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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAGAGAAGGCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtcatcttgttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcag

Basic information

species Oryza sativa
transcript LOC_Os09g20820.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g20820.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G034848_T01 (Zea mays), 5'ss of exon 3
TGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAGAGAAGGCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtcatctt----gttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcag
||| ||||||||||| || ||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||| |||||| ||| ||   ||||||     |||| |||  |||| | ||  ||   |  | | |  |||| ||||| |  ||| || |          |||||| |||||
TGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAGAGAGGGTCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAATGgtgtgatatcatctaactagtttcattggccacttgtttgatt--gttctcttgattttattttgaattttaaaaca---------aatcctaatgcag

upper sequence: LOC_Os09g20820.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G009030_T01 (Zea mays), 5'ss of exon 3
TGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAGAGAAGGCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtcatctt----gttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcag
||| ||||||||||| || ||||||||||||||||||||||||||||| || ||| ||||||||||||||||||||||||||||||||||| ||||||| || ||   ||||||     |||| |||  |||| | ||  ||        |  | || ||||||   ||||  |||  |    ||  |||||| |||||
TGTCGGAGATGAAGGAGGTTTTGCTCCTAATGTTCAAGACAACAGAGAGGGTCTTATCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACACTGGAAAAgtgtgatatcatctaactagtttcattggccacttgtttgat------tgctctcttgtttttt---actttaaatgttaaacacaaatcctaatgcag

upper sequence: LOC_Os09g20820.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA18G22780.1 (Glycine max), 5'ss of exon 4
TGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAGAGAAGGCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtcatcttgttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcag
||||||||||||||| || |||||||| ||||||||||| ||||| || || ||||| || || |||||||||||||| ||||| || ||  |||| |||||  |     | |||   |||||||       |    ||   |    ||| |  |  | || || | | || ||  ||   |             
TGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAGGGAGGGGCTTGTTTTACTCATGGATGCCATTGACAAGGCTGGTTATACTGGCAAGgtgggtga--agctttgattatttctgttgcataatttgaaaattcacttgtgctgatctggaaat-aaaaaacaatggtgcag-----------

upper sequence: LOC_Os09g20820.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G23080.1 (Glycine max), 5'ss of exon 3
TGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAGAGAAGGCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtcatcttgttttatttcccacct--tttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcag
||||||||||||||| || |||||||| ||||||||||| ||||| || || |||||||| || |||||||| |||||||| || || ||  |||| |||||  |   |  | |  || | | |   || |  ||| ||| |    ||| | |  |  | | | ||  || || ||  ||   |             
TGTTGGAGATGAAGGAGGATTTGCTCCCAATGTTCAAGATAACAGGGAGGGGCTTGTCTTACTCATGGATGCTATTGAGAAAGCTGGTTATACTGGCAAGgtgggtgatgctttgattatttctgttacataatttgaatat---tcacttgtgctgatctggaaa--taaaaaacaatggcgcag-----------

upper sequence: LOC_Os09g20820.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G24920.1 (Glycine max), 5'ss of exon 2
TGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAGAGAAGGCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtc--tgcagtcatcttgttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcag
||||||||||||||| || |||||||| | ||||||||| ||||| || ||  |||| || ||  ||||||||||||||||||| || ||  |||| |||||   || |||  |  |  ||| | |  ||   ||| ||| |  ||      |  | |     |||   | |||  ||                   
TGTTGGAGATGAAGGAGGATTTGCTCCCAGTGTTCAAGATAACAGGGAGGGGTTTGTTTTACTCGTGGATGCCATTGAGAAGGCTGGTTATACTGGCAAGgtgggtgaagttttgattatttctgttgcataatttgaatattcacttgtgctgatctggaaataaaaaacaatggtgcag----------------

upper sequence: LOC_Os09g20820.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G25390.1 (Glycine max), 5'ss of exon 4
TGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAGAGAAGGCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtc--tgcagtcatcttgttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctactgcag
   ||||||||| || || |||||||| ||||||||||| ||||| || || ||||| || || |||||||||||||||||||| || ||  || | |||||   || ||   |  |  ||| | |  ||   ||| ||| |  ||      |  | |     |||   | |||  ||                   
---TGGAGATGACGGAGGATTTGCTCCCAATGTTCAAGATAACAG-GAGGGTCTTGTTTTACTCATGGATGCCATTGAGAAGGCTGGTTATACTAGCAAGGTGGgtgaagctttgattatttctgttgcatactttgaatattcacttgtgctgatctggaaataaaaaaaaatggtgcag----------------

upper sequence: LOC_Os09g20820.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G74030.1 (Arabidopsis thaliana), 5'ss of exon 3
TGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAGAGAAGGCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgca-gtcatcttgttttat----ttcccaccttttcaa--tgtggaccaccttttttttttttg-taacttataatactgt--gaacccatcctactgcag------------------------
||| ||||||||||| || ||||| || ||||||||||| |||||||| || || ||  |||| || ||||| ||||| ||||| || ||| ||||||||||   || ||  ||||  ||| |     |   || |  | ||  ||     || || | |||   |    ||||| |   |   |  |   | ||| |||  ||                         
TGTCGGAGATGAAGGAGGGTTTGCGCCGAATGTTCAAGATAACAGAGAGGGACTAGTTCTGCTCATAGATGCAATTGAAAAGGCCGGTTACACTGGAAAGgtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcag

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|88688642|gb|CI732218.1|CI732218
EST:     GCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAG                         ATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGA
genomic: GCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtc ... cctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGA
EST: gi|88690860|gb|CI734939.1|CI734939
EST:     GCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAG                         ATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGA
genomic: GCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtc ... cctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGA
EST: gi|58604385|gb|CK014913.1|CK014913
EST:     GCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAG                         ATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGA
genomic: GCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtc ... cctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGA
EST: gi|88691935|gb|CI735510.1|CI735510
EST:     GCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAG                         ATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGA
genomic: GCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtc ... cctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGA
EST: gi|88693829|gb|CI735332.1|CI735332
EST:     GCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAG                         ATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGA
genomic: GCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtc ... cctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGA

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: 55 (upstream exon), 75 (downstream exon)
Score: 21

TGTTGGAGATGAAGGTGGCTTTGCTCCTAATGTTCAAGACAACAGAGAAGGCCTTGTCTTGCTTATGGATGCCATTGAGAAGGCAGGCTACTCTGGAAAGgtctgcagtc ... cctactgcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGAAGCTATGACTTAAACTTTAAGAATCAGCCTAATGATGGAGCTCATGTTC




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