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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctttttatgttacatttgagctagctgtgtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgcatatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT

Basic information

species Oryza sativa
transcript LOC_Os10g33275.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G119671_T01 (Zea mays), 3'ss of exon 3
gctttttatgttacatttgagctagctgt---gtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgcatatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT
 || |||||      ||     |  || |    |||||  |  ||||  ||  |  ||| |     || |||||  ||||   | |   | |||| ||| ||| ||||||||||||||||| || ||||| || || ||||| || |||||||||||||||||||| ||||||||||                          
-ctctttataaatggttaacaattcctttcagatcttatcgagtaattttagatccttttacttttct-tattgtctattaacggtttgtttgtaattt-cagAAAAATTGTTTTGGCAACCAACATTGCGGAGAGTAGTATCACTATAGATGATGTTGTCTATGTGATTGATTGTG--------------------------

upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 12
gctttttatgttacatttgagctagctgt---gtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgcatatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT
 || |||||      ||     |  || |    |||||  |   |||  ||  |  ||| |     || |||||  ||||   | |   | |||| ||| ||| ||||||||||||||||| || ||||| || || ||||| || |||||||||||||||||||| ||||||||||| || || ||||| ||||| ||||||
-ctctttataaatggttaacaattcctttcagatcttatcgagaaattttagatccttttacttttct-tattgtctattaacggtttgtttgtaattt-cagAAAAATTGTTTTGGCAACCAACATTGCGGAGAGTAGTATCACTATAGATGATGTTGTCTATGTGATTGATTGTGGTAAGGCCAAGGAGACAAGCTATGAT

upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G052798_T01 (Zea mays), 3'ss of exon 4
----------------gctttttatgttacatttgagctagctgt---gtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgcatatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT
                ||| |||||      ||     |  || |    |||||     ||||  ||  |  ||| |     || |||||  ||||     |   | |||| |||     ||||||||||||||||| || ||| | || || ||||| || |||||||||||||||||||| ||||||||||| || ||                   
gtttgaactaattgtagctctttataaatggttaacaattcctttcagatcttatcaagtaattttagatccttttacttttct-tattgtctattaacagTTTGTTTGTAATTTCAGAAAAAATTGTTTTGGCAACCAACATTACGGAGAGTAGTATCACTATAGATGATGTTGTCTATGTGATTGATTGTGGTAAGGCC------------------

upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA10G10180.1 (Glycine max), 3'ss of exon 12
gctttttatgttacatttgagctagctgtgtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgc-atatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT
   |   ||| |   |       ||  || | ||  |     ||  |   || | | | ||   |    |   | ||    |||  || | | | ||  || ||||||||  | |||||||||||||| || || || || || |||||||| ||||| ||||| || || ||||||||||||||||| || || ||||||
-tatcagatgatcagtaaagatgaggggtattttgctcatatatatttgattttctcatcattttagcatctatgttttgattgttatttttctgttgtagAAAAATTGTGCTAGCAACAAATATTGCTGAGAGTAGCATCACCATAGATGACGTTGTGTATGTCATAGACTGTGGCAAAGCAAAGGAGACCAGCTATGAT

upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 10
gctttttatgttacatttgagctagctgtgtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgcatatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT
| |     | | |  | |    | |   | ||||  |   | || ||  ||| |   | |||| | | |     | ||||  |||       ||||  |||||||| |||||||| ||||| ||||| || || ||||||||||| ||||||||||| |||||  | |||||||| |||||||||||||| || ||||||
gttagccctctgagctatcgattcgtcatttcttcttttatcattctgctttgt---agcaacttttctaagcgaatgct-ctgc-------ttttgtagGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTACAATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGAT

upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 3'ss of exon 10
gctttttatgttacatttgagctagctgtgtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgcatatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT
       ||  | ||| | |   |||  | | |  ||   | || |   |  |   ||  |   |  | | || | |    |||||| | |    |  |||||||||||  | || ||||| |||||||| || ||||| || |||||||||||||| || || || || ||||| || ||||||||||||||||| |||
-gcaagcatccttcatct-actaagccttctatctattagtgatgcatctgaaacagattatttttcaattctaaattgctttgcatctat----tgtagGAAAATTGTGCTAGCCACAAACATTGCAGAGAGTAGTATCACCATAGATGATGTTGTATACGTCATAGACTGTGGAAAGGCAAAGGAAACAAGTTACGAT

upper sequence: LOC_Os10g33275.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S36_206V6.1 (Physcomitrella patens), 3'ss of exon 11
gctttttatgttacatttgagctagctgt---gtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgcatatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT
  || |   |||  |    |   |   |    || |  ||| ||| |        || | | ||   | || |||| | ||||||||    |     ||  |||||||||||  |||| || || || || || |  |||||||| || |||||||| ||||| || ||||||||||| || |||||||| ||||| ||||| 
-tttctctagttgaacactaataaaacggacagtttctatg-ctagtatacagggatatcagcagagtctaatgct-agtgctgttgaccttcctggttgtagGAAAATTGTGCTGGCCACCAACATAGCCGAGACTAGTATTACGATCGATGATGTAGTCTACGTGATTGATTGTGGGAAGGCAAAGGAGACAAGCTATGAC

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|112786422|gb|EE590731.1|EE590731
EST:     CCCACTGTCAATCAGCGTGAAATTTTTGATAGACCACCAGCCAATATGAG                         GAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGA
genomic: CCCACTGTCAATCAGCGTGAAATTTTTGATAGACCACCAGCCAATATGAGgtaaatcacc ... tatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattttatttgaacaacctgtattgcttattgctgttgcatatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT
                                             tatttttc  CT-rich tract
                                        atatgtatttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctttttatgttacatttgagctagctgtgtcttaatggctaatcctattttatttgaacaacctgtattgcttattgctgttgcatatgtatttttcagGAAAATTGTTTTGGCAACAAATATTGCAGAAAGCAGTATTACAATAGATGATGTTGTCTATGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA