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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgcctaagattttttgcaactatatggatgtatactgactgctcgacactatgtagtctgtactaatcctcaagggttactccttgtaacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGAGAGGTTTAGTGAGAACAGAGGAAAGCAAACAAAAGATTGGTGGAGGCAA

Basic information

species Oryza sativa
transcript LOC_Os03g60740.1
intron # 1
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|88573949|gb|CI665718.1|CI665718
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|33818132|gb|CF334892.1|CF334892
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|33686688|gb|CF314927.1|CF314927
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|163927224|gb|EG710262.1|EG710262
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|88370280|gb|CI587670.1|CI587670
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|33660167|gb|CF291134.1|CF291134
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|88395066|gb|CI609382.1|CI609382
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAAAATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|88308413|gb|CI650822.1|CI650822
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGNACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|88762303|gb|CI771859.1|CI771859
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|117234788|gb|CT847886.1|CT847886
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|88353303|gb|CI654569.1|CI654569
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|87006111|gb|CI291307.1|CI291307
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|88764490|gb|CI773608.1|CI773608
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|33821837|gb|CF336729.1|CF336729
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|33817945|gb|CF334801.1|CF334801
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|88348311|gb|CI638970.1|CI638970
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|42592251|gb|CK738737.1|CK738737
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
EST: gi|88576382|gb|CI670527.1|CI670527
EST:     GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAG                         GAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA
genomic: GAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 125

CCTCGTGAACTCGTCGCCTTCGTCTTCGTCTCGATCTCCATGGCGGACTCGAGCGCGGCCCGCCCCACCGTCCTCGTCACCGGCGCCGGCGGCCGCACAGgtgggtactc ... aacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGAGAGGTTTAGTGAGAACAGAGGAAAGCAAACAAAAGATTGGTGGAGGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgacactatgtagtctgtactaatcctcaagggttactccttgtaacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGAGAGGTTTAGTGAGAACAGAGGAAAGCAAACAAAAGATTGGTGGAGGCAA
                  tactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgcctaagattttttgcaactatatggatgtatactgactgctcgacactatgtagtctgtactaatcctcaagggttactccttgtaacttgtcagGAAACATTGTCTACAACAAGCTCAAGGAAAGGTCTGACCAGTTTGTTGTGAGAGGTTTAGTGAGAACAGAGGAAAGCAAACAAAAGATTGGTGGAGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- gtgccta
- - - - - - - ttttgca
- - - - - - - - - - - - - atggatg
- - - - - - - - - - - - - - - - - - - - -ctgctcg