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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG

Basic information

species Oryza sativa
transcript LOC_Os11g33240.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 12
gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctc--ttcatcccatacttgtgatattcaattaca----gGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
  | || ||  ||   || |  | | || | ||  |   | |  || |   ||  ||| |  |    |    | |||   |  |  || || |||   |||    |||||||||||||||||||||||||||||||||||| ||| |  |  ||||||| |||||||| ||| | || ||||| || ||||||
-ctttaattgcttgcaacct--gctagctactgtgt---ttttttgtcatgtccttggcccttgggtttgacttatcttctgttcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCATCATCTGTGAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
gatatactttttttttacttttgttggccattgcctatctc-tcatg-actcatctctgggcactaacctcttcatcccatacttgtgat-attcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
  | || ||  ||   || |  | | || | ||  | | |   ||||    ||| ||   |   |   ||  || ||   |  | ||  | || ||  | |||||||||||||||||||||||||||||||||||||| ||||| || || ||||| |||||||| ||| | || ||||| || ||||||
-ctttaattgcttgcaacct--gctagctactgttttttttgccatgtgaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 13
gatatactttttttttacttttgttggccattgcctatctctcatgactcatct-ctgggcactaacct---cttcatcccatacttgtgatattcaattaca----gGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
        |||||||| || || |   ||  |   |   |   |      | || ||| |   |  |||   |||||||   | ||  ||||| |||   |||    |||||| ||||||||||||||||||||||||||||| ||||| || || |||||  ||||||| ||| |||| ||||| || ||||||
--------ttttttttgctattttaatcctataattgcttgcaacctgctagctactgtgtcttccccttgacttcatcttctgctaatgatactcatccacatgcagGTTGGGAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGCTAGCTGGGCCACTGCATGGCCTTGCAAATCAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
---------------------------------------------------------------gatatactttttttttacttttgttggccattgcctat-ctctcatgactcatctctgggcactaacctcttcatcc---catacttgtgatattcaatta----------------cagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
                                                                | |   ||||||  ||  | |  |||  |  |||| |  | | || |   || | |    |   |  | |  ||      |||  | |  || |  |||                 |||||||  ||| | || ||||||||||||||| | |||||||||||  ||||||| |||||||| ||  |||| ||  |||| ||||||
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatgtattgtactgtgtgttcccgtcagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 13
gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
  |||   | |  | | | | |||      |     ||      ||||  | ||   |   ||||    |   |  |  |    |  | ||||  |  ||||||| ||||| || ||||| || ||||| || |||||||||||| | |||||||||||||| ||| | || ||  |||||||||||
-gtatgtatatactctccatgtgtcaattttaaaggat------tgacctacctgaagtttctaatggttcttttgctaaaaattcttgttca--tgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 12
-gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattac--agGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
  || || ||      |  | ||| ||  ||| |   || | |    ||| ||         || |    |   |      ||  |||| ||   | ||  ||||||| ||||| || |||||||| |||||||| ||||| |||||| |||||||||||||||| ||| | || ||  |||||||||||
gtatgtatttgccacatgatcttgatg--cat-gataatgttttg-aacttatagacattt-ctgatggttctgtttttggctaatgatgtttcttcacttagGTTGGGAGTGCACTTTCAGATCCATATCTTTCATTTGCTGCTGCATTGAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 13
-------------------------------------------------------------------------------------------------gatatactttttttttacttttgttggccat-tgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
                                                                                                  ||  | || |   | |  |||   | |  | ||  | |   |  | | | |||  ||   |  ||  |  ||     |    | | ||  |||||| |||||||  |||||  || |||||||||| ||||| |||||||||||| | |||||| ||||||| ||| | || ||  ||||||| |||
gtaagtgagcctagattcgttctaattagttaaatggaaatgtgtaattttgttgtatttccgagggtaaagtcattattttatcctgaagttatttaatggaattatggctcatattttcagtcagtgtgtttgttattatttagtgatca-tgaagaggaatgttctctattgactgatattatgctcaatt-cagGTTGCTAGTGCATTGGCAGATCCTTACCTTTCATTTGCAGCTGCATTAAATGGTCTAGCTGGCCCACTCCATGGTTTGGCTAACCAG

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|3758954|gb|C96653.1|C96653
EST:     TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattg ... tcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
EST: gi|38470398|gb|CF954529.1|CF954529
EST:     TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT
genomic: TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTGgtaattattg ... tcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG
              cactaac  putative branch site (score: 1)
                                         atattcaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatatactttttttttacttttgttggccattgcctatctctcatgactcatctctgggcactaacctcttcatcccatacttgtgatattcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA