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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttctctacttttgccaagctaaattctcctaagatgttagcttatggaccactgcttgatgaagaacctgatttaaaattgtatcttaaattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGTGTCGCTGTCCAG

Basic information

species Oryza sativa
transcript 13114.m00108
intron # 3
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|14980697|gb|BI305375.1|BI305375
EST:     TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAG                         TTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
genomic: TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAGgtgtgttctt ... aattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
EST: gi|66916796|gb|CX103644.1|CX103644
EST:     TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAG                         TTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTAT
genomic: TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAGgtgtgttctt ... aattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTAT
EST: gi|38481179|gb|CF965268.1|CF965268
EST:     TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAG                         TTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
genomic: TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAGgtgtgttctt ... aattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
EST: gi|14980567|gb|BI305245.1|BI305245
EST:     TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAG                         TTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
genomic: TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAGgtgtgttctt ... aattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
EST: gi|13420795|gb|AU174885.1|AU174885
EST:     TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAG                         TTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGG
genomic: TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAGgtgtgttctt ... aattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGG
EST: gi|29668134|gb|CB664409.1|CB664409
EST:     TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAG                         TTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
genomic: TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAGgtgtgttctt ... aattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
EST: gi|58690258|gb|CK078945.1|CK078945
EST:     TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAG                         TTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
genomic: TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAGgtgtgttctt ... aattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
EST: gi|33679460|gb|CF307699.1|CF307699
EST:     TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAG                         TTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
genomic: TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAGgtgtgttctt ... aattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
EST: gi|58609210|gb|CK037243.1|CK037243
EST:     TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAG                         TTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT
genomic: TCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAGgtgtgttctt ... aattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGT

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: 50 (upstream exon), 63 (downstream exon)
Score: 34

GATGAAGTTGTCAAATATTCACCTCATGCTCGCGCCATCAGGGATGTCGAGGATGAGGAGCTTCGCAGCTTCTTCTATGGCATGTCACCATGGCAGgtgtgttctt ... aattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGTGTCGCTGTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggaccactgcttgatgaagaacctgatttaaaattgtatcttaaattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGTGTCGCTGTCCAG
                      acctgat  putative branch site (score: 34)
                         tgatttaaaattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttctctacttttgccaagctaaattctcctaagatgttagcttatggaccactgcttgatgaagaacctgatttaaaattgtatcttaaattttgcagTTCATTCTTATTGTAACTGCTAGCTCAATTGGAGAGGAGCTATTCTATCGTGTCGCTGTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT