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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGAGTACGTCCCTGAGACACTCTACCGTGTGCTCAAGCACTACAGCAATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagccaccatgttaacacctctctgattgccactatgcttctcattgcttctctaaagatacttttgctatgcttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g10840.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G472625_T02 (Zea mays), 5'ss of exon 4
TATGGAGTACGTCCCTGAGACACTCTACCGTGTGCTCAAGCACTACAGCAATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagccaccatgttaacacctctctgattgccactatgc-ttctcattgcttctctaaagatac----ttttgctatgcttgcag
 ||||| |  ||||| ||||| || |||||||| || |||||||||||||| || |||||| |||||||  | ||||| || ||||| ||||| |||||||||||| | ||| ||| |||||   | |     ||| | | ||   | |||||| ||  ||||   |      |||||  ||| | ||||
CATGGAATTTGTCCCCGAGACCCTGTACCGTGTCCTGAAGCACTACAGCAACGCGAACCAGAGGATGCCTCTTATCTACGTCAAGCTCTACATGTATCAGgtttgtgaaccagcatcttaacttatatgaagctgctaatgtgtgctttcattgttttgctaactgtctctttttttgtaatgttcgcag

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 4
TATGGAGTACGTCCCTGAGACACTCTACCGTGTGCTCAAGCACTACAGCAATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagccaccatgttaacacctctctgattgccactatgc-ttctcattgcttctctaaagatact-------tttgctatgcttgcag
 ||||| | |||||||||||| || ||||| || || ||||||||||||||||| |||||| |||||||  | ||||| || ||||| ||||| |||||||||||||| ||| ||  ||||| | | |  || ||||| |  |   |||||||| ||  ||||   |  |       ||||  ||| ||||||
CATGGAATTCGTCCCTGAGACTCTATACCGAGTCCTGAAGCACTACAGCAATGCGAACCAGAGGATGCCTCTTATCTACGTCAAGCTCTACATGTATCAGgtttgtcaaccagcagcttaactcttgtgagactgccaatgcgtgctctcattgttttgctaattgtcttcttcttttttgtgatgtttgcag
















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|33675956|gb|CF304195.1|CF304195
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTNTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|218490531|gb|FG951644.1|FG951644
EST:     ATGCTAACCAGCGGATGCCCTTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCA
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCA
EST: gi|112786757|gb|EE591387.1|EE591387
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTCTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|58595981|gb|CK006509.1|CK006509
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGGTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|58695322|gb|CK084009.1|CK084009
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|88329587|gb|CI650042.1|CI650042
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|88305351|gb|CI653078.1|CI653078
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|84117624|gb|CD151391.1|CD151391
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|58666731|gb|CK055417.1|CK055417
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTC
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTC
EST: gi|218491874|gb|FG949273.1|FG949273
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|218498171|gb|FG949783.1|FG949783
EST:     ACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|58668898|gb|CK057584.1|CK057584
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|29616355|gb|CB621367.1|CB621367
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|88306430|gb|CI638217.1|CI638217
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|2317560|gb|C22614.1|C22614
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGG
EST: gi|58661958|gb|CK050638.1|CK050638
EST:     ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAG                         CTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTC
genomic: ATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTC

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), 51 (downstream exon)
Score: 37

TATGGAGTACGTCCCTGAGACACTCTACCGTGTGCTCAAGCACTACAGCAATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagc ... atgcttgcagCTTTTCAGAGGGTTAGCTTATATTCATACTGTTCCAGGAGTCTGCCACAGGGATGTGAAACCACAAAATGTTTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGAGTACGTCCCTGAGACACTCTACCGTGTGCTCAAGCACTACAGCAATGCTAACCAGCGGATGCCATTGATCTATGTGAAGCTTTACATCTATCAGgtttgtcagccaccatgttaacacctctctgattgccactatgcttctcattgcttctctaaagatacttttgctatgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC