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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttcccataattttgttatgttttctttgataatatagatacagatatgatactcatattattatgtaattttaaatgtgcttttatgccatatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g64770.5
intron # 4
splice site 3'
intron type U2

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|29656748|gb|CB653023.1|CB653023
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|88344519|gb|CI677575.1|CI677575
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|88722525|gb|CI746035.1|CI746035
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCAC
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCAC
EST: gi|88334859|gb|CI648634.1|CI648634
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|33798640|gb|CF325178.1|CF325178
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|88355035|gb|CI615916.1|CI615916
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|88362576|gb|CI607334.1|CI607334
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATA
EST: gi|88426086|gb|CI604375.1|CI604375
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|88309155|gb|CI654774.1|CI654774
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|88348634|gb|CI634229.1|CI634229
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|88308532|gb|CI650941.1|CI650941
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|88390459|gb|CI607495.1|CI607495
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGA
EST: gi|88326048|gb|CI651098.1|CI651098
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|88403282|gb|CI571023.1|CI571023
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATC
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATC
EST: gi|88400865|gb|CI616870.1|CI616870
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTAGTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
EST: gi|88347482|gb|CI637422.1|CI637422
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGAC
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGAC
EST: gi|33798687|gb|CF325201.1|CF325201
EST:     TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAG                         GGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA
genomic: TCTGCTGTGAATGTGATCCAATACTACAATACAATTCAACCCAGTGTAAGgtaagcttgt ... catatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgatactcatattattatgtaattttaaatgtgcttttatgccatatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAG
         tcatattattatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcccataattttgttatgttttctttgataatatagatacagatatgatactcatattattatgtaattttaaatgtgcttttatgccatatattagGGGAAGAAATGTTTACTTGCAATATTCATCCCACCAAGAATTGACTACTGATCAGAGCTCTCATGGACGAAATCCTGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA