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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG

Basic information

species Oryza sativa
transcript LOC_Os05g50120.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgca----ttaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
| ||| | || ||| | ||||| ||| || | | | || | | || ||| || | | || | | || |||| |||||||||||||| ||||| |||||||||||||| ||||| ||||||||||| || |||| ||||| |||||||||||||||||||| |||||||||||||| ||||
-------------------------------------------------------------------------tacttgaa-cagtgtgtacatagtgtg--gagtttgatgtatcagcttgttttacaaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG

upper sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
| ||| | | || | || | | | ||| ||| || |||| || | ||| |||| || || ||| ||||| | || ||| ||||||||||| ||||| |||||||| |||||||| | ||||| ||||||||||| |||| | || |||||| | ||||| || |||||||| ||||| |||||||
--------------------------------------------ctcttcaatcctcctctaccaggattgtgtat---gatttatgaag----------ttgaatatat----ttaagtattg---cagtacgtg----tacgatttcaa----atccttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG

upper sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
| | || | ||| || | | || || || || || | || || || ||| | || || | | |||| | |||| | ||| | || |||||||||||||||||||||||||||||||||| | || || ||||||||||| |||| || || |||||| | ||||| ||||||||||||||||| |||||||
----------------------------------------------gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaatt-gaacatgctt-----gatat-attgaattatgca----tgcaattttaaatttat--ttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG

upper sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
| ||| | | || || | | | ||| ||| || |||| || | ||| |||| | | || || || | || | || ||||||||||| || |||||||||||||||||||| | ||||| ||||||||||| |||| | || |||||| | ||||| || |||||||| ||||| |||||||
-------------------------------------------cctcttcaatcctcctctaccgggattgtgtat---gatttatgaag----------ttgaatatat----ttaagtattgcactagtgtgtaat-------ttcaaatcct-----tgtcttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG

upper sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 4
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
| | || || ||| || ||||| || | | |||| || | |||| | || | || | | || | | | || |||| || || | | |||||| | | ||||||||||||| || ||||||||||||||||| | ||||| ||||||||||| |||| || || |||||| | ||||| ||||||||||||||||| |||||||
------------------------------gtaagtttcttcttttttttaacatcttttcttgggttgaatataatttaagcaattgaaca----tacttggtgtat------tgaaatat----gcat---gtaat-tttaaatttatttcct---------ttttgcagTACACTCCAGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG

upper sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
|| | | | || | | ||| | || | | || | | || || | |||| | | |||| | | | |||| | ||| | | ||||||| || ||||| |||||||| ||||| ||||||| ||||||||||| |||| || || |||||| | ||||| ||||| ||||| ||||| |||||||
---------------------------------------------------------gtaaaatgcaattctctattttcttttttgcaaaagttgtctgattcacatattat----gacaccacaacctgaggttaaaacg-gattattgctttctt------tgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG

upper sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0011g04920.t01 (Vitis vinifera), 3'ss of exon 4
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
| ||||| || ||| | |||| || || | | | || ||| || | | | | | | | || || | | || | || |||| |||||||||||||||||||| |||||||||||||| |||||||||||||||| || ||||||| |||||||| | ||||| || |||||||| || || |||||||
------------------------------------------------------gttttatactaatatc-tgtgtt---atttatttcg----attgaactgatcatacaccataatccctc------tgaaatggtacagtt-tctaaagcttttcat---cttttgcagTACACCCCTGCTATTGATATTTGGAGCATAGGATGTATATTTGCGGAAATGCTTACTGGAAAGCCCTTGTTTCCTGGTAAAAATGTGGTCCAGCAATTGG

upper sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggc-ttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
|||| ||| | | | || ||| || || | ||| |||| |||| | | || | | | | |||| |||||||| ||||| |||||||||||||| ||||||| ||||||||||| ||||||||||||| || || ||||| ||||||||||| ||||| || ||||
-------------------------------------------------------------------------cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG

upper sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagca-acagtgttttgagaatgttctcttagacattgtcgcattaggtgatatct--tgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
|| | | || | | | | || | | || | || || || | || | |||| | | | ||||| | | | | | || |||| | |||| ||||| || ||||| || ||||| |||||| |||| ||||||||||| || || | || ||||||||||| || || ||||| |||||||| ||||| |||
--------------------------------------------------------gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagt-tattgggtagaacatatttg---tgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGG

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: 33 (upstream exon), 66 (downstream exon)
Score: 7

GATTATGTGGCAACTAGATGGTATCGTGCCCCAGAGTTGTGTGGCTCCTTTTTTTCAAAGgtaagggaat ... gcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
                      tcttgat  putative branch site (score: 7)
 cttttgc  putative PPT
 tgatatcttgatttat  TA-rich tract