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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcagtctaacataaccaacaatgtttccaggtttcgccatctcacttctcatggctcctctcatcctcggtcggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCGGCCGTGGGCGTGGTCGATTCTAAGATGAAATCAGGAGGAGGTGCCCTTG

Basic information

species Oryza sativa
transcript LOC_Os11g06760.1
intron # 8
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|88992823|gb|CI035785.1|CI035785
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|38474629|gb|CF958762.1|CF958762
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88984917|gb|CI011814.1|CI011814
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88479193|gb|CI416464.1|CI416464
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88843823|gb|CI011081.1|CI011081
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|86259091|gb|CI010392.1|CI010392
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88200101|gb|CI199951.1|CI199951
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|66916064|gb|CX102912.1|CX102912
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|8527588|gb|AU092403.1|AU092403
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88511355|gb|CI438861.1|CI438861
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88485024|gb|CI422295.1|CI422295
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|86259367|gb|CI008044.1|CI008044
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTTCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|13818900|gb|AB060279.1|AB060279
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTTCGC
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGT-CGC
EST: gi|88489408|gb|CI426680.1|CI426680
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88991427|gb|CI034762.1|CI034762
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|86422775|gb|CI060348.1|CI060348
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|29677610|gb|CB673885.1|CB673885
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88488478|gb|CI425749.1|CI425749
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|4714353|gb|AU058320.1|AU058320
EST:     AGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: AGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88209667|gb|CI209516.1|CI209516
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88282600|gb|CI403996.1|CI403996
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|8527776|gb|AU092591.1|AU092591
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88841488|gb|CI005568.1|CI005568
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTNCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|86541902|gb|CI182108.1|CI182108
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTGCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
EST: gi|88502833|gb|CI430339.1|CI430339
EST:     TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTG                         GACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG
genomic: TCAGGGCGAATACTTTGAAGAACCAGAGGACTACCCCCCTCCAGGCCGTGgtaagctcag ... ggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggtttcgccatctcacttctcatggctcctctcatcctcggtcggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCGGCCGTGGGCGTGGTCGATTCTAAGATGAAATCAGGAGGAGGTGCCCTTG
           atctcac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctcagtctaacataaccaacaatgtttccaggtttcgccatctcacttctcatggctcctctcatcctcggtcggcttcacagGACGTGGCAGGGGAAGAAGGGGCGGAGGACCGGGACCATTCCGTGGTCGCGGCCGTGGGCGTGGTCGATTCTAAGATGAAATCAGGAGGAGGTGCCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG