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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG

Basic information

species Oryza sativa
transcript LOC_Os05g48960.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G031827_T05 (Zea mays), 3'ss of exon 1
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------
  ||| |||  ||||  | ||| |  ||||| |    |||     ||||        | | ||     ||||   ||    ||  |||  ||  |  | | ||||  |  |   |  || |    |||||||      |||     | ||||||||||||| |||||||| || ||||| || |||||||| ||||| |||||||| ||||||||||||        
--attccttgatccccatggtt-cttgataa-caggccatgagtttatac-------cccctcc----attt---caccttatattgaagatgatact-attcttgcttatgcttgaagGT----TGTCAGTCTGCAAGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G031827_T06 (Zea mays), 3'ss of exon 1
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------
||||| |||  ||||  | ||| |  ||||| |    |||     ||||        | | ||     ||||   ||    ||  |||  ||  |  | | ||||  |  |   |  || |    |||||||      |||     | ||||||||||||| |||||||| || ||||| || |||||||| ||||| |||||||| ||||||||||||        
gtattccttgatccccatggtt-cttgataa-caggccatgagtttatac-------cccctcc----attt---caccttatattgaagatgatact-attcttgcttatgcttgaagGT----TGTCAGTCTGCAAGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G031827_T02 (Zea mays), 3'ss of exon 1
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG----------------
           ||||  | ||| |  ||||| |    |||     ||||        | | ||     ||||   ||    ||  |||  ||  |  | | ||||  |  |   |  || |    |||||||      |||     | ||||||||||||| |||||||| || ||||| || |||||||| ||||| |||||||| ||||||||||||                
----------atccccatggtt-cttgataa-caggccatgagtttatac-------cccctcc----attt---caccttatattgaagatgatact-attcttgcttatgcttgaaggt----tgtcagTCTGCAAGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTTGGTACCGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGCTTGTCGTC

upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G025014_T01 (Zea mays), 3'ss of exon 2
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------
                 | ||| | |||||| | |  |||     || ||  |  | | | |||    || |   ||    ||  |||  ||  ||||| ||  | || || | |     | |||  || | ||    | |||     | ||||||||||||| |||||||| || || || ||||||||||| ||||| |||||||| ||||||||||||        
---------------catggtt-ctagataa-caaaccatgagtttacat-cattatcccctct----atct---caccttatattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGAGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G020928_T02 (Zea mays), 3'ss of exon 3
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------
||||| |||  ||||  | ||| | |||||| | |  |||     |||||  |  | | | |||    || |   ||     |  |||  ||  ||||| ||  | || || | |     | |||  || | ||    | |||     | ||||||||||||| |||||||| || || || ||||||||||| ||||| |||||||| ||||||||||||        
gtattccttgatccccatggtt-ctagataa-caaaccatgagtttatat-cattatcccctct----atct---caccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G020928_T03 (Zea mays), 3'ss of exon 2
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAG--TGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG--------
                 | ||| | |||||| | |  |||     |||||  |  | | | |||    || |   ||     |  |||  ||  ||||| ||  | || || | |     | |||  || | ||    | |||     | ||||||||||||| |||||||| || || || ||||||||||| ||||| |||||||| ||||||||||||        
---------------catggtt-ctagataa-caaaccatgagtttatat-cattatcccctct----atct---caccttgtattgaacatggtttttgatactattcttctttgtgcttgaagGTTGCCGGTCTGCGGGTT----GAATCATGGCGGAGCACTTGGCTTCGATCTTCGGCACTGAGAAGGACAGGGTCAACTGCCCTTTTTACTTCAAGATTGGGGC

upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G27650.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaatt-ctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG----------------
                 ||||| |  | | |    ||         |||| ||  |     | || |  ||  | | |||  || || |  || || || |||     || | | |  | |||| |     || ||| |  |      | |||||||||||||||||||||||| ||||| |||||||| || || || || ||||| || |||||||||                
----------------ttagtttcttgttgatgtttttg-------atatctaccaatctcttttcaatttatgtctatatgttgctaaatatcttgttcaatgac--tgatttcttaaactcagG-----GTGGAAATTCT------GCCATGGCGGAGCATTTGGCTTCAATCTTTGGTACTGAGAAAGACAGAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTC

upper sequence: LOC_Os05g48960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G27650.2 (Arabidopsis thaliana), 3'ss of exon 1
gtatttctttctccctgtagttaccagataagccattcatatacatatatatagaagcacttcttgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTT---TGAAAGTCATGGCGGAGCATTTGGCT--TCAATATTTGGGACTG-AGAAGGATAGGGTTAACTGCCCCTT-TTACTTCAAG
                    || | | |||     ||||   ||  || | |  ||       | || |||  | ||           || ||   || ||||||  || ||   | |     || || | |||   | | |   | ||  |    ||    | |   | |   |  |  | | | ||  | ||   |      | || |||     | ||||   
--------------------ttgctaaatatcttgttcaatgactgatttcttaaactcagggtggaaattctgccat---ggcggagcatttggcttcaatctt--tggtactgagaaagacagAGTGAATTGCCCTTTCTACTTCAAGATTGGCGCTTGCCGTCATGGTGACCGGTGCTCGCGTCTTCACAACCGTCCTACCATCTCCCCAACACTCCTTCTT-

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|29685226|gb|CB681501.1|CB681501
EST:     TGTTGTCTACTTTTTCTGTATGTAATGCGCTATGACGACTCTAGATCGAG                         CTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC
genomic: TGTTGTCTACTTTTTCTGTATGTAATGCGCTATGACGACTCTAAATCGAGgtatttcttt ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTC




















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: 68 (upstream exon), 72 (downstream exon)
Score: 8

GTTAAAAATGATAACATATGAACTTGTTTTTATTTAGCATATGCTCCCTTTGTTGTCTACTTTTTCTGTATGTAATGCGCTATGACGACTCTAAATCGAGgtatttcttt ... ttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagatttggacaataaattctgacaattttttttaatctttttgttatgtacagCTCAAGTGTCAGTTGAAGTGTTTTGAAAGTCATGGCGGAGCATTTGGCTTCAATATTTGGGACTGAGAAGGATAGGGTTAACTGCCCCTTTTACTTCAAG
                                     tctttttgtt  CT-rich tract
            aataaattctgacaat  TA-rich tract