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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcttgaaaaccgttgaattgcgatcagtcgtcgcgtcggtttcaagtggttttgtttgtgaatgtactgacgtgactaaattatggtgtgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGACTATTACAAGATTCGTGAGCTTCTTTACTCTCAGTTCTACTTGTTGTAAA

Basic information

species Oryza sativa
transcript LOC_Os09g39590.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39590.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G036050_T03 (Zea mays), 3'ss of exon 18
--cctcttgaaaaccgttgaattgcgatcagtcgtcgcgtcggtttcaagtggttttgtttgtgaatgtactgacgtgactaaattatggtgtgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGACTATTACAAGATTCGTGAGCTTCTTTACTCTCAGTTCTACTTGTTGTAAA
   |   |   |||| |   ||| ||  |           | ||||   |           |  | | |||    ||||    |||||  | |   ||||||||||||||||| ||||||||||| || ||||| || ||||| || |||||||||||||||||  | |||||||| ||||| |||||||||||| ||| | 
actccactctgaacctt--gatttcgcacgtctaaaaatgcagtttgttgataccaaacaaggtattatacgtctgtgatgcgattattatatatattgcagGGCAGCACAGGGTCCCAGCAGATCGTCATCGAGGGCCCCCTCTGCGAGGACTATTACAAGATCAGGGAGCTTCTGTACTCGCAGTTCTACTTGCTGTGAG

upper sequence: LOC_Os09g39590.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv16s0050g00590.t01 (Vitis vinifera), 3'ss of exon 17
-----------------------------------------------cctcttgaaaaccg---ttgaattgcgatcag--tcgtcgcgtc--ggtttcaagtggttttgtttgtgaatgtactgacgtgactaaatta--tggtgtgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGACTATTACAAGATTCGTGAGCTTCTTTACTCTCAGTTCTACTTGTTGTAAA
                                               ||||||    || |   |  ||     |  ||    ||  | ||    ||       |     || |   |  |   ||| ||| ||||     || | |  || |   ||  |  |       ||||| |||||||| ||||||||||||||||| || ||||| |||||  | |||    | || || || |  |||||| | |   
gtgagtaacttataagaaaacctgattgttgcaataggttcaaaatccctcttactgactggaatcaaagatttactagatctgttccatccaaattcttgaaagcccatttagcagaaatcaagac-tgattaaaagggctgatttatgtagGGTGGTGGTGCCATAATTCAGCAAATTGTGATGGAAGGGCCCCTGTGTGACGAATATTATAAGATCAGGGAGTACTTGTATTCACAATATTACTTGCTTT---
















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|88541812|gb|CI471105.1|CI471105
EST:     GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAG                         GGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
genomic: GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAGgtaagtagtg ... tgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
EST: gi|88829475|gb|CI074345.1|CI074345
EST:     GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAG                         GGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
genomic: GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAGgtaagtagtg ... tgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
EST: gi|88527394|gb|CI455552.1|CI455552
EST:     GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAG                         GGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
genomic: GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAGgtaagtagtg ... tgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
EST: gi|88535348|gb|CI464143.1|CI464143
EST:     GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAG                         GGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
genomic: GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAGgtaagtagtg ... tgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
EST: gi|88531680|gb|CI460090.1|CI460090
EST:     GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAG                         GGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
genomic: GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAGgtaagtagtg ... tgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
EST: gi|88964230|gb|CI045423.1|CI045423
EST:     GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAG                         GGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
genomic: GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAGgtaagtagtg ... tgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
EST: gi|29672566|gb|CB668841.1|CB668841
EST:     GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAG                         GGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
genomic: GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAGgtaagtagtg ... tgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
EST: gi|88560284|gb|CI490933.1|CI490933
EST:     GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAG                         GGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC
genomic: GGTGTGGTGAATACATCACACTGCGCAAGATTGGTGATGCTGGCCAAAAGgtaagtagtg ... tgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtggttttgtttgtgaatgtactgacgtgactaaattatggtgtgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGACTATTACAAGATTCGTGAGCTTCTTTACTCTCAGTTCTACTTGTTGTAAA
                               actaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctcttgaaaaccgttgaattgcgatcagtcgtcgcgtcggtttcaagtggttttgtttgtgaatgtactgacgtgactaaattatggtgtgggttgcagGGCAGCACAGGTTCCCAGCAGATTGTGATCGAAGGGCCCCTGTGTGAGGACTATTACAAGATTCGTGAGCTTCTTTACTCTCAGTTCTACTTGTTGTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- tcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaatg