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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctttctcgtcagattgtagcgttatcatttccaatggaatgaacatcaagccatgcctgataactcaactcccaactggtggccgtggcttctatcttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g71256.1
intron # 6
splice site 5'
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|88476623|gb|CI413894.1|CI413894
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88474576|gb|CI411847.1|CI411847
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88519353|gb|CI447007.1|CI447007
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88473139|gb|CI410410.1|CI410410
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGGTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88501874|gb|CI429380.1|CI429380
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88478004|gb|CI415275.1|CI415275
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88284730|gb|CI406176.1|CI406176
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88831405|gb|CI083799.1|CI083799
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88515283|gb|CI442937.1|CI442937
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88503548|gb|CI431054.1|CI431054
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88482756|gb|CI420027.1|CI420027
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88281624|gb|CI403020.1|CI403020
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88217255|gb|CI217104.1|CI217104
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
EST: gi|88477716|gb|CI414987.1|CI414987
EST:     TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAG                         GTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT
genomic: TCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGAT

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: 66 (upstream exon), 47 (downstream exon)
Score: 5

GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctt ... tatcttgcagGTATCGTCTTTTTTCAGGATAAAACCGTGTGAAGTGTCCGCGAGTCTTGATAAATTAGGTACTATGCAACAAAGCGTATTATTGTACATAAATCCTTATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTGAGGTGTTTGAATCAGAGCTTGTGCTTAATGGTATTGTCACCCAGAAGCTAGAATTTGAAAGgtacgctctttctcgtcagattgtagcgttatcatttccaatggaatgaacatcaagccatgcctgataactcaactcccaactggtggccgtggcttctatcttgcag

- - - - - - - - -  AGAGCT
- - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - AGAAGC