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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctattttgtttttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat...

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 27
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GRMZM2G115138_T01 (Zea mays), 5'ss of exon 11
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctattttgtttttgtgttgaatatttag------catgtagtatgctgcattaacttgtaac---att-gccatctcttctagttat-----------
 |||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| || |||||||| || ||||| || |||||||||||  |||||   ||  | |||||    ||   |  || | | |   |   || ||         ||  || |    || |   |||| |     ||| |  | | | || | | ||           
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGAAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgcattctgattagtaaacgcatccaatcatatgtaatgcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 4
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctattttgtttttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctc-ttctagttat--------------------------
 || |||||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| || |||||||| || |||||||| ||||| || || ||||||   || || |||||   | |  | |     | || |   |    | |||   |   ||   |   ||   |||    ||| |||  | ||||  |||                           
ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTGTATTTTATCGAGCAGgtttggttgaaacccattc-tattgactgataatatgagactagcgataagctaatt-cataaggtcctagtctgtctacttggcattgcattctgattagcaaatccatccattcatgtaacacag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 4
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctattttgtt------tttgtgttgaat--atttagcatgtagtatgctgcattaacttgtaacattgccatctc-ttctagttat--------------------------
 || |||||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| || |||||||| || ||||||||||||||||| || ||||||   || || |||||    ||   |  | ||       | ||| | |    ||| || ||      |   |   ||   |||    ||| |||  | ||||  |||                           
ATCAAAGAAAGATAACATGTACAAGGATTGTATGGAGACATGCTCACAATCTGGTGACCGTGAACTGTCAGAGGACTTGCTTGTCTATTTCATCGAGCAGgtttggttcaaacccattcccttgactgatattacgagactagtgataagctaattcagtatacgccgtaaggtcctagtctgtctacttggcatagcattctgattagcaaacacatccaatcatgtaacacag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 25
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctattttgtttttgtgttgaatatttagcatgtagtatgctgcattaa-cttgta---acattgccat-------ctcttctagttat-----------
 |||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| || |||||||| || ||||| || ||||||||||| ||||||   ||  | |||||    ||   |  || | | |   |   || ||   ||    ||| | |||  || ||| |     ||||   ||       | | || | | ||           
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattca-atactatatacagcaaaaagcttatgcttgcattctgattagtaaacacatccaatcatatgtaatgtag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 12
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctattttgtttttgtgttgaatatttagcatgtagta--tgctgcattaacttgt--aacattgccatctcttctagttat
 |||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| || |||||||| || || || || ||||||||||| ||||||   ||  | |||||    ||   |  || | | |||| |    ||    |   ||      |||     ||  ||  ||  | ||    |   | ||    
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTTCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatat-gtgtcggcgtttcgagaccgaggggtccctgggccgacgagtgaaatgtcgctgcgtgccccagc---

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 12
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctattttgtttttgtgttgaatatttag------catgtagtatgctgcattaacttgtaac---att-gccatctcttctagttat-----------
 |||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| || || ||||| || ||||| || ||||||||||| ||||||   ||  | |||||    ||   |  || | | |   |   || ||         ||  || |    || |   |||| |     ||| |  | | | || | | ||           
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTATCAGAGGACTTGCTCGTGTATTTCATTGAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgcattctgattagtaaacgcatccaatcatatgtaatgcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 7
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctattttgtttttgtgttgaatatttag------catgtagtatgctgcattaacttgtaac---att-gccatctcttctagttat-----------
 |||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| || |||||||| || ||||| || ||||||||| | ||||||   ||  | |||||    ||   |  || | | |   |   || ||         ||  || |    || |   |||| |     ||| |  | | | || | | ||           
ATCGAAGAAAGACAACATGTACAAGGACTGCATGGAGACATGCTCACAATCTGGCGACCGTGAACTGTCAGAGGACTTGCTCGTGTATTTCATTAAGCAGgtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgcattctgattagtaaacacatccaatcatatgtaatgcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 27
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta--agcccataaatttctattttg--tttttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat
||| || ||||||||  | |||||||| || ||||| || ||||| || ||||||||||| || || ||||| ||||||||||| || || ||||| |||||  | |||   |  || |   ||   || |     | || | || |    | |  |  | |   |  |    |   || ||  |  ||    || | | ||  
GTCAAAAAAAGACAATCTTTACAAGGACTGTATGGAAACTTGCTCTCAATCTGGTGACCGTGAACTCTCAGAGGATTTGCTTGTTTACTTTATTGAGCAGgtctattttcttattcccttccttgaaatatcaaactcttctattcatatctcaaaaccttgccag--gtcccactgtgcaatttgacctctgctacaaatt--

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 27
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgt-tcaatttaa--gcccataaatttctatttt---gtttttgtgtt-gaatatttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat----------------------------------------------------------------------------------------
||| |||||||||||  | |||||||| || ||||| |||||||| || ||||||||||| || || || ||||||||||||||||| || ||||| ||||| |  ||||    | || |    ||    | |     | | || || | | |||    |   | || | |  |     |||  | | |||  | |   |  | |                                                                                          
GTCAAAGAAAGACAATCTTTACAAGGACTGTATGGAAACATGCTCTCAATCTGGTGACCGTGAACTCTCGGAAGATTTGCTTGTCTACTTTATTGAGCAGgtgtttattttcttgtccttttccttaagatctcaaactctggtattcgtaaattagatactaactaggttagacccttttggcatagtgcactttgaccctgcttcacttagaaatgattttgctgctttctttcctcacctcccgcaccagtttttctctcttaattaacaaagggattatattgatttgcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 27
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgt-tcaatttaa--gcccat-------aaatttctattt----tgtttttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat------------------------------------------------------------------------------
||| |||||||||||  | |||||||| || ||||| |||||||| || ||||||||||| || || ||||||||||||||| |||| || ||||| ||||| |  ||||    | || |       | || || |  |    | ||  |   ||  ||| | |  | ||   |   |     |   || |      |    ||   |||  ||                                                                              
GTCAAAGAAAGACAATCTTTACAAGGACTGTATGGAAACATGCTCTCAATCTGGTGACCGTGAACTTTCAGAAGATTTGCTTATCTACTTTATTGAGCAGgtgtttattttcttgtccttttccttaagatatcaaactccagtattcgtaaattagatactaactaggttagaccttttggcatagtgcagtgaccctgcttcacttagaaattattttgctgctttctttcttcacctccagtgctggttcttttcttttaattaacaaagggattatattgatttgcag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 26
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttc--aatttaagcccataaatttctattttgtttttgtgttgaat-atttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat
||| |||||||| ||| | ||||| |||  ||||||||||  |||||| ||||||||||| || ||  | || || |||||||| ||||||||||| ||||| |  |||| ||   ||      | || ||  |||||  |    ||     ||||| |   ||    |||    || |   |   | |        || || 
GTCAAAGAAAGATAACCTTTACAAAGATGCCATGGAGACAGCCTCACAATCTGGTGACCGTGAACTTGCTGAGGAGTTGCTTGTTTATTTCATTGATCAGgtaccaaattcaatttcaacggcatataattcattttttagcaacattgcccagcat-tctcatttaacat-gttttatttgaagactaagatgctaagcta-

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 27
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctatt--ttgtttttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat--
||| |||||||||||| | ||||| |||   |||||||||||||| |||||||| || || || ||  |||| || |||||||| ||||||||||| |||||   | | |    ||    | | ||     ||   ||| | | |||  | | ||  |  ||    |  | ||  |    | ||   |  | ||||| || |  
GTCAAAGAAAGACAACCTATACAAAGATGCGATGGAGACATGCTCTCAGTCTGGGGATCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGCAGgtatgagtcatatacacttgtctataaaagctgaaattgagat-aatcatcatcaaatgctaaatagtgtgaatgtt---ccttcataaattttctaattttta

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 27
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 15
GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaatttaagcccataaatttctatt-----ttgtttttgtgttgaatatttagcatgtagtatgctgcattaacttgtaacattgccatctcttctagttat---------------------
||| |||||||||||| | |||||||||   |||||||| |||||||||||||| || || |||||  | || ||  |||||   |  ||| | ||  ||||   | ||    | ||   | |||        |||   |||     || || ||   |   |    ||     | | |   | | |   ||   || |   |                       
GTCCAAGAAAGACAACTTATACAAGGATGCAATGGAGACTTGCTCACAGTCTGGAGATCGTGAGCTTGCTGAGGAGCTGCTTACATTCTTCGTGGACAAGgtaagaattc--tctatttgtgtctgcgggcaattgaagttgaaagaaacatctacactactgatgtctatgacaccctaagaaaattttataatttttttctgcgttgtaatttgtgatgtacag

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|12622957|gb|AU173170.1|AU173170
EST:     CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAG                         GGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGNTATGACTTGATC
genomic: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta ... tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
EST: gi|29685119|gb|CB681394.1|CB681394
EST:     CTGGTGACCGCAAGCTGTCAAAAGATTTGCTTGTCTATTTCATTGAACAG                         GGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
genomic: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta ... tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
EST: gi|29627717|gb|CB632728.1|CB632728
EST:     CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAG                         GGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
genomic: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta ... tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
EST: gi|29664581|gb|CB660856.1|CB660856
EST:     CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAG                         GGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC
genomic: CTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta ... tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATC

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: 75 (upstream exon), 70 (downstream exon)
Score: 110

GTCGAAGAAAGACAACATGTACAAGGATTGCATGGAGACATGCTCACAGTCTGGTGACCGCGAGCTGTCAGAAGATTTGCTTGTCTATTTCATTGAACAGgttcaattta ... tgtattgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT




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