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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgtccatgttcatagctagaaatagctacattttgggacgagcatagcatatcattagttatattatcatgtttagtcgccaacttactttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g15870.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15870.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135816_T01 (Zea mays), 3'ss of exon 5
acttgtccatgttcatagctagaaatagctacattttgggacgagcatagcatatcattagttatattatcatgtttagtcgcc--aacttactttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG
  ||  || |    |  ||||    | |        ||  |   |  | |    | |  |  ||| ||| |   |||  |  |   | ||  || |   ||||||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||| || || ||||||||||
gttttaccgttcctagggctaatggttggaggtcactgttatt-gtgtgggtactaaccaaatat-ttaccgcatttcatgacttgacctccctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG

upper sequence: LOC_Os02g15870.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G135816_T03 (Zea mays), 3'ss of exon 5
acttgtccatgttcatagctagaaatagctacattttgggacgagcatagcatatcattagttatattatcatgtttagtcgcc--aacttactttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG---------------
  ||  || |    |  ||||    | |        ||  |   |  | |    | |  |  ||| ||| |   |||  |  |   | ||  || |   ||||||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||| || || ||||||||||               
gttttaccgttcctagggctaatggttggaggtcactgttatt-gtgtgggtactaaccaaatat-ttaccgcatttcatgacttgacctccctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA

upper sequence: LOC_Os02g15870.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 5
acttgtccatgttcatagctagaaatagctacattttgggacgagcatagcatatcattagttatattatcatgtttagt--cgccaacttacttta--cccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG
    |||   |   |     |    ||    ||  ||  |   |||      |||      || || ||||||||||  |   |    ||| ||||   || |||| || ||||||||||||  ||||||||| ||||| || || || ||||| |||||||| |||||||| || |||||||| | ||
----gtcatagactacttgaaattgtattgccaactttagttaagctatttttatgcggtcttgtaatatcatgtttcttaatgttgcctttcttttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG

upper sequence: LOC_Os02g15870.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G42290.1 (Glycine max), 3'ss of exon 5
acttgtcca-tgttcatagctagaaatagctacattttgggacgagcatagcatatcattagttatattatcatgtttagt--cgccaacttacttta--cccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG
  |  |  | |  |   |  |  |  ||   | | ||| |       ||   ||    |   || || |||||| |||  |   |    ||| | ||    | |||| || ||||||||||||  ||||||||| |||||||| || || ||||| |||||||| || ||||| || |||||||| | ||
-gtcatagactacttgaaattgta--taagcaaactttagttaagctattttatggggtc--ttgtactatcatatttcttaatgttgtctttcctttgttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG

upper sequence: LOC_Os02g15870.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G31955.1 (Arabidopsis thaliana), 3'ss of exon 5
acttgtccatgttca-tagctagaaatagctacattttgggacgagcatagcatatcattagttatattatcatgtttagtcgccaacttacttta---cccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG-----------
    ||   | || | | |||  |  |   |  |          |  | | | |  |  |  || |  | ||    ||       || | ||  |      ||||| || || |||||||||  ||| ||||| ||| |||| |||||||| || || |||||||| ||||| ||||||||||||| ||           
----gtaagtatttagttgcttcatctgattttacgaaccagtcaagaaatctttcctctgtttttcgtttctgtattgacttaaaattcacaatgggtttcagGTGAAGAGAAAGAAAGCTGCACACGCTGGAATGCTTGACATTGCTAAAACAGCTAATAGACCAATGATACACATTGGTGGCTAAGCTCCGGTGAAC

upper sequence: LOC_Os02g15870.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0156g00170.t01 (Vitis vinifera), 3'ss of exon 7
acttgtccatgttcatagc--tagaaatagctaca-ttttgggacgagcatagcatatcattagttatattatcatgtttagtcgccaacttactttacc-cagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG
    | ||| | |||| ||  |  || |  || ||  |||     |  | |  |   || ||   ||     |  |   || |        |  ||  |  ||||| || ||||||||||||   |||||||| |||||||| ||||| ||||| |||||||| || ||||| || |||||||||| ||
----ggccaagatcattgccctgaaattcacttcagctttcaagtgtccttgtctggtctttgcctaatacgtttttcatatttcttgttcttgttggctgcagGTCAAGAGGAAGAAAGCTTCTCATGCTGGAATGTTTGACATTGCAAAGACCGCAAATAGGCCCATGATACATATTGGTGGCTAAG

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|29664100|gb|CB660375.1|CB660375
EST:     TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
genomic: TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtatgtgtag ... ctttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
EST: gi|29687345|gb|CB683620.1|CB683620
EST:     TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
genomic: TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtatgtgtag ... ctttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
EST: gi|29686873|gb|CB683148.1|CB683148
EST:     AATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
genomic: AATAATAAGCGCTGCGgtatgtgtag ... ctttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
EST: gi|86597930|gb|CI276716.1|CI276716
EST:     TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
genomic: TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtatgtgtag ... ctttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
EST: gi|25806204|gb|CA762165.1|CA762165
EST:     TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
genomic: TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtatgtgtag ... ctttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
EST: gi|86493550|gb|CI136183.1|CI136183
EST:     TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
genomic: TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtatgtgtag ... ctttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
EST: gi|29674321|gb|CB670596.1|CB670596
EST:     TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
genomic: TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtatgtgtag ... ctttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
EST: gi|29631794|gb|CB636803.1|CB636803
EST:     TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
genomic: TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtatgtgtag ... ctttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
EST: gi|29675364|gb|CB671639.1|CB671639
EST:     TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCG                         GTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG
genomic: TTCGAGCTGGTGTTGATGATGCTGGACTCAGAGAAATAATAAGCGCTGCGgtatgtgtag ... ctttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagcatatcattagttatattatcatgtttagtcgccaacttactttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG
                                       aacttac  putative branch site (score: 2)
                                         cttacttt  CT-rich tract
      atatcattagttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttgtccatgttcatagctagaaatagctacattttgggacgagcatagcatatcattagttatattatcatgtttagtcgccaacttactttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - gtccatg
- - - - - - - - - - - - - -gctacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcatgt