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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgctgtccttgatccgtctcattgtcagtaagcattcacagcattggggattagtaggtattgtgtgctcatttgttgcttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGGTTGTGCGTCACGGGATAGCATGAAAGCTGTTATGAAGCTGCCACGTCTT

Basic information

species Oryza sativa
transcript LOC_Os12g27520.1
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|58030560|gb|CX728103.1|CX728103
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|86250790|gb|CI007653.1|CI007653
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|29632958|gb|CB637967.1|CB637967
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|86421246|gb|CI057235.1|CI057235
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|88849216|gb|CI087738.1|CI087738
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|29670716|gb|CB666991.1|CB666991
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|88333223|gb|CI641066.1|CI641066
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|86494975|gb|CI137608.1|CI137608
EST:     TATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: TATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|88981415|gb|CI027033.1|CI027033
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|13895818|gb|C23622.2|C23622
EST:     TGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: TGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCT-CAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|88226612|gb|CI226528.1|CI226528
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|88841022|gb|CI000984.1|CI000984
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|86416061|gb|CI030072.1|CI030072
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|88216486|gb|CI216335.1|CI216335
EST:     TGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: TGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|88958327|gb|CI095846.1|CI095846
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|88845676|gb|CI008673.1|CI008673
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|86433131|gb|CI093474.1|CI093474
EST:     CTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: CTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|88985455|gb|CI002972.1|CI002972
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|89183315|gb|CI045880.1|CI045880
EST:     GGAGAGGGTTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAG
genomic: GGAGAGGG-TATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCA-GAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAG
EST: gi|29675908|gb|CB672183.1|CB672183
EST:     ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: ATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|86487600|gb|CI130233.1|CI130233
EST:     GAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
genomic: GAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGG
EST: gi|86860035|gb|CI321984.1|CI321984
EST:     TGGAGAGGGTATTTTGTCCTTTGCCATGTCACATGCTCAAAAGGGCCAGA                         CCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAG
genomic: TGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGG-CAGAgtatgttgct ... ttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacagcattggggattagtaggtattgtgtgctcatttgttgcttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGGTTGTGCGTCACGGGATAGCATGAAAGCTGTTATGAAGCTGCCACGTCTT
               attagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgctgtccttgatccgtctcattgtcagtaagcattcacagcattggggattagtaggtattgtgtgctcatttgttgcttgtatgtagCCGGCATTCCGAGAAATATGTCAGAAAAGGCCGTTTAAACTGGCCTGAAGGTTGTGCGTCACGGGATAGCATGAAAGCTGTTATGAAGCTGCCACGTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC