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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTAAGTTTGGTGCTGTATGCAAGTTCCATCATCCCAAGGAGAGAATTATCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagtcttttatagcattgtacaccctaagttcctaagttcatgtattcttagcaacatggtcatttaattttttgctgtatgctgccttagctt...

Basic information

species Oryza sativa
transcript LOC_Os11g28270.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g28270.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G146514_T02 (Zea mays), 5'ss of exon 6
CTGTAAGTTTGGTGCTGTATGCAAGTTCCATCATCCCAAGGAGAGAATTATCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagtcttt-tatagcattgtacaccctaagttcctaagttcatgtattcttagcaacatggtcatttaattttttgctgtatgctgccttagctt---
|||||||||||||||||||||||||||||||||||||| |||| |||| || |||||||| || |||||  ||||  ||||||| || ||  |||| |||||||| |    | |  ||  | ||        || | ||   |    | |||||    ||||  |      |  |||| |     |||  || ||| |  |   
CTGTAAGTTTGGTGCTGTATGCAAGTTCCATCATCCCAGGGAGCGAATAATTCCTACTCCCAATTGTGCACTGAGTCCATTAGGCCTACCTTTGCGCCCGgtaagagttagtatacatgtctttaagttaattatgctctctaagatacgtatt----gcaatttttggggtagatttgtctggctatcttggcttcgtctttt

upper sequence: LOC_Os11g28270.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G100794_T01 (Zea mays), 5'ss of exon 6
CTGTAAGTTTGGTGCTGTATGCAAGTTCCATCATCCCAAGGAGAGAATTATCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaaggg--agtct---tttatagcattgtacaccctaagttcctaagttcatgtattcttagcaacatggtcatttaattttttgctgtatgctgccttagctt
||||||||||||| |||||||||||||||||||||||| |||| |||| || |||||||| || |||||  | ||  ||||||| || ||  |||| |||||||| |  ||| |   | | |   | | |   | ||||| |    | | ||  | ||   |   |  ||      ||  | || | |  ||| |   |||    
CTGTAAGTTTGGTTCTGTATGCAAGTTCCATCATCCCAGGGAGCGAATAATTCCTACTCCCAATTGTGCACTAAGTCCATTAGGCCTACCTTTGCGCCCGgtaagagttagtatacatgtctttaagtattttctctaagatatgtattgcaattttttggatagatttgtgtggcta--tcttggtttcatgtttttttat---
















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|87026842|gb|CI259495.1|CI259495
EST:     TCCGTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCG                         GGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
genomic: TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagt ... ctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
EST: gi|58694326|gb|CK083013.1|CK083013
EST:     TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCG                         GGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
genomic: TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagt ... ctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
EST: gi|87037579|gb|CI192201.1|CI192201
EST:     TCCCTACTCCAAACTGTGCTTTGAGCTCATTAGGTCTTCCACTGCGTCCG                         GGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
genomic: TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagt ... ctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
EST: gi|58682235|gb|CK070922.1|CK070922
EST:     TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCG                         GGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
genomic: TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagt ... ctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
EST: gi|218478406|gb|FG958094.1|FG958094
EST:     TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCG                         GGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
genomic: TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagt ... ctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
EST: gi|88255387|gb|CI354211.1|CI354211
EST:     TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCG                         GGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
genomic: TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagt ... ctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
EST: gi|218478656|gb|FG958102.1|FG958102
EST:     TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCG                         GGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
genomic: TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagt ... ctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
EST: gi|87037426|gb|CI192048.1|CI192048
EST:     AACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCG                         GGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
genomic: AACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagt ... ctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGT
EST: gi|58679009|gb|CK067696.1|CK067696
EST:     TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTACG                         GGAGAGCCCATATGCACATTCTATTCTCGCTATG
genomic: TCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagt ... ctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATG

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: 73 (upstream exon), 33 (downstream exon)
Score: 25

CTGTAAGTTTGGTGCTGTATGCAAGTTCCATCATCCCAAGGAGAGAATTATCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagt ... ctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGTCCGAATTGCAAATTTGATCATCCAATGGGAACTGTGATGTATGGTCTCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTAAGTTTGGTGCTGTATGCAAGTTCCATCATCCCAAGGAGAGAATTATCCCTACTCCAAACTGTGCGTTGAGCTCATTAGGTCTTCCACTGCGTCCGgtaagggagtcttttatagcattgtacaccctaagttcctaagttcatgtattcttagcaacatggtcatttaattttttgctgtatgctgccttagctt

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