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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagatcaatttggaatggagggagtacgacattaagatagatagattagattagattaattaatgacctgcacattgatttgaatgcatatgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG

Basic information

species Oryza sativa
transcript LOC_Os02g01150.3
intron # 5
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|38477990|gb|CF962123.1|CF962123
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCGCTGTGACATGGAAG
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGC-CTGTGACATGGAAG
EST: gi|29682997|gb|CB679272.1|CB679272
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|58693460|gb|CK082147.1|CK082147
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|10794734|gb|AU108700.1|AU108700
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|11442863|gb|BF430762.1|BF430762
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|86906454|gb|CI294577.1|CI294577
EST:     AGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: AGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
EST: gi|38481826|gb|CF965897.1|CF965897
EST:     GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAG                         CTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA
genomic: GATCTACTACGACCTGTATCAGTCCACGCGCCTTGAGAAATTCGTCACAGgtatgcatcc ... atgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagattagattaattaatgacctgcacattgatttgaatgcatatgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG
     attagattaattaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatcaatttggaatggagggagtacgacattaagatagatagattagattagattaattaatgacctgcacattgatttgaatgcatatgcatgtagCTTACGGGCAGTTCCTGAAAGCAAACGGAGAGCAGCCTGTGACATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG