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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgttttctcatttctgtgattcataggggcccttaatcttggaagtgtgagcttgatgcttttgccgttggcctaaccagttcttcaacttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCATCTCCTGTCATGTGGAAGAGACTAAGGTGCAGTGTTTAGCTACTGACAGT

Basic information

species Oryza sativa
transcript LOC_Os05g16660.3
intron # 7
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|88380233|gb|CI516220.1|CI516220
EST:     CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTG-AACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
EST: gi|86495724|gb|CI138357.1|CI138357
EST:     CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
EST: gi|38476674|gb|CF960807.1|CF960807
EST:     CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
EST: gi|88449484|gb|CI534043.1|CI534043
EST:     CTNACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
EST: gi|88269002|gb|CI380300.1|CI380300
EST:     CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
EST: gi|88436960|gb|CI523910.1|CI523910
EST:     CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
EST: gi|88419994|gb|CI516443.1|CI516443
EST:     CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
EST: gi|86837852|gb|CI343257.1|CI343257
EST:     CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
EST: gi|88463857|gb|CI527184.1|CI527184
EST:     CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
EST: gi|89169545|gb|CI109904.1|CI109904
EST:     CTGACTACTTCGACATCGAGATTGAAAGCAAGAAGTTGTGAAACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
EST: gi|88436059|gb|CI516595.1|CI516595
EST:     CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAG                         GCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT
genomic: CTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAAACTCTGAGgtaagatgtc ... ttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgagcttgatgcttttgccgttggcctaaccagttcttcaacttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCATCTCCTGTCATGTGGAAGAGACTAAGGTGCAGTGTTTAGCTACTGACAGT
                          gcctaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgttttctcatttctgtgattcataggggcccttaatcttggaagtgtgagcttgatgcttttgccgttggcctaaccagttcttcaacttgtatccagGCTGCATTTGAGGAAGGCCGAAGGTACCTTTTGGTTGGGAAGATGTTTCATCTCCTGTCATGTGGAAGAGACTAAGGTGCAGTGTTTAGCTACTGACAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA