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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacttcctcttgtatcgtatggtaccccctcttaccctccttgcccttccccactctattcatgttctctaatgcttgaatttatataacatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAGAGGGTAACAATGAAGATTGGCGCAGGACATTTTGAGCCAAGCGGCCCCA

Basic information

species Oryza sativa
transcript LOC_Os01g51754.1
intron # 10
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|87010794|gb|CI312486.1|CI312486
EST:     TAAATTAATTTCTATTAGAAATCGCCAAAAGATTCCATTGCCGTAGCAAG                         ATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAAGAGATTGATGA
genomic: TAAATTAATTTCTATTAGAAATCGCCAAAAGA-TCCATTGCCGTAGCAAGgtaaaacttc ... acatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGC-AGAGATTGATGA
EST: gi|86478038|gb|CI120671.1|CI120671
EST:     CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAG                         ATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
genomic: CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAGgtaaaacttc ... acatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
EST: gi|218500833|gb|FG957608.1|FG957608
EST:     CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAG                         ATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
genomic: CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAGgtaaaacttc ... acatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
EST: gi|25806949|gb|CA762910.1|CA762910
EST:     CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAG                         ATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
genomic: CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAGgtaaaacttc ... acatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
EST: gi|86480605|gb|CI123238.1|CI123238
EST:     CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAG                         ATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
genomic: CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAGgtaaaacttc ... acatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
EST: gi|29678997|gb|CB675272.1|CB675272
EST:     CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAG                         ATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
genomic: CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAGgtaaaacttc ... acatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
EST: gi|66923399|gb|CX110247.1|CX110247
EST:     CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAG                         ATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
genomic: CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAGgtaaaacttc ... acatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
EST: gi|86479747|gb|CI122380.1|CI122380
EST:     CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAG                         ATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
genomic: CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAGgtaaaacttc ... acatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
EST: gi|29677516|gb|CB673791.1|CB673791
EST:     CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAG                         ATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG
genomic: CTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAGgtaaaacttc ... acatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAG

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: 24

TCCTGCAATCTTCTATGATCATATATTTTCGCATTTACAGCCAGAGATTGCTAAATTAATTTCTATTAGAAATCGCCAAAAGATCCATTGCCGTAGCAAGgtaaaacttc ... acatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAGAGGGTAACAATGAAGATTGGCGCAGGACATTTTGAGCCAAGCGGCCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttccccactctattcatgttctctaatgcttgaatttatataacatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAGAGGGTAACAATGAAGATTGGCGCAGGACATTTTGAGCCAAGCGGCCCCA
                                        atataac  putative branch site (score: 24)
                                ttgaatttatataaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacttcctcttgtatcgtatggtaccccctcttaccctccttgcccttccccactctattcatgttctctaatgcttgaatttatataacatttacagATCAAGATACTGAAAGCAGAGGGAAATTTATATGCGGCAGAGATTGATGAGAGGGTAACAATGAAGATTGGCGCAGGACATTTTGAGCCAAGCGGCCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA