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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttatctccaatatttctgattctgttcatcgtgtatgttgagccatcaaacttgatgctgtttccctattatttatttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACTGGATGTGTCTTTAGAAGACAGGCGCTGTATGGTTATGATGCCCCCAAAT

Basic information

species Oryza sativa
transcript LOC_Os03g62090.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62090.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G113137_T01 (Zea mays), 3'ss of exon 10
gtaagatttatctccaatatttctgattctgttcatcgtgtatgttgagccatcaaacttg--atgctgtttccctattatttatttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACTGGATGTGTCTTTAGAAGACAGGCGCTGTATGGTTATGATGCCCCCAAAT
||||||| | ||  ||| |||||| |     | | | || ||   |||  |||  |||||   |||||||||||||| | ||   ||| | ||||||||||||||||||||||||||||| || ||||| || ||||| ||||||||||||||||| ||||| |||||  | ||||| || ||||| |||||| 
gtaagatctgtcatcaaaatttctaagaagttcccttgtctaacatgatacattgaacttacaatgctgtttccctaatgttacattcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACTGGATGTGTCTTCAGAAGGCAGGCATTATATGGCTACGATGCTCCCAAAA

upper sequence: LOC_Os03g62090.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 3'ss of exon 10
--------------gtaagatttatctccaatatttctg--attctgttcatcgtgtatgttgagccatcaaacttg-atgctg---tttccctattatttatttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACTGGATGTGTCTTTAGAAGACAGGCGCTGTATGGTTATGATGCCCCCAAAT
               |   || |  |  || |  |||||   |||| ||| | ||     |     ||   | |||| ||||      |    |   |  | |   || ||||| |||||||||||||| ||||| |||||||| ||||| ||||| || ||||||||||| || ||||| || ||||| |||||||||||||| || ||  
gtgagcatgcacttctttcatattgcctcatttcttctgctgttcttttctttgttctcataacatcaattatcttgtatgccaagactaatttgcaaactctactttccagATTAACATGAAAGGTTTAGATGGCATTCAAGGACCCATATATGTTGGGACTGGATGTGTGTTCAGAAGGCAAGCGCTATATGGTTATGATGCTCCAAAGA

upper sequence: LOC_Os03g62090.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 10
gtaagattt--atctccaatatttctgattctgttcatcgtgtatgttgagccatcaaacttgatgctgtttccctattatttatttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACTGGATGTGTCTTTAGAAGACAGGCGCTGTATGGTTATGATGCCCCCAAAT
|||||  |    |   | |||| | |||| ||  |  |  |   | | ||||  |   |     ||    ||    ||  ||||| |     |||||||||||||||| ||||| || |||||||| ||||| ||||| |||||||| ||||||||||||||||||||  | |||||| ||||||| || ||| 
gtaagcctgcagttctccatatct-tgatgctagttttgata-gtttagagcttttctatcgattg--acttggtcat--tttatatgcactagATCAACATGAAAGGCTTGGACGGAATTCAAGGACCCATTTATGTGGGTACTGGGTGTGTCTTTAGAAGACAGGCATTCTATGGTAATGATGCTCCAAAAA

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|58673633|gb|CK062319.1|CK062319
EST:     ATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGAT                         ATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
genomic: ATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGATgtaagattta ... tttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
EST: gi|428504|gb|D24655.1|D24655
EST:     GCATTGACCGTCATGATCGATATGCTAATAGGNATGTCGTCTTTTTCGAT                         ATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
genomic: GCATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGATgtaagattta ... tttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
EST: gi|58653950|gb|CK042630.1|CK042630
EST:     GCGTTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGAT                         ATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
genomic: GCATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGATgtaagattta ... tttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
EST: gi|58661513|gb|CK050193.1|CK050193
EST:     GCATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGAT                         ATCAACATGAAAGGTTGGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
genomic: GCATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGATgtaagattta ... tttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
EST: gi|300215913|gb|HO088539.1|HO088539
EST:     GCATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGAT                         ATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
genomic: GCATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGATgtaagattta ... tttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
EST: gi|58598457|gb|CK008985.1|CK008985
EST:     GCATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGAT                         ATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
genomic: GCATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGATgtaagattta ... tttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACT
EST: gi|58673488|gb|CK062174.1|CK062174
EST:     GGAATGTCTGTCTTTTTCTGAT                         ATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTAC
genomic: GGAATGTC-GTCTTTTTC-GATgtaagattta ... tttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTAC

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: 62 (upstream exon), 75 (downstream exon)
Score: 20

CTTGGTAGGAAAGAAAGTTTGTTATGTGCAGTTCCCACAAAGATTCGATGGCATTGACCGTCATGATCGATATGCTAATAGGAATGTCGTCTTTTTCGATgtaagattta ... tttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACTGGATGTGTCTTTAGAAGACAGGCGCTGTATGGTTATGATGCCCCCAAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtatgttgagccatcaaacttgatgctgtttccctattatttatttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACTGGATGTGTCTTTAGAAGACAGGCGCTGTATGGTTATGATGCCCCCAAAT
                   acttgat  putative branch site (score: 20)
                              tttccctattatttat  putative PPT
                                    tattatttatttctt  TA-rich tract