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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgtccctgaactcaaccactgtgttggacacaatttttttttctactgctagttttctgtaactatgttatgcatcaccttcatccatgtgccttgtagaaggctagacactgctcacatccgctgacgagtacttctatgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACGATCTTCAGAGCTTGGTGGCATCAGAGCTTTGCTCCCTGCTCAAAAACGT

Basic information

species Oryza sativa
transcript LOC_Os03g61950.1
intron # 16
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|86488405|gb|CI131038.1|CI131038
EST:     TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|88546559|gb|CI476210.1|CI476210
EST:     GCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: GCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|86599110|gb|CI355727.1|CI355727
EST:     TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|44668058|gb|CR281492.1|CR281492
EST:     CCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: CCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|88547608|gb|CI477916.1|CI477916
EST:     CACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATANCTGCATACATGGCATGCTTTCACG
genomic: CACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|86503558|gb|CI146191.1|CI146191
EST:     TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|25806211|gb|CA762172.1|CA762172
EST:     TGCTTTCCACCTGAGGCTGGGATAGCATTTTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|27577131|gb|CA999825.1|CA999825
EST:     TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|58676211|gb|CK064898.1|CK064898
EST:     TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|88262375|gb|CI366149.1|CI366149
EST:     TTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: TTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|88259975|gb|CI363185.1|CI363185
EST:     GTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: GTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
EST: gi|27547744|gb|CA767413.2|CA767413
EST:     TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTG                         AGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG
genomic: TGCTTTCCACCTGAGGCTGGGATAGCATCTTAGTTCTGACTCTTTACTTGgtaagcgtcc ... atgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagaaggctagacactgctcacatccgctgacgagtacttctatgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACGATCTTCAGAGCTTGGTGGCATCAGAGCTTTGCTCCCTGCTCAAAAACGT
                                        cttctat  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgtccctgaactcaaccactgtgttggacacaatttttttttctactgctagttttctgtaactatgttatgcatcaccttcatccatgtgccttgtagaaggctagacactgctcacatccgctgacgagtacttctatgtcatcagAGAACATTAGAAGGCAAGGAAGCATAGCTGCATACATGGCATGCTTTCACGATCTTCAGAGCTTGGTGGCATCAGAGCTTTGCTCCCTGCTCAAAAACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT