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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaattttgttgtagtcctgaaatgaaaatcacagtgccctatttattaagatgtaatctggttgccttaatgtctcctatgtaattgttcttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTGCTCTCCAAGCCTGCCAAGGGTGTAGAGAAGTCGTTCGCTCTTCTTTCCC

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42884.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G149751_T06 (Zea mays), 3'ss of exon 1
-----------------------tgaattttgttgtagtcctgaaatgaaaatcacagtgccctatttattaagatgta-atctggttgccttaatgtctcctatgtaattgtt-cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTGCTCTCCAAGCCTGCCAAGGGTGTAGAGAAGTCGTTCGCTCTTCTTTCCC
                       | | ||    | |  |  |  | |     |      | |  |  ||| || |  |   | |  |||| |  ||| ||  || |   ||||| |||| |||||||||| ||||| |||||||||||||||||||||||||| || ||| |||||||||| ||||||||||||||||| ||||||   ||| ||||||||||||
gtgcatacagagtggcattactataatttggactctcattatttattttgtgttgtttagtctgaaatataaaaacatgtgtttttttgcttgtatggcttataaggtgttgttgcttcttgcagCTCGGTGTTGATACCGTGCCAGTACTTGTTGGACCAGTCTCGTACCTGTTGCTCTCAAAGCCTGCCAAGGGTGTGGAGAAGGGATTCCCTCTTCTTTCCC

upper sequence: LOC_Os12g42884.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G149751_T01 (Zea mays), 3'ss of exon 3
tgaattttgttgtagtcctgaaatgaaaatcacagtgccctatttattaagatgta-atctggttgccttaatgtctcctatgtaattgtt-cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTGCTCTCCAAGCCTGCCAAGGGTGTAGAGAAGTCGTTCGCTCTTCTTTCCC
  | ||    | |  |  |  | |     |      | |  |  ||| || |  |   | |  |||| |  ||| ||  || |   ||||| |||| |||||||||| ||||| |||||||||||||||||||||||||| || ||| |||||||||| ||||||||||||||||| ||||||   ||| ||||||||||||
--atttggactctcattatttattttgtgttgtttagtctgaaatataaaaacatgtgtttttttgcttgtatggcttataaggtgttgttgcttcttgcagCTCGGTGTTGATACCGTGCCAGTACTTGTTGGACCAGTCTCGTACCTGTTGCTCTCAAAGCCTGCCAAGGGTGTGGAGAAGGGATTCCCTCTTCTTTCCC
















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|29620902|gb|CB625913.1|CB625913
EST:     TGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|58668944|gb|CK057630.1|CK057630
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|29636000|gb|CB641009.1|CB641009
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|58611543|gb|CK039255.1|CK039255
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTGGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|27334367|gb|CA882818.1|CA882818
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGT
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGT
EST: gi|58664132|gb|CK052818.1|CK052818
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|29633667|gb|CB638676.1|CB638676
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|88360108|gb|CI610222.1|CI610222
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|117239956|gb|CT849487.1|CT849487
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|58686304|gb|CK074991.1|CK074991
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|58612621|gb|CK040333.1|CK040333
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|58669089|gb|CK057775.1|CK057775
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|88358234|gb|CI605159.1|CI605159
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|300216097|gb|HO088723.1|HO088723
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
EST: gi|58607018|gb|CK035051.1|CK035051
EST:     TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAAGCG                         CTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG
genomic: TCTCCTACTCTTCCCACAAGGCTGTGAATGAATACAAGGAGGCCAAGGCGgtaagataat ... cttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaagatgtaatctggttgccttaatgtctcctatgtaattgttcttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTGCTCTCCAAGCCTGCCAAGGGTGTAGAGAAGTCGTTCGCTCTTCTTTCCC
                    ccttaat  putative branch site (score: 4)
                                        ttgttcttc  putative PPT
                                 tatgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaattttgttgtagtcctgaaatgaaaatcacagtgccctatttattaagatgtaatctggttgccttaatgtctcctatgtaattgttcttcatgcagCTCGGCGTTGACACCGTGCCAGTACTTGTTGGACCAGTTTCATACTTGTTGCTCTCCAAGCCTGCCAAGGGTGTAGAGAAGTCGTTCGCTCTTCTTTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT