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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCATGGGCGTCGAGCAGGACGGCAAGTTCAGCATGACGAGCCTCCTGTGGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaaccacgaacgacctcgtcatgcctctcgctcacatttcgtttggaattttgcag

Basic information

species Oryza sativa
transcript LOC_Os05g37470.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g37470.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G067022_T02 (Zea mays), 5'ss of exon 1
-GGCCATGGGCGTCGAGCAGGACGGCAAGTTCAGCATGACGAGCCTCCTGTGGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaaccacga-acg---acctcgtcatgcctctcgctcacatttcgtttggaattttgcag------------------------------------
 |   |   ||  || | | | ||||||| ||||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  |   ||||  |||    |  || |  |  |         |  |||  ||||   | ||                                      
CGCTGAGCAGCAGCGCG-ACGGCGGCAAGGTCAGCATGAAGAGCCTGCTGTGGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgcacgggcacggcacgctagctgcggccggtgtgctagagtaacgtcgcatggaggatcgcgcgctcacgcggtggcgtgtttcggcgttcgtccgcag

upper sequence: LOC_Os05g37470.3 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S90_46V6.1 (Physcomitrella patens), 5'ss of exon 1
GGCCATGGGCGTCGAG-CAGGACGGCAAGTTCA-GCATGACGAGCCTCCTGTGGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaaccacgaa--cgacctcgtcatgc-ctctcgctcacatttcgtttggaat--tttgcag---------------------------------
    |||| | |   | |  | |    |||      |||| | |||| || ||||| || |||||||||||||| ||||||||||||  |||||||||||||||    |||  ||| |     | ||||  ||||  |||| ||| ||||||    |  |   |||||||                                 
--GGATGGCCCTTACGACGTGTCCATGAGTGGGCAGATGAAGCGCCTGCTTTGGCATGGTGGCTCCGTCTGGGATGCCTGGTTCAGCGCCGCCTCCAACCAGgtcattccattcaccatgctcagctcga-atgcattctcactcccatttccaacgacacactttgcagtagtatccaacgagattgcttgcatccgatttc

upper sequence: LOC_Os05g37470.3 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S211_67V6.1 (Physcomitrella patens), 5'ss of exon 1
GGCCATGGGCGTCGAGCAGGA-CGGCAAGTTCAGC-ATGACGAGCCTCCTGTGGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgta----------cgaccaaccacgaac----gacctcgtcatgcctct-cgctcacatttcgtttggaattttgcag----------------------
    | || | ||  |  |   ||   |||  |   |||| | | ||||||||||| ||||||||||||||||| ||||||||||||  ||| |||||||||||           || ||| |  |  |      |     | ||  |||| | ||||| |||           ||                          
--AGAGGGCCCTCACGATGTCTCGATGAGTGGAAAGATGAAGCGGCTCCTGTGGCATGGCGGCTCCGTCTGGGATGCCTGGTTCAGCGCCGCGTCCAACCAGgtgatcattcttccggccagcagcagatcgaaaaatggattatagctctactctcacctttaaaccaatgccttatgatgggcggctgatgggaattctc

upper sequence: LOC_Os05g37470.3 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ18760 (Selaginella moellendorffii), 5'ss of exon 1
GGCCATGGGCGTCGAGCAGGACG-GCAAGTTCAGCATGACGAGCCTCCTGTGGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgacc---aaccacgaacgacctcgtcatgcct--ctcgctcacatttcgtttggaattttgcag--------------------------------
 |    |   || ||  |   |  || || ||  |   | ||  ||||| |||||||| || |||||||  || || ||||| ||||||||||||||||||||  |       | | | || |||| |  | | | |      ||  |||  | |       |||||                                  
AGATGGGCTTGTGGATAACTCCATGCGAGCTCT-CGCCAAGAAGCTCCTCTGGCACGGTGGATCCGTCTACGATGCTTGGTTTAGCTGCGCCTCCAACCAGgtgagtagtgagagctcaaaagaccactcctttcttgctcttcttgcatagcttccccgcctttgcttcgattccttccactcgcagtataaaaaccaaa

upper sequence: LOC_Os05g37470.3 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ36050 (Selaginella moellendorffii), 5'ss of exon 1
GGCCATGGGCGTCGAGCAGGACG-GCAAGTTCAGCATGACGAGCCTCCTGTGGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacg-accaa-----ccacgaacgacctcgtcatgcctctcgctcacatttcgtttggaattttgcag-------------------------------
 |    |   || ||  |   |  || || ||  |   | ||   |||| |||||||| || |||||||  || || ||||| ||||||||||||||||||||  | |   |     | | ||||   |   || |||   ||   || |  |     |   ||     |                               
AGATGGGCTTGTGGATAACTCCATGCGAGCTCT-CGCCAAGAAGTTCCTCTGGCACGGTGGATCCGTCTACGATGCTTGGTTTAGCTGCGCCTCCAACCAGgtgagtagtgagagctcaaagaacactcctttcttgctcttcttgcatagcttccccgcgtttgcttcgattccttccagtcgcagtataaaaaccaaag

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|88585887|gb|CI703558.1|CI703558
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88371817|gb|CI680927.1|CI680927
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88583175|gb|CI700640.1|CI700640
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTANTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88579751|gb|CI691736.1|CI691736
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88578093|gb|CI674724.1|CI674724
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88401031|gb|CI685010.1|CI685010
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCACCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGNCGTANTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88583386|gb|CI700863.1|CI700863
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|95100978|gb|CI692704.1|CI692704
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88394229|gb|CI684904.1|CI684904
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88313368|gb|CI671479.1|CI671479
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88468865|gb|CI696867.1|CI696867
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88593124|gb|CI711280.1|CI711280
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88419567|gb|CI686784.1|CI686784
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
EST: gi|88584222|gb|CI701761.1|CI701761
EST:     GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAG                         GTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG
genomic: GGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaa ... aattttgcagGTGGCGCAGGTGCTCCTGACGCTGCCGTACTCCTTCTCGCAGCTCGGGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCATGGGCGTCGAGCAGGACGGCAAGTTCAGCATGACGAGCCTCCTGTGGCACGGCGGCTCCGTCTGGGACGCCTGGTTCAGCTGCGCCTCCAACCAGgtacgaccaaccacgaacgacctcgtcatgcctctcgctcacatttcgtttggaattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC