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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTCTTCGCTGGCCTCGTTTATGTCCAATCAGGAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgcttttacataatatatattttctatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g02756.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02756.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G453794_T01 (Zea mays), 5'ss of exon 3
TGTTTCTTCGCTGGCCTCGTTTATGTCCAATCAGGAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgcttttacataatatatattttctatttcatgag--tcatttcaagttacatactgtcaacatttggaa----ttcttttgcag
|||||| || |||||||| |||||||| |||||||| || |||||||| ||||| |||||||||||||| || || || |||||||||||||||||||||| ||| | || | | |  ||||||  |||  | || ||   |   || || |  || ||    |||||||| ||
TGTTTCCTCCCTGGCCTCATTTATGTCTAATCAGGAGACAAGTTTTGTGACATTAGGACAGCGTGTTCTTGCTAACCCGCTGAAgtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtag

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 40
TGTTTCTTCGCTGGCCTCGTTTATGTCCAATCAGGAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgc-ttttacataatatatattttctatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcag
||| || ||  | || || |||||||||||||| |||||||||||||| || ||||| ||||| ||| | || |||||| |||||||||  | ||||| || | |||    ||     ||| || |||    ||||   | | ||      | |  |            
TGTCTCATCTTTAGCATCATTTATGTCCAATCAAGAAACTAGTTTTGTGACTTTGGGGCAGCGAGTTTTAGCAAATCCATTGAAgtaagcccattttaaattaaataatgatttctcgtcaagattcaaactaagtatgacaatgatgctctattcag-----------

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA10G44150.2 (Glycine max), 5'ss of exon 38
TGTTTCTTCGCTGGCCTCGTTTATGTCCAATCAGGAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgc-ttttacataatatat--attttctatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcag
||| || || || || || |||||||||||||| |||||||||||||| || || || ||||| ||| | || |||||| |||||||||  | ||||| || | |||   ||||  | | ||| || |||    ||||   | | ||      | |  |            
TGTCTCATCTCTAGCGTCATTTATGTCCAATCAAGAAACTAGTTTTGTGACTTTAGGGCAGCGAGTTTTAGCAAATCCATTGAAgtaagcccattttaaattaaataatgatttcttttgtcaagaatcaaactaagtatgacaatgatgctctatttag-----------

upper sequence: LOC_Os03g02756.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 5'ss of exon 35
TGTTTCTTCGCTGGCCTCGTTTATGTCCAATCAGGAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgcttttacataatatatattttctatttcatga---gtcatttcaagttacatactgtcaacatttggaattcttttgcag-------
||| |||||  | ||||  |||||||||||||| |||||||| ||||| ||  | || |||||||||||||| || ||  | |||||||| | |||| || |   |     | ||||| |||     |||||| || ||    |          |  ||| |||||   |        
TGTCTCTTCTTTAGCCTTATTTATGTCCAATCAAGAAACTAGCTTTGTTACTCTAGGCCAGCGTGTTCTGGCAAAACCTTTAAAgtaagttcattta-attaagcaagcaatttatttgatgtcatatcattttaaatttgggataactggagct--gaaatctttaataatggccag

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|300216075|gb|HO088701.1|HO088701
EST:     GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAA                         AGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
genomic: GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgctt ... tcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
EST: gi|88399969|gb|CI588273.1|CI588273
EST:     GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAA                         AGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
genomic: GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgctt ... tcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
EST: gi|33679231|gb|CF307470.1|CF307470
EST:     GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAA                         AGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
genomic: GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgctt ... tcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
EST: gi|29675246|gb|CB671521.1|CB671521
EST:     GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAA                         AGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT
genomic: GAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgctt ... tcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATAT

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), 71 (downstream exon)
Score: 39

TGTTTCTTCGCTGGCCTCGTTTATGTCCAATCAGGAAACTAGTTTTGTCACATTGGGACAGCGTGTTCTGGCCAATCCACTGAAgtaagtgctt ... tcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG




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