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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgtgtgaactgctccatacttgttcatgtcataactcattagagatttttttttttgcttgtgtatttgtgttcaagtagaggttcttcttttctatttttgaattatcagTCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCGACAAGGTTCTATTTCAGCTGGACCAGGAGTGTTTGGATGTCTACAAGCGGAAAGTTGATC

Basic information

species Oryza sativa
transcript LOC_Os02g48830.1
intron # 2
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|86850277|gb|CI305516.1|CI305516
EST:     CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAG                         TCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGC
genomic: CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAGgtatgcgtgt ... gaattatcagTCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGC
EST: gi|88364157|gb|CI610501.1|CI610501
EST:     CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAG                         TCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCGACAAGGTTCTA
genomic: CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAGgtatgcgtgt ... gaattatcagTCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCGACAAGGTTCTA
EST: gi|88393226|gb|CI616710.1|CI616710
EST:     CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAG                         TCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACC
genomic: CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAGgtatgcgtgt ... gaattatcagTCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACC
EST: gi|58673175|gb|CK061861.1|CK061861
EST:     CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAG                         TCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCGACAAGGTTCTA
genomic: CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAGgtatgcgtgt ... gaattatcagTCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCGACAAGGTTCTA
EST: gi|88584957|gb|CI702552.1|CI702552
EST:     CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAG                         TCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCG
genomic: CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAGgtatgcgtgt ... gaattatcagTCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCG
EST: gi|88316618|gb|CI622864.1|CI622864
EST:     CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAG                         TCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCGACAAGGTTCTA
genomic: CTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAGgtatgcgtgt ... gaattatcagTCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCGACAAGGTTCTA

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: 69 (upstream exon), 64 (downstream exon)
Score: 4

TTTATAGAGCCATACAGCTCCGACAAAAGGATTCACCTATTCCAGAATGTCTGCTTTGCTCCGTGAAACTTCGTGTGGATCATTGCTGCAAAAACTGCAGgtatgcgtgt ... gaattatcagTCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCGACAAGGTTCTATTTCAGCTGGACCAGGAGTGTTTGGATGTCTACAAGCGGAAAGTTGATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgtgtatttgtgttcaagtagaggttcttcttttctatttttgaattatcagTCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCGACAAGGTTCTATTTCAGCTGGACCAGGAGTGTTTGGATGTCTACAAGCGGAAAGTTGATC
                           ttcttcttttctattt  CT-rich tract
                              ttcttttctatttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcgtgtgaactgctccatacttgttcatgtcataactcattagagatttttttttttgcttgtgtatttgtgttcaagtagaggttcttcttttctatttttgaattatcagTCGGTATGGGATGAAGTTGGTGAAAGCGAGGAGGACCGCGACAAGGTTCTATTTCAGCTGGACCAGGAGTGTTTGGATGTCTACAAGCGGAAAGTTGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA