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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatgttttaccacttatcttcttatgattataacatcaatatgaatgctactattaacttgtcttatcatttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATATTTTTGCATTCGGAGTGGTCATGTTGGAGACTGTCGCTGGGAGA

Basic information

species Oryza sativa
transcript LOC_Os05g17604.3
intron # 21
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|29680540|gb|CB676815.1|CB676815
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGN
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGG-
EST: gi|29676653|gb|CB672928.1|CB672928
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
EST: gi|29624376|gb|CB629387.1|CB629387
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
EST: gi|29664574|gb|CB660849.1|CB660849
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
EST: gi|29630956|gb|CB635965.1|CB635965
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGNG
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAG-G
EST: gi|29672836|gb|CB669111.1|CB669111
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
EST: gi|29627532|gb|CB632543.1|CB632543
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCGGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
EST: gi|29622648|gb|CB627659.1|CB627659
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
EST: gi|29675944|gb|CB672219.1|CB672219
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
EST: gi|29627200|gb|CB632211.1|CB632211
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
EST: gi|29628147|gb|CB633158.1|CB633158
EST:     CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATT                         GGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC
genomic: CTCTACGATGAGAATCAAACTCATGTGAGCACTAGAATTGCAGGCACATTgtaagaatgt ... catttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgattataacatcaatatgaatgctactattaacttgtcttatcatttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATATTTTTGCATTCGGAGTGGTCATGTTGGAGACTGTCGCTGGGAGA
                             tattaac  putative branch site (score: 1)
                                            tcattttt  putative PPT
     ttataacatcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatgttttaccacttatcttcttatgattataacatcaatatgaatgctactattaacttgtcttatcatttttaagGGGCTATCTAGCTCCTGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATATTTTTGCATTCGGAGTGGTCATGTTGGAGACTGTCGCTGGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA