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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgttactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag

Basic information

species Oryza sativa
transcript LOC_Os03g02756.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G453794_T01 (Zea mays), 5'ss of exon 11
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgt-tactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag----
|||||||||| ||||| || || ||||| || ||| |||||||| | ||||||||||||||||| ||  |||| || ||||||||||||||||||||||||||||| || ||||||| | || || | | |||| |  ||  | | |||   | |  ||   || ||  || |||  | |||| |      
CAGTTGGCTATATTTTACTCTCTATAAGCAGTTGGATTATGGCATTGTCTTGGCTTTTTGCTCCCTATTTATTTAACCCATCTGGATTTGAATGGCAGAAgtaagcagccaagcattttgtgtatctatgtactataagt--tcaaattgtcattatgag--attagatttcaaacccttctccctcttag

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA10G44150.1 (Glycine max), 5'ss of exon 46
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgttactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag
|| |    || ||| |  |    ||||| || |||||||||||  | || ||| | |||||||||||  ||||||| || ||||||||||| ||||| ||||||| |  ||     |||||  || |   ||| ||   |   || | | |   |   ||| ||      | | |   | | |   
CACTCTCATATATTCTTTTGAGTATAAGCAGTTGGTTTATGGCTCTATCCTGGTTGTTTGCTCCATATTTATTCAACCCGTCTGGATTTGAGTGGCAAAAgtaag-tatta-----tctatttatcttgaactttg-acaggcatgtctcatgatt--attttccctcacacagtgtttttttag-

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA20G38860.1 (Glycine max), 5'ss of exon 48
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgttactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag
|| |    || ||| |  |    ||||| || |||||||||||  | || ||| | |||||||||||  ||||||| |||||||||||||| ||||| ||||||| |  ||   ||| |||   ||| ||  ||   | |  | | |    | |    |||||     || |     || | | ||
CACTCTCATATATTCTTTTGAGTATAAGCAGTTGGTTTATGGCTCTATCCTGGTTGTTTGCTCCATATTTATTCAACCCATCTGGATTTGAGTGGCAAAAgtaag-tattatctatt-tatctttgtattcttcctggca--tgtctcatgagtcatgattattttccttcacggtgcttttttag

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 5'ss of exon 45
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgttactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag
| |||  ||||||  ||||  |  | || ||||||||| |||| ||||||||||| |||||||| ||| ||||||| ||  | |||||||| |||||||||||||  |      ||  |||  || |  |  |  | ||      |  ||    || | | | ||  | ||||||    || ||||
CGGTTTCCTACATCCTGCTGACAGTTAGCAGCTGGTTTTTGGCTGTTTCTTGGCTGTTTGCTCCGTACCTATTCAACCCTGCCGGATTTGAGTGGCAGAAgtaagtggt--gctatcttatttatatcatgttgagtgttgagtaacgtgtttctc-attgaacaacaataaaattatgctttcag

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 5'ss of exon 43
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgttactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag
|| |    |||||| | |||  ||| || || ||||| |||||  ||||||||||||||||||| ||  | |||||||||||||| ||||| |||||||||||||      | |||| |    || |  |       | | ||     ||   |   ||  ||     ||    |||| || | ||
CACTATCGTACATTCTTCTTAGCATTAGCAGTTGGTTCATGGCTCTTTCTTGGCTTTTTGCTCCCTATTTGTTCAATCCATCTGGTTTTGAGTGGCAGAAgtaagt-----atcatttttctaattttctctctcatggatttgctcatgttttattaaccat-----ttgttttaccccttttag

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S88_136V6.1 (Physcomitrella patens), 5'ss of exon 44
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgttactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag----------------------------------------------------
||||    |  || |||||  |  | |||   |||||  | ||  | || |||||||| || || |||||||| ||||||||||| ||||| ||||| ||||||||           || ||  | |||| |  || | ||   |||| |  |    |||||    |  ||  |||    | |||                                                     
CAGTCACTTTTATCTTGCTGACGTTCAGTTCTTGGTTCCTAGCTTTATCCTGGCTTTTCGCACCCTACATATTTAATCCATCTGGTTTTGAGTGGCAAAAgtaagcacgattcttccctttgattatgtttcattg-ggaaccttattggttagc--aattaaacagggtacgatattcttttcacgttgaaaccttgagtacaatgacaattgaggatgtgaatttatgtgctgcag

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S67_70V6.1 (Physcomitrella patens), 5'ss of exon 41
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagc----attctatgcatgtgttactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag---------------------------------------------------------------------------------------
|||||   |||||||||||  |  | |||  ||||||  ||||  |||| ||||| ||||| |||||  | ||||| |||||||| || |||||||||||||||||     |||     || |     ||| ||  ||   || || || | ||  |||| | || | || |  ||        |   ||                                                                                       
CAGTTACTTACATTTTGCTCACATTCAGTTCCTGGTTCCTGGCGCTTTCGTGGCTCTTTGCGCCATATGTTTTCAACCCATCTGGCTTCGAATGGCAGAAgtaagcactacagctcttgttttcgttttgtattgatcaatgtcatgatgtctgccattc-atttgtaagcaacaagtgttacatgatagtttgtgtcctctgaggtcttacgttgtaggagtggtctttcgctcaataatctatttggtcttacaaaatgtaaaattttgatacag

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S67_234V6.1 (Physcomitrella patens), 5'ss of exon 47
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgttactctgcgtaatta----tat-ttgaaattcgaattatcaggattaaaatacctctctcag-----------------------------------------------
| |   |||||||| |     |  | ||||| |||||| | ||  | || ||| | | |||||||| ||| |||||||| || || ||||||||||||||||||| |    |   ||  ||  |  ||  | |   |    ||     ||| |||||  ||    | |  || |  |  ||  || |                                                   
CTGCCAGCTACATTCTCAGCACGTTTAGTAGTTGGTTTCTAGCTCTCTCATGGTTATATGCTCCATTCATCTTCAATCCTTCAGGGTTTGAATGGCAGAAgtaagataaccattcttgaatatacatggcagttgtcaatgttggccttatattgaatatcatggtttttggctggacgtatttcacaagtcccacaactcaggacacgatgttctaattttcacttttcaactttag

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S18_300V6.2 (Physcomitrella patens), 5'ss of exon 24
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgctaagcattctatgcatgtgttactctgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag------------------------------------------------------------------
| |   |||||||| | ||  |  | || || |||||| ||||  |||| ||| | |||||||| | | | |||||||| || ||||||||||||||||||||||   | | | |   | |  |  | || |  |||||  ||   || |    |   |||  || | ||    | ||    ||||                                                                  
CTGCCAGCTACATTCTTCTCACATTTAGCAGTTGGTTTCTGGCTCTTTCATGGTTATTTGCTCCTTTCGTCTTCAATCCTTCAGGATTTGAATGGCAGAAgtaagaaaccacgaacattcttgacctttttcgatgcgtttttcatttgggtccttcgattgacatggttcct-ttccgacttcagtcttaaaagtgggtggcctattgacttcgggcaccaggttctgattttcttcctcaataaattcag

upper sequence: LOC_Os03g02756.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S40_186V6.2 (Physcomitrella patens), 5'ss of exon 30
CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctg-ctaagc--attctatgcatgtgttactc-tgcgtaattatatttgaaattcgaattatcaggattaaaatacctctctcag---------------------------------------------------
  |   |||||||| | ||  |  | ||||| |||||| | ||  | || ||| | |  ||||| | ||| |||||||| |||||||| |||||||||||||||| |  || | |  ||  |   ||||||  ||      || ||| |       | |   | || || | ||    | |       ||                                                   
ATGCCAGCTACATTCTTCTCACATTTAGTAGTTGGTTTCTTGCTCTCTCATGGTTATACGCTCCTTTCATCTTCAATCCTTCTGGATTCGAATGGCAGAAgtaagataactcaaccaatcttgatcatgtgcgacagacttgtcattgttggccctacttagactagcatggttttcttccaggatgtagttcggatattccagatgtgaagtgattctaattttcattctgtaacttcag

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|568436|gb|D39285.1|D39285
EST:     TGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAA                         GGTCGTTGAGGATTTCAGAGACTGGACGAATTGGCTGTTTTACCGAGGTGG
genomic: TGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgct ... cctctctcagGGTCGTTGAGGATTTCAGAGACTGGACGAATTGGCTGTTTTACCGAGGTGG




















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: 70 (upstream exon), 56 (downstream exon)
Score: 35

CAGTTGGCTACATTTTGCTTTCCATAAGTAGCTGGTTTATGGCAGTTTCTTGGCTTTTTGCTCCATACATATTCAATCCATCTGGATTTGAATGGCAGAAgtaagctgct ... cctctctcagGGTCGTTGAGGATTTCAGAGACTGGACGAATTGGCTGTTTTACCGAGGTGGTATTGGGGTTAAGGGAGAAGAAAGTTGGGAAGCCTGGTGGGATGAAGAA




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