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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtggcaccaacattccatttccgtaactttattattatggtatcaattgtgggtcatgacgagcaattctttctacacatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC

Basic information

species Oryza sativa
transcript LOC_Os02g08544.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
gtacgtggcaccaacattccatttccgtaactttatta--ttatggtatcaattgtgggtcatgac-gagcaattctttctacacatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC
||| ||| ||| |      ||| |   |  | |  | |  || || |||||  |  || ||||  | || | | |||||    |   || ||||||||||||||||| || ||||||||||||||||| || || || ||||| || ||||| |||||||| |||||||||||||| |||||||| |||||||
gtatgtgacactacggcgacatata-attccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
gtacgtggcaccaacattccatttccgtaactttatta--ttatggtatcaattgtgggtcat-gacgagcaattctttctacacatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC
||||||| |||   |    ||  |   |  | |  |||  || || |||||  |  || |||| || |||||| |||||    ||   | |||||||||||||||||| | |||||||||||||||||||| || || |||||||||||||| |||||||||||||||||||| || |||||||| |||||||
gtacgtgacac---cgcgtcaacttaattccctcgttagcttctgctatcaggttcggctcattgatgagcaactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
---gtacgtggcaccaacattccatttccgtaactttattattatggtatcaa----ttgtgggtcatgacgagcaattctttctaca---catattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC
    |||     |   |   | |        || ||||  |||    | |  |    |  |   |  || |   |||||  |||| ||     | ||||||| || || ||||| ||  |||||||||||||||| || || || ||||| ||||| |||||||| || || ||| | ||  | ||||||||||||||||
aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S77_59V6.1 (Physcomitrella patens), 3'ss of exon 5
---gtacgtggcaccaacattccatttccgtaactt----tattattatggtatcaattgtgggtcatgacgagcaattctttct---acaca---tattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC
    ||   || |  |   |||    | |||  |||      ||  ||   |||||       | |  |   | || ||  |||    |||||    | |||||| || || || |  |   |  | ||||| || || ||  | || |||||| ||||||| ||||| || ||||| || || |||||||||||||||||||
tgcataaccggtag-actcttctgaatgcgtggcttatgacgtttctagcatatcatcaaaacgcccagt--aacattttgttccgggacacaatgcaatcagGAGGATGAGAAAGAACAATTAATACAGGAGACAGGATTGGAGCTCAAGCAAGTCAACAACTGGTTTATAAACCAGCGAAAGCGAAACTGGCATAGCAACC

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S154_83V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------gtacgtggcaccaacattccatttccgtaactttattattatggtatcaat-tgtgggtcatgacgagcaattctttctacacatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC
                                                                ||||     ||  |||||||||   ||  | |||     |  |    |  ||  | |  |  |       | || |    |  |  ||||| || || ||||  || ||| | ||||| || || ||  || |||||||| | || ||||||||||| ||||||||||| || |||||||| ||||| |
gtatcaaaaaattcatcaggaatcctgaactacgtatatccattcatgctttatgttctagttcacgtaatttcagaattccatttatatatatatatatacgtattggtgacatgctgatttttccacctctgttttgcactcctcaaccagGAGGATGAAAAGGAGCGGCTGATTCAGGAGACAGGTTTGGAATTGAAGCAAGTGAATAATTGGTTCATAAACCAACGCAAGCGGAACTGGCACAGCAATC

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ05363 (Selaginella moellendorffii), 3'ss of exon 4
gtacgtggcaccaacattccatttccgtaactttat-tattatggtatcaattgtgggtcatgacgagcaattctttctacacatatt-cagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC
                          || | || |   ||| |   | || |  ||| ||||  ||| |    ||   || | || |  ||||| ||||| ||||| || ||||| || || || ||| |  | || |||||||||||||| |||||||| ||||| ||||| || ||||||||   | |||
--------------------------gtgagttcacgcattct--cagcattgctggatcat--cgatct-cactaggtagagatgtggcagGAGGACGAGAAGGCGCGGCTGGTCCAAGAGACCGGGCTGGAGCTCAAGCAAATCAACAACTGGTTCATCAACCAGCGCAAGCGCAACTGGCACCACCACC

upper sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ06200 (Selaginella moellendorffii), 3'ss of exon 4
gtacgtggcaccaacattccatttccgtaactttat-tattatggtatcaattgtgggtcatgacgagcaattctttctacacatatt-cagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC
                          || | || |   ||| |   | || |  ||| ||||  ||| |    ||   || | || |  ||||| ||||| ||||| || ||||| || || || ||| |  | || |||||||||||||| |||||||| ||||| ||||| || ||||||||   | |||
--------------------------gtgagttgacgcattct--cagcattgctggatcat--cgatct-cactaggtagagatgtggcagGAGGACGAGAAGGCGCGGCTGGTCCAAGAGACCGGGCTGGAGCTCAAGCAAATCAACAACTGGTTCATCAACCAGCGCAAGCGCAACTGGCACCACCACC

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|29670827|gb|CB667102.1|CB667102
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
EST: gi|29640689|gb|CB645698.1|CB645698
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
EST: gi|29663726|gb|CB660001.1|CB660001
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
EST: gi|87016643|gb|CI275645.1|CI275645
EST:     CTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
EST: gi|29661445|gb|CB657720.1|CB657720
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAA
EST: gi|88302049|gb|CI667895.1|CI667895
EST:     CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACT                         GAAGACGACAAGGCCCGCCTGGTGCAG
genomic: CTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggca ... acatattcagGAAGACGACAAGGCCCGCCTGGTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattatggtatcaattgtgggtcatgacgagcaattctttctacacatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC
         tatcaatt  TA-rich tract