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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatagatgacagatggttccttaagtccttaaatttgttattcaaaaagcttttattttactaacggtttgaaggccatttgatgtccttttactaattccaaccattgtttattagATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGTTTTCTGGGGATGGGGAGGCTCAAGATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g66850.1
intron # 3
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|33671653|gb|CF299892.1|CF299892
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACTGGAACAGAG
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAACTGGAACAGAG
EST: gi|88340205|gb|CI652554.1|CI652554
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACTGGAA
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAACTGGAA
EST: gi|33664175|gb|CF295142.1|CF295142
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGT
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGT
EST: gi|13420831|gb|AU174921.1|AU174921
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGT
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGT
EST: gi|88417949|gb|CI596626.1|CI596626
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACGTGGAAGAGAGTTTT-ATAAG
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAAC-TGGAACAGAGTTTTCATAAG
EST: gi|88718484|gb|CI741994.1|CI741994
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGT
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGT
EST: gi|88417964|gb|CI596641.1|CI596641
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACTGGAACAGAGTTTTCATA
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAACTGGAACAGAGTTTTCATA
EST: gi|88368321|gb|CI577592.1|CI577592
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACCTGGAACAGAGTTTTCATAAGATACTGCGATGGA
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAAC-TGGAACAGAGTTTTCATAAGATACTGCGATGGA
EST: gi|163921121|gb|EG710147.1|EG710147
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACTGGAACAGAGTTTTCATAAGATACT
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAACTGGAACAGAGTTTTCATAAGATACT
EST: gi|88417991|gb|CI596668.1|CI596668
EST:     AGCAGTAGAGTT-AACGGGATACTCAGCAATGACCAACAACTGACTTCTG                         ATTTTTACAAAGTGGAAGAGAGTTTTCATAAGA
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAAC-TGGAACAGAGTTTTCATAAGA
EST: gi|66914214|gb|CX101062.1|CX101062
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGT
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGT
EST: gi|88342448|gb|CI645970.1|CI645970
EST:     AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTG                         ATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCA
genomic: AGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 73 (downstream exon)
Score: 63

GATTGTTCCAAACGCAAAATGAGCGCGTATGGTTCATCGAAATTCATGCGAGCAGTAGAGTTCAACGGGATACTCAGCAATGACCAACAACTGAATTCTGgtacatatag ... tgtttattagATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGTTTTCTGGGGATGGGGAGGCTCAAGATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacggtttgaaggccatttgatgtccttttactaattccaaccattgtttattagATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGTTTTCTGGGGATGGGGAGGCTCAAGATCAG
                          ttttactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatatagatgacagatggttccttaagtccttaaatttgttattcaaaaagcttttattttactaacggtttgaaggccatttgatgtccttttactaattccaaccattgtttattagATTTTTACAACTGGAACAGAGTTTTCATAAGATACTGCGATGGAGCATCGTTTTCTGGGGATGGGGAGGCTCAAGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA