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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtattggttaagctattttgggctagggtgaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaattatttactgtatatctcttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
gtaatgtattggtt-aagctattttgggct-agggtgaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaattatttactgtatatctct---tttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
|||||   ||  || |||| |  ||||||| |  ||||  || ||   ||||||  ||   |  ||   |||||| |   ||||   |  || | |||  || | |   || ||||||||||||||||||||||  | |||||||||||||||||||| || |||||||| || ||||| ||||| ||||||||||||||||||
gtaattggttattttaagcaaacttgggcttaatgtgaggtattc--atttgtttggtacatgttt--cttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 14
--------------------------gtaatgta--ttggttaagctattttgggctagggtgaaatactctgctttgttctgtgggttgttg--atttttatttgcaaaattaatt---atttactgtatatctctt--ttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
                           | || ||  ||  |||    |   ||  | |        ||     | || |||| ||  |  |||  || | | ||  |||  |    |   | ||||  | |   | ||  ||  ||||| ||||| || |||||  | |||||||| ||||||||||| ||  | |||||||||||||| || |||||||||||||| ||||||
gtgtgagagaaacctctgcagtttatattatataatttttttagttgaacctgaaccatttctttgtagctccccttattctctgtctccttgttatatctgttgacaatgtctgctgacagttaccattttcattttgatttgcagGGCGCTGTTAATTTTGCATTAATGATGTCTCAAATGGAGGGAGGTAGCCCAGTTGATTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 14
gtaatgtattggttaagctattttgggctagggtgaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaattatttactgtatatctcttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
  |  | | |  |  | |||||||    |    | ||    | |||     |   | | ||||  |   | |||    || ||  || || |       | |   || | |||| ||||| || |||||  | |||||||| ||||||||||| || || |||||||||||||| || ||||||||||| || ||||||
acatggaaattctataactatttttttttcatctcaa----tttgcagaaattaatag-ttgtataaactaattcaagaactttctttttca-------ttttggtttctagGGTGCTGTTAATTTTGCATTAATGATGTCGCAAATGGAGGGAGGTTGCCCAGTTGATTACAACACCATAACTGATCTGTTTCTTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 12
gtaatgtattggttaagctattt--tgggctagggtgaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaattatttactgtatatctcttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
      ||||| ||| | |  ||     | ||   | | | | | |    | |  ||   |||  |  | ||| |||    | ||  |||||||  | |    | || |  ||||| ||||| || ||||| || |||||||| |||||||||||||| || || ||||| || || || ||||| |||||||| ||||||
------tattgtttatgatgcttacctagttacctttatacaatatctaatatcttgccagtt--tactcttttttt----atttgtttattta--gaactcgttttattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTATAACACAATAACCGATCTCTTTCTTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 14
gtaatgtattggttaagctattt--tgggctagggtgaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaattatttactgtatatctcttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
    | ||||| ||| | |  ||     | ||   | | | | | |   || |  ||   ||| |    |||||||||         |||||||     | | || ||   ||||| ||||| || ||||| || |||||||| |||||||||||||| || || ||||| ||||| || |||||||||||||| ||||||
---ctatattgtttatgatgcttgcctagttacctttatacaatatcaattatcttgctagtt-tactcttttatttgt--------ttatttagaacttgtttcatt--gcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 14
-----------------------------------------------------------------gtaatgtattggttaagctattttggg--ctagggtgaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaatt---atttactgtatatctctt--ttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
                                                                       |||||  |  |   || |     ||  ||| |     | || ||||  | ||   |   |   ||   ||  |||  |    |   | ||||  | |   | ||  ||  ||||| ||||| || |||||  | |||||||| ||||||||||| ||  | |||||||||||||| || |||||||||||||| ||||||
gtgtgagagaaacctctgcagttcatacaatttttttatttgaacctgaaccatttctttgtagctccccttattgtctgcgtccttgttatatctgtggtaactgtttttgttttgaacagtatatg--tacattaagttgacaatgtctgctgacagttaccattttcattttgatttgcagGGCGCTGTTAATTTTGCATTAATGATGTCTCAAATGGAGGGAGGTAGCCCAGTTGATTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 14
gtaatgtattggttaagctattttgggctagggt--gaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaattatttactgtatatctcttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
       ||   | ||      || |  || | |  | |  |  |   ||  || | |    | ||  ||| | | |   || |    ||||| |   |  |   || |  ||||||||||| || ||||| || |||||| | |||||||| || || || ||  |||| ||||| || |||||||||||||| ||||||
-------atctctgaaatctggtttgtttaagttttgtagcatccaagttgatttttt---cttttagtttatgtatagtaagta---tattt-caaaactttctttattgcagGGAGCTGTAAATTTTGCTCTGATGATGGCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 14
------------------------------------------------------------------------gtaatgtattggttaagctattt-tgggctagggtg-aaatactctgctttgttc--tgtgggttgttgatttttat--ttgcaaaa------ttaattatttactgtatatctctt--ttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
                                                                         ||||  |||  | ||  ||| | |   ||    || |||| || |   |  |||        |||  ||  || ||  ||| ||||      | ||  | || || | |   | ||  || | |||| ||||| || |||||  | |||||||| ||||||||||| || || |||||||||||||| || ||||||||||| || ||||||
gtatgagagaatcctctgtagttcatattaactatttctttgtatttctcccattgtctgccacactgttggataattgatta-tcaaattatatattttctgacatggaaattctataactatttcatctcaatttgcagaaattaatagttgtaaaaactaattcaacaactttcttttttcattttggtttctagGGTGCTGTTAATTTTGCATTAATGATGTCGCAAATGGAGGGAGGTTGCCCAGTTGATTACAACACCATAACTGATCTGTTTCTTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaatgtattggttaagctattttgggctagggtgaaatactctgctttgttctgtgggttgttgatt-tttatttgcaaaattaattatttactgtatatctcttttac---cagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
                ||| || |     | |   || ||  ||  ||||  ||||      |  ||  | | |||       ||||||| | || | | |  ||  ||    |||||||| || || |||||  | |||||||| |||||||| || || ||||||||||| ||||| ||||| |||||||| |||||||||
------------gcctgctgttgtttatcaagc--aactaagct--tttgccctgtaaaagatcaatagtcttttttttctgctaattatcttcttttttttcctgctaattgcagGGAGCAGTAAATTTTGCTTTAATGATGTCCCAAATGGAAGGAGGTTGTCCAGTTGACTACAACACTATCACTGATCTTTTCCTTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 14
gtaatgtattggttaagctattttgggctagggtgaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaatta---tttactgtat------atctcttttac-----cagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
||| || |    ||   ||| | |  ||     |    |        ||||||         |    ||  |||| |||| |  || |   ||| |||  |      || | ||||       ||||||||||| || |||||||| |||||||| ||||||||||| || |||||  ||||||  ||||| |||||||||||||| ||||||
gta-tgcaagcctttttctagtgtttgcagattttccttttatgaaattgttccagaaaggatcagcttaaattt-caaattggataaaattttcctgagtggaggcatttatttttgggttgcagGGAGCTGTAAATTTTGCGCTAATGATGTCTCAAATGGAGGGAGGTTGTCCCATTGATTTTAATACGATAACTGATCTCTTTCTTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 14
gtaatgtattggttaagctattttgggctagggtgaaatactctgctttgttctgtgggttgttgatttttatttgcaaaattaattatttactgtatatctcttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
    || |||| ||    | | ||    ||   |  | |  ||||   |         ||||       ||  |     |    || ||| ||   || | |    |  ||||| || || || |||||  | |||||||| |||||||| || || || |||||||||||||| || ||||| ||||| |||||||||
----tggattgcttg---tctcttctcatacactccattcttctgaagttggactccagttgaaatcacttgctgatggag--gataattcac---attttttggatggcagGGGGCAGTTAATTTTGCTTTAATGATGTCTCAAATGGAAGGAGGTTGCCCAGTTGATTACAACACAATAACAGATCTATTCCTTCAG

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: 60 (upstream exon), 73 (downstream exon)
Score: 106

GTTGGATACACCCCTGACTACCTCTTCCTCCTCCAGACCATTTTACGTACGGATCCACAGgtaatgtatt ... cttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgttgatttttatttgcaaaattaattatttactgtatatctcttttaccagGGAGCTGTCAACTTTGCGCTCATGATGTCACAAATGGAGGGGGGCTGTCCAGTTGATTACAATACTATAACTGATCTCTTCCTTCAG
                      aattaat  putative branch site (score: 106)
                                          tctcttttacc  putative PPT
     ttgatttttatttgca  TA-rich tract