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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttctacatttaatttccagtcattggcttatttttgtgtggttttcacaataatagagacatgtaaaaatgtttgctttcatgcag

Basic information

species Oryza sativa
transcript LOC_Os06g40650.4
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G071659_T01 (Zea mays), 5'ss of exon 8
CCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttctacatttaatttccagtcattggcttatttttgtgtggttttcacaataatagagacatgtaaaaatgtttgctttcatgcag
|||| |||| ||||||||||| ||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||| ||| || ||||  | ||||| | |      |  | | || ||   ||   | |  || |   |    |    || |||  |||  |||||
CCCCCTGTCAATTGTTCTTGTCGGGGTTGGTGATGGACCATGGGACATGATGCACCAGTTTGATGACAATATACCTGCTCGGTCATTTGACAATTTCCAGgtaacttttttacagattatttctaatatgcaacaaaatattctg--attcataaatgaacaagcatgactcttcat-tttttttttttgcag

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G345544_T02 (Zea mays), 5'ss of exon 8
CCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttctacatttaatttccagtcattggcttatttttgtgtggttttcacaataatagagacatgtaaaaatgtttgctttcatgcag
|||| |||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||    ||||| | |      |  | | || ||     |||| ||    | |  |||| || |||  ||   || ||||||
CCCCCTGTCAATTGTTCTTGTTGGGGTTGGTGATGGACCATGGGACATGATGCACCAGTTTGATGACAATATACCTGCTCGGTCATTTGACAATTTCCAGgtgattgttctacagactatttctaatacgaaacgaaatattctgg----ttcaaaaatgaataagcatggaagaattcttcactttatgcag

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv00s0780g00040.t01 (Vitis vinifera), 5'ss of exon 8
CCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttctacatttaatttccagtcattggcttatttttgtgtggttttcacaataatagagacatgtaaaaatgtttgctttcatgcag---
|||| |||| || ||||| ||||| || || ||||| ||||||||  ||||||| |||||||||||||| || ||| |  |  | ||||||||||||||||| |     | | | | |   |       |||        ||||||    |||| | |  ||| | |    |    |||||  ||     | |   
CCCCCTGTCAATAGTTCTGGTTGGCGTTGGGGATGGGCCATGGGATGTGATGCAGCAGTTTGATGACAACATTCCTTCCAGGGCTTTTGACAATTTCCAGgttaggaagcaaaactga---taagactcttgaaaccaacttgtgtcaacttca-agttttag-gtctctaatggttgtttatttgtccactgtag

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ27121 (Selaginella moellendorffii), 5'ss of exon 7
CCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgact--gttctacatttaatttccagtc--attggcttatttttgtgtggttttcacaataatagagacatgtaaaaatgtttgctttcatgcag
 || |||||||| ||||||||||| || || ||||| ||||||||||||||||  |||||||| || || || |||   || |  |||||||| ||||| ||      | | |  || |  |||| ||    | || |||| | |    ||   | ||                                       
TCCGTTGTCTATAGTTCTTGTTGGTGTTGGAGATGGGCCATGGGACATGATGCGACAGTTTGACGATAACATTCCTCAGCGATTGTTTGACAACTTCCAAgtattctcgctttctatgttgtttctagcgcgactgacttaatctctcttgtcgtgcag--------------------------------------

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ21520 (Selaginella moellendorffii), 5'ss of exon 7
CCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgact--gttctacatttaatttccagtc--attggcttatttttgtgtggttttcacaataatagagacatgtaaaaatgtttgctttcatgcag
 || |||||||| ||||||||||| || || ||||| ||||||||||||||||  |||||||| || || || |||   || |  |||||||| ||||| ||      | | |  ||    |||| ||    | || |||| | |    ||   | ||                                       
TCCATTGTCTATAGTTCTTGTTGGTGTTGGAGATGGGCCATGGGACATGATGCGACAGTTTGACGATAACATTCCTCAGCGATTGTTTGACAACTTCCAAgtattctcgctttctatggtgtttctagcgcgactgacttaatctctcttgtcgtgcag--------------------------------------

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|116875559|gb|EC366067.1|EC366067
EST:     TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAG                         TTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAGCTGACAGGAAG
genomic: TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttc ... tttcatgcagTTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAGCTGACAGGAAG
EST: gi|58692386|gb|CK081073.1|CK081073
EST:     TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAG                         TTTGTGAATTTCACGGAC
genomic: TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttc ... tttcatgcagTTTGTGAATTTCACGGAC
EST: gi|13420773|gb|AU174863.1|AU174863
EST:     TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAG                         TTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAGCTGACAGGAAG
genomic: TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttc ... tttcatgcagTTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAGCTGACAGGAAG
EST: gi|66928286|gb|CX115134.1|CX115134
EST:     TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAG                         TTTGTGAATTTCACGGACATCATGTCCAAGAGCATAGCAG
genomic: TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttc ... tttcatgcagTTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAG
EST: gi|125863438|gb|EL586714.1|EL586714
EST:     TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAG                         TTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCACCTGACAGGAAG
genomic: TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttc ... tttcatgcagTTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAGCTGACAGGAAG
EST: gi|116875525|gb|EC366033.1|EC366033
EST:     TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAG                         TTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAGCTGACAGGAAG
genomic: TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttc ... tttcatgcagTTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAGCTGACAGGAAG
EST: gi|58678137|gb|CK066824.1|CK066824
EST:     TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAG                         TTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAGCTGACAGGAAG
genomic: TGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttc ... tttcatgcagTTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAGCTGACAGGAAG

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), 74 (downstream exon)
Score: 26

CCCCTTGTCTATTGTTCTTGTTGGGGTGGGTGATGGACCATGGGACATGATGCATCAGTTTGATGACAATATACCTGCTCGCTCATTTGACAATTTCCAGgtgactgttc ... tttcatgcagTTTGTGAATTTCACGGACATCATGTCAAAGAGCATAGCAGCTGACAGGAAGGAGGCAGAATTTGCACTATCCGCCTTGATGGAAATCCCAACACAATACA




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