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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgttcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcag

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G119725_T02 (Zea mays), 5'ss of exon 8
GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgt-------tcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcag
|||||||||| || ||||||||||| |||||||||||| ||||||| ||||| ||||||||||||||||| |||||||| ||||||||||| ||||||||||||| ||| ||| |||         |  | | |||||| | |  ||||||   |||  |   ||    ||  || |  ||| |||
GGTATGCAAAACGATTTTTGCATCCCGATGTTGTTGCCAGATATGATTACATTTTCATCTGGGATGAGGATCTAGGTGTAGAGCATTTCAACGCAGAGAAgtaagcactacatatttccattcttgttttctttctgttcagcaggtgttcattttgattaaaatgtccttcctatt--tttacag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G006507_T02 (Zea mays), 5'ss of exon 8
GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgt-------tcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcag
|||| ||||| || ||||||||||| || ||||||||| ||||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||||||||||| ||| ||| ||||        |  | | |||||| |  | ||||||   ||   |  |||    ||  || |  ||| |||
GGTACGCAAAACGATTTTTGCATCCCGACGTTGTTGCCAGATATGATTACATTTTCATCTGGGATGAGGATCTAGGTGTAGAACATTTCAATGCAGAGAAgtaagcactacatatttgcattcttgttttctttctgttcagttggtgttcatttttattaagatgcccttgctatt--tttacag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G08040.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgttcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcag
||||||||||| | ||||||||||||||||||||  |    ||||| || ||||| || |||||||| || || || || ||||| ||||||||||| | ||  ||| | | | | ||    | ||  ||  || |  |||     |||   | | ||| |  || ||    |||||||
GGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGATAGgt--gaattacttgtctgaaattgtagttgcagatca-gtgacaatctt---tacaatttttattttaaa--ttttcag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 5'ss of exon 8
GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgttcctttatctgttgac--cttgtgttccacttgggtgcgattatg----tttgtactctttttcag------------
||||||||||  |||| ||||||||||||||||||||    ||||| || || || || |||||||| ||||||| |||  |||| ||||||| |||||||||||       ||||| | || | | |   |||    |  || || | |||       |||      |||||  |||  ||| |            
GGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAGAAgtaag-------tttttttcccataaaccagtgatagttcctggtcaaattgaaaatttttacacttctttgtgttctgcttccgatgatcttccag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S129_53V6.1 (Physcomitrella patens), 5'ss of exon 8
GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactgcatttttgttcctttatctgttgaccttgtgttccacttgggtgcgattatgtttgtactctttttcag---------------------------------------------------------------------------------------------
||||||| |||||||||||||| || ||||| || || |  ||||| ||||| ||||| ||||||||||| || | | |   |||||| ||| |  ||| | ||| ||  |  |   ||   ||  || |   | ||  |    |  ||  ||         |  | |   |||   ||                                                                                             
GGTATGCCAAGCGGTTTTTGCACCCCGATGTAGTGGCGCCGTATGAGTACATCTTCATTTGGGATGAGGATCTTGATTTGAGGCATTTTAATCCTAAGAGgcaagtacatc--tgccgtatattactccgactagctcattcgtcgatttagtaaagcctcatacgcatgttttagaaggattccttttcgcggttgctctcaaagagaaaagtgagacttgaaacttctgaagattttggatttattgatacgggtggactggcttcgcag

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|38475807|gb|CF959940.1|CF959940
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
EST: gi|33795503|gb|CF323621.1|CF323621
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
EST: gi|33675555|gb|CF303794.1|CF303794
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
EST: gi|86906524|gb|CI294647.1|CI294647
EST:     ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAA                         GTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT
genomic: ATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTT

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), 75 (downstream exon)
Score: 24

GGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAGAAgtaagaactg ... tctttttcagGTATATTGAACTTGTTAGGAAGCATGGGCTAGATATCTCTCAGCCTGGTTTGCAACCTGACAAGGGACTGACATGGCAAATGACAAAACGGCGAGGTGAT




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