAG-CGTCGGATGAAAgtaaggattc ... attggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgcaatctttgaataattttactttaacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT
                      ctttaac  putative branch site (score: 3)
                                       tcttctatt  putative PPT
     atctttgaataatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggattctctggcttctcaccacttgattcatcgaacgcaatctttgaataattttactttaacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG