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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT

Basic information

species Oryza sativa
transcript LOC_Os01g01710.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G036290_T02 (Zea mays), 3'ss of exon 10
aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatt-tgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
| || |   | | |    | ||||||    |      |  ||      |    | | ||     ||  ||      | |   || | |   | ||||||||| ||||||| ||||| |||||||||||||||||||| ||||||||||| ||||| || || || ||||||||  | ||||||||||||||||||||||||
agaaaacgaaaacgggttataaaattaaacaccgcacgatctcttaaatagtaagcattccatgtta-acagtttttgagcgttcactgacgttaatgcagGTTGGGTTCGCTGACGTTCAAAGCTCCTGACAATGTAAAATACCCGTCAATGGACCTAGCGTACGCAGCTGGGCGGGCTGGGGGCACCATGACAGGAGTT

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 10
------aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
       |||||  |  |  |  |  | | |  ||||    ||| | |||  | ||   ||  ||||| |     |    | |||| ||  | || | ||||||||| ||||||||||||||||||||||||| ||||| || |||||||| || ||||| || ||||||||||||||  | ||||||||||||||||||||||||
ctgcattaaagatgttaagacttcgcacagtc-ttaaacagtaggaatta--catggtaacagtttttgagcattca---gattaagttccagttggttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTT

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 10
aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataat--gcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
    |   | ||| ||   |||    |||| |    | | | | | |    ||   |     | |   || ||  |||  ||   | | ||    |  |||| || |||||| |||| |||||    || ||||||||||||||||| || |||||||| || ||||| |||||| ||||||| ||||| ||||| ||||||
ttttggtgtggat-cagttaaactgggttaggac-cactgccttatctatcagcattcagcacctaaaaccaaaagttgtttacaattgtggattttggcagACTCGGTTCATTGACTTTCAAGAAACCAGACAATGTGAAATACCCATCCATGGATCTTGCTTATGCTGCTGGACGAGCTGGAGGCACAATGACTGGAGTT

upper sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 10
aaaagaactagatgcaacaaaaaattgttaagttatagtacttaa---ccgtgaagaccttttttcattgcacga-agggtt-aatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
       | ||||  ||||| ||||  |   || | | || | ||     |  |  |  || ||   ||||  || | | || || ||  |||   ||  |||||||| || ||||||||||| ||| ||||||||||||||||||| || || |||||||| |||||||| |||||| | ||||| ||||||||||||||||||
----tttccagattaaacaataaat-atggtgtgaaaataatgaaaacttgcaatcagtttattagtttgcttgacatgattgaaattggaatggaatggtgcagGCTTGGGTCACTGACATTTAAAACTCCTGACAATGTGAAATATCCATCCATGGATCTTGCCTATGCTGCTGGACGGGCTGGAGGCACCATGACAGGAGTT

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|58653081|gb|CK041761.1|CK041761
EST:     GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
EST: gi|38478000|gb|CF962133.1|CF962133
EST:     GACAGAATCTATTGCTCAGAGATCACCTGGCCCCGACTAGATCTTTGCAA                         GCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT
genomic: GACAGAATCTATTGCTCAGAGGTCACCTGGCCCCGACTAGATCTTTGCAAgtacaggctc ... gataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT
                               ttaatttttaatttga  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT