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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatcttaatccttgatcttcaagttccaattttgggctcttattgccctcttgcagtgactgactttgggaccatggaatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g67850.1
intron # 3
splice site 5'
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|33677048|gb|CF305287.1|CF305287
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|41884252|gb|BX929083.1|BX929083
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|88741864|gb|CI764369.1|CI764369
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGG
EST: gi|33693004|gb|CF321243.1|CF321243
EST:     CTCTATATCCACCAATATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|33654303|gb|CF276917.1|CF276917
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|88349124|gb|CI678094.1|CI678094
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|88442752|gb|CI693758.1|CI693758
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|88588287|gb|CI706094.1|CI706094
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGA
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGA
EST: gi|88762905|gb|CI772461.1|CI772461
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGA
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGA
EST: gi|88740582|gb|CI764090.1|CI764090
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAA
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAA
EST: gi|55410340|gb|CV722716.1|CV722716
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|66920252|gb|CX107100.1|CX107100
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|33688529|gb|CF316768.1|CF316768
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACACCTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|33680394|gb|CF308633.1|CF308633
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|33693589|gb|CF321828.1|CF321828
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|157650563|gb|EX450197.1|EX450197
EST:     CCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|33679207|gb|CF307446.1|CF307446
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|88851912|gb|CI679470.1|CI679470
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAG
EST: gi|33685055|gb|CF313294.1|CF313294
EST:     CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATG                         CTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGAT
genomic: CTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGAT

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: 70 (upstream exon), 74 (downstream exon)
Score: 43

GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatctt ... tggaatgcagCTGTAATATATCCATTCTTGCAACAACTCGAGGGGAATTTGATGGAGAAAGACTGCAACGAGAAAGGATGGTGCAAGGAGGCGGCCTCCGGTGGCGGCGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATATGTTGATGAGGATGCCTCTATATCCACCAACATTGAAAGGAGAGCAAGCCTCAAGGAATTCTATGgtatgatcttaatccttgatcttcaagttccaattttgggctcttattgccctcttgcagtgactgactttgggaccatggaatgcag

- - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA