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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAATCAGACGATGGTCTTCTTGAAATATTTGGATTGAAGCAAGGGTGGCATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAGgtacttttgctccctgcacaagatctgaatagcagaaggtattttaatgcattactgttcaatttggagctcaaaggttaaaaatgtagtagtaaatttt...

Basic information

species Oryza sativa
transcript LOC_Os08g15090.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g15090.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G073380_T01 (Zea mays), 5'ss of exon 5
TCAATCAGACGATGGTCTTCTTGAAATATTTGGATTGAAGCAAGGGTGGCATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAGgtacttttgctccctgcacaagatctgaatagcagaag---gtattttaatgcattactgttcaatttggagctcaaaggtta---aaaatgtagtagtaaatttt--
 |||||||| |||||||||||||| ||||||||| |||||||||||||||||||||| || |||||||||||||| |||||||| ||||||||||||||||||  ||    |||   |||| | |  || |  || |     ||   ||  | |  | | || | |       ||| | |      | ||| | ||  |||  ||   
CCAATCAGATGATGGTCTTCTTGAGATATTTGGACTGAAGCAAGGGTGGCATGCATCTCTCGTGATGGTTGAACTTATATCTGCCAAGCACATAGCTCAGgtaacttgctcccccaaacaaaaacaaaaaaaaagtattctataaactatagaaagaatatttattacttcattcagaagcaccgcataatttggtgctaatgttcag

upper sequence: LOC_Os08g15090.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA17G07480.1 (Glycine max), 5'ss of exon 11
TCAATCAGACGATGGTCTTCTTGAAATATTTGGATTGAAGCAAGGGTGGCATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAGgtacttttgctccctgcacaagatctgaatagcagaaggtatttt---aatgcattactgttcaatttggagctcaaaggttaaaaatgtagtagtaaatttt
| |    | |||||| ||  | ||| ||||||| || || ||||| |||||||||||  |||| ||||||||||| || ||||| |||||| ||| ||||||||    | |   ||   | | |||  |  | |     || |||   |||  |  | | || || ||     ||   | ||     ||   |   |  ||  
TGATGTTGCCGATGGGCTCTTGGAAGTATTTGGTTTAAAACAAGGATGGCATGCATCATTTGTTATGGTTGAACTGATCTCTGCTAAGCACTTAGTTCAGgtaccacagtttattgtttatgttcttgagtgaattgcttacttttcaaattaaaaaattttgaactttagattccctgattgcttttgc--tgagaggttg-

upper sequence: LOC_Os08g15090.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA18G22370.1 (Glycine max), 5'ss of exon 4
TCAATCAGACGATGGTCTTCTTGAAATATTTGGATTGAAGCAAGGGTGGCATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAGgtac--------ttttgctccctgcacaagatctgaatagcagaaggtattttaatgcattactgttcaatttg-gagctcaaaggttaaaa-atgtagtagtaaatttt
 |||   || ||||| ||| | |||||||||||  | || ||||| |||||||||||  |||| |||  |||||| || ||||||||||| |||||||||||||        |||  |    |  |     | ||| | |      || ||||| | ||  | |||  ||| |  || |||||   ||  ||    ||||          
ACAAGTTGATGATGGACTTTTAGAAATATTTGGTCTAAAACAAGGATGGCATGCATCATTTGTCATGAGTGAACTTATTTCTGCAAAGCATATAGCTCAGgtaccatattaatttgacgtattttattctttgtgatttgggttgtgttttttacttcaaaattgtaaaatatatgaactcaatttttttaatgcttagt----------

upper sequence: LOC_Os08g15090.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA13G01360.2 (Glycine max), 5'ss of exon 11
TCAATCAGACGATGGTCTTCTTGAAATATTTGGATTGAAGCAAGGGTGGCATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAGgtacttttgctccctgcacaagatctgaatagcagaaggtatttt---aatgcattactgttcaatttggagctcaaaggttaaaaatgtagtagtaaatttt
| |    | |||||| ||  | ||| ||||||| || || ||||| ||||| |||||  |||| ||||| ||||| || ||||| |||||| ||||||||||||    | |   ||   | | |||  |  | |     |  |||   ||||||  | | || || ||     ||   |  |    ||||  |   |  ||  
TGATGTTGCCGATGGGCTCTTGGAAGTATTTGGTTTAAAACAAGGATGGCACGCATCGTTTGTCATGGTGGAACTGATCTCTGCTAAGCACTTAGCTCAGgtaccacagtttattgtttatgttcttgagtgaattgcttgcttttcaaatgcaaaaat-ttgaactttagattccctgactgcttatgtc-tgagaggttg-

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|88484940|gb|CI422211.1|CI422211
EST:     ATGCATCCCTTGTGATGGTTGAACTAATATCTNCAAAGCACATAGCTCAG                         GCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATAC
genomic: ATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAGgtacttttgc ... ctgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATAC
EST: gi|29676335|gb|CB672610.1|CB672610
EST:     ATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAG                         GCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATAC
genomic: ATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAGgtacttttgc ... ctgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATAC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAATCAGACGATGGTCTTCTTGAAATATTTGGATTGAAGCAAGGGTGGCATGCATCCCTTGTGATGGTTGAACTAATATCTGCAAAGCACATAGCTCAGgtacttttgctccctgcacaagatctgaatagcagaaggtattttaatgcattactgttcaatttggagctcaaaggttaaaaatgtagtagtaaatttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctgc