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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatagatagatagatagatagatgttctaatgtgcttatcatgtcatttggtacctgtacttttcaaaaagtttttaaaaattgttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA

Basic information

species Oryza sativa
transcript LOC_Os06g40170.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S8_170V6.1 (Physcomitrella patens), 3'ss of exon 6
ataatagatagatagatagatagatgttctaatgtgcttatcatgtcatttggtacctgtacttttcaaaaagtttttaaaaattgttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
          | | | |  | |    ||  |  ||| | ||||  || ||||      |   | |||  |  |   |    |||| || |  ||   |||| ||||| ||||||||||| ||||| || |||||||||||| |||| ||  || ||||    || ||||| || || ||||||||||| | ||||||| |
----------gtttgtttaagatgcatttcacggtgttcatca-atcgtttg----tcgatttcttctcatggcaatgtgtaatt-tttgcctg---cagTGGATGATGAGTACATCATAGTGGGTTCTGCCAACATCAACGAGAGATCCCTGAACGGTTCGCGTGACTCCGAAATTGCCATGGGAGCTTACCAGCCATA

upper sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S58_143V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------ataatagatagatagat--agatagatgttct------aatgtgcttatcatg-tcatttggtacctgtact--tttcaaaaagtttttaaaa-----attgttcgtt--tgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
                 ||  | ||| |    ||   ||  |  ||| |      | |||   ||| ||  ||  |  |||| |||     | ||  | | | |||| ||     ||| ||  ||  |||| |||| ||||| ||||||| |||| | ||||| || ||||| ||||||||||||||||||||    || ||||| || |||||||| ||||| | ||| ||  |
gtaagtcccattactcaatgctcgattgccgaatttggagtgccgttttcctttaattgtatatataatcctcgatgagtacatgtctcagtatctgagaatatttagaatgacgattcttttttgttgttgcagTGGATGATGAGTACACCATCATCGGATCAGCGAACATTAACCAGAGGTCGATGGACGGTTCTCGTGACTCTGAAATCGCCATTGGAGCCTACCAACCTTA

upper sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S94_36V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------ataatagatagatagatagatagatgttct----aatgtgcttatcatgtcatttggtacctg--tacttttcaaaaagtttttaaaaattgttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
                 || ||   ||||   |  ||  | | |      || | | ||   |||||||||| | |||   ||||  | |  ||   |||      |||| | |   | |||| |||||||||||||| || ||||| || |||||||||||| |||| ||  || |||| |  || ||||| || || ||||||||||| |  ||||| ||
gtgagtatttttatgtgtactactcagatttgtttattcacgcttacaaaaaggagttttcgatgtcatttgttcccttgctactggtgacgaacgcttt------tgtt-gctgcctgcagTGGATGACGAGTACATAATAGTGGGGTCAGCCAACATCAACGAGAGATCCTTGAACGGTGAACGCGACTCCGAAATTGCCATGGGAGCTTATCAGCCTCA

upper sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S94_26V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------ataatagatagatagatagatagatgttct----aatgtgcttatcatgtcatttggtacctg--tacttttcaaaaagtttttaaaaattgttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
               |  ||   ||||  ||  ||  | | |      || |   ||   |||||||||| | |||   ||||  | |  ||   |||      |||| | |   | |||| |||||||||||||| || ||||| || |||||||||||| |||| ||  || |||| |  || ||||| || || ||||||||||| |  ||||| ||
gtgagtatttttatgtcttactcagattcatttattcacgcttacaaaaaagaattttcaatgtcatttgttcccttgctactggtgacgaacccttt------tgtt-gctgcgtacagTGGATGACGAGTACATAATAGTGGGGTCAGCCAACATCAACGAGAGATCCTTGAACGGTGCACGCGACTCCGAAATTGCCATGGGAGCTTATCAGCCTCA

upper sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ26601 (Selaginella moellendorffii), 3'ss of exon 2
------ataatagatagatagatagatag--atgttctaatgtgctta-tcatgtcatttggtacctgtacttttcaaaaagtttttaaaaattg--ttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
       |   ||     | | |   |    | | || ||  | |    ||  |||  | |  |    |  | ||| |  |   || |   | |    |   | ||  |||| || ||||||||||||||||| || |||||||||||||||||| | || |||||||||||||| ||||||||||||||||||||||| | ||||||   
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagcacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACTCGGAGATCGCCATGGGAGCGTACCAGCCGTT

upper sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ34754 (Selaginella moellendorffii), 3'ss of exon 2
ataatagatagatagatagatagatgttctaatgtgcttatcatgtcatttggtacctgtacttttcaaaaagtttttaaaaattgttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
                                   |     ||       | ||  |     |||  |   |  ||   | ||  | ||  |||   |||| || || || |||||||| || |||||||| || || |||||| | || ||||| |||||||| ||| ||||||||||||||||||| | ||||||| |
-----------------------------------gtaagccagcctgcctcgtttcaaagttttctagcgaacttacgagaa--gatctcttgcg-cagTGGACGATGAATACATCATAGTTGGATCGGCGAATATAAACCAGCGCTCCATGGATGGCGGCCGCGACACGGAGATCGCCATGGGAGCTTACCAGCCATA

upper sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ24056 (Selaginella moellendorffii), 3'ss of exon 2
ataatagatagatagata-gatagatgttcta-atgtgcttatcatgtcatttggtacctgtacttttcaaaaagtttttaaaaattgttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
    | ||| | | | |  |||   | | ||  |||   || || | ||||   |     ||  | |   |   |     |    || ||   |  ||  ||| || ||||||||||| ||||| ||||| || |||||||||||| | || |||||||| || || ||| |||||||||||||||| || | |||||| | 
--cttcgatcgcttggtttgattcctttcctctatgcttttctcctatcatactggtttcgtgatatctcactggaaaaaactcgtttttttctccttgtagTGGACGACGAGTACATAATCGTTGGATCCGCTAACATCAACCAGCGATCAATGGACGGGGGGCGCGACACGGAGATCGCCATGGGCGCGTACCAGCCGCT

upper sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ35104 (Selaginella moellendorffii), 3'ss of exon 2
ataatagatagatagatagatagatgttctaatgtgcttatca--tgtcat-ttggtacctgtacttttcaaaaagtttttaaaaattgttcgtttgtttc-----agTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
    | ||| | | | |         |||   | ||||| ||   | ||||  ||||  |   |  | |||          |||| | |||  ||| | ||     ||| || ||||||||||| ||||| ||||| ||||||||||||||| | || |||||||| || || ||| |||||||||||||||| || | |||||| | 
----ttgatcgcttggtttgcttcctttcctctatgcttttctcctatcatactggtttcgtgatatctcactggaa----aaaactcgtttttttttctccttgtagTGGACGACGAGTACATAATCGTTGGATCCGCCAACATCAACCAGCGATCAATGGACGGGGGGCGCGACACGGAGATCGCCATGGGCGCGTACCAGCCGCT

upper sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ30966 (Selaginella moellendorffii), 3'ss of exon 2
ataatagatagatagatagatagatgttctaatgtgcttatcatgtcatttggtacctgtacttttcaaaaagtttttaaaaattgttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
                                     | | |  |     | ||  |     |||  |   |  ||   | ||  | ||  |||   |||| || || || |||||||| || ||||| || || || |||||| | || ||||| |||||||| ||| ||||||||||||||||||| | ||||||| |
------------------------------------gtaagccagctgcctcgtttcaaagttttctagcgaacttacgagaa--gatctcttgcg-cagTGGACGATGAATACATCATAGTTGGATCAGCGAATATAAACCAGCGCTCCATGGATGGCGGCCGCGACACGGAGATCGCCATGGGAGCTTACCAGCCATA

upper sequence: LOC_Os06g40170.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ06378 (Selaginella moellendorffii), 3'ss of exon 2
------ataatagatagatagatagatag--atgttctaatgtgctta-tcatgtcatttggtacctgtacttttcaaaaagtttttaaaaattg--ttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
       |   ||     | | |   |    | | || ||  | |    ||  |||  | |  |    |  | ||| |  |   || |   | |    |   | ||  |||| || ||||||||||||||||| || |||||||||||||||||| | || |||||||||||||| ||| ||||||||||||||||||| | ||||||   
gtaagtcttccagccttttcgttttctttccacgctcaaactttcacggtcgagtccatagtcatagtttttgttctagtacacttgactgactagactttctcgtaacagTGGACGACGAGTACATCATCGTCGGGTCGGCCAACATCAACCAGCGCTCCATGGACGGCGGCCGCGACACGGAGATCGCCATGGGAGCGTACCAGCCGTT

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|87041060|gb|CI195682.1|CI195682
EST:     ACAAAAGACGCGCCGGTTCATGATCTATGTCCACTCCAAGATGATGATAG                         TCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGA
genomic: ACAAAAGACGCGCCGGTTCATGATCTATGTCCACTCCAAGATGATGATAGgtatgctcaa ... tttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGA
EST: gi|36355297|gb|CF589234.1|CF589234
EST:     ACAAAAGACGCGCCGGTTCATGATCTATGTCCACTCCAAGATGATGATAG                         TCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGA
genomic: ACAAAAGACGCGCCGGTTCATGATCTATGTCCACTCCAAGATGATGATAGgtatgctcaa ... tttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttggtacctgtacttttcaaaaagtttttaaaaattgttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA
                                             tttgtttc  CT-rich tract
              tacttttcaaaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatagatagatagatagatagatgttctaatgtgcttatcatgtcatttggtacctgtacttttcaaaaagtttttaaaaattgttcgtttgtttcagTCGATGACGAGTACATCATCGTGGGATCGGCCAACATCAACCAGAGGTCGATGGACGGCGGCCGAGACTCGGAGATCGCCATGGGAGCATTCCAGCCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - aatgtgc
- - - - - - - - - - - - - - - - - - - -atcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - gtacctg