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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT

Basic information

species Oryza sativa
transcript LOC_Os06g14540.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G04840.1 (Glycine max), 3'ss of exon 1
gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtgg-cagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
                     |   | ||| ||||||   || ||          ||||||| | | ||   ||  |||  | |||    ||  ||   | |   | | | || |  |   ||||||||| |||  |||||||||||||||||||| || ||| | ||||||||||| ||||||||||||||| ||||| |  |||||||| |  ||||||| |
--------------------gtaagtttct-tgttctgttatgaa----------aatgtag-attgatagagaatatgatgatga----ttaatgaggtaggcacattgtgttgtttactcagGTGGACTTGAGTGGAGGGTACTACGACGCCGGGGATAACATAAAGTTCGGGTTTCCGATGGCGTTCACGACGACGATGCTGTCGTGGAGCGTGATCGATT

upper sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
                                    ||   ||  |  | ||||   || |   |||||   |     |    ||| | ||  |  |  ||||    ||   |    |  ||||||||| |||  |||||||||||||||||||| |||||| | ||||||||||| |||||||||||| || ||||  |  |||||||| |  ||||||| |
-----------------------------------gtaa-gtttttctgttttgttctgaaagggtaata--ggtagagaaaatgatgattaatgaggttggtacattgtgtttttttctcagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT

upper sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
                         |   |||  ||||    |||      || |||  |  |  |  |  | |     || || ||  || |       |  |   |  |      |  ||||| ||| |  | || || |||||||||||||| |||||| | |||||||| || ||||||||||||||  | ||| |  | || ||| |  | ||||| |
------------------------gtaagtctactcta---ctaacatacatttcaaacttctccttcttctaa-----tctctaacttttcc-------gacgatatttca-aaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT

upper sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgca---atgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
                              |   | | |   ||    |  | ||  |     |||  |      | |  |||  |     | | | | |    ||  ||  | |   |      ||||  | | ||| |     | | |   ||||| ||  |||  ||||||||||||||||| || |||||||| ||||||||| | || ||||| ||||  |   |  |  |||| |||||   | | || |
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttg--acgatggtggactcttgtg---cagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT

upper sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
                                       | |||      |||||       | | |||| |     ||| | | ||    | |      | | |  |  ||  ||    |||||| | || |||||||| ||||||||  | ||||||||||| ||||| || ||||||||||||||||||   |||||  |||||||| |  || | || |
------------------------------------gtaccttagaatcttttgc---tcgtttgaaatgtttttcttgtggtttac---ctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT

upper sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ08014 (Selaginella moellendorffii), 3'ss of exon 1
gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
                                      | |  | |    | |         | | |||| |     ||| | | ||    | |      | | |  |  ||  ||    |||||| | || |||||||| ||||||||  ||||||||||||| ||||| || ||||||||||||||||||   |||||  |||||||| |  || | || |
--------------------------------------gtacca-tagaatcttttgctcgtttgaaatgtttttcttgtggtttac---ctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCCGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT

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|58686981|gb|CK075668.1|CK075668
EST:     GCCTCCGCTGGCGCCGTGACTCCGCCCTCAACGACGGCGCCACCGCCGGC                         GTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGTGACTCCGCCCTCAACGACGGCGCCACCGCCGGCgtacggacca ... ggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
EST: gi|58672594|gb|CK061280.1|CK061280
EST:     GCCTCCGCTGGCGCCGTGACTCCGCCCTCAACGACGGCGCCACCGCCGGC                         GTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGTGACTCCGCCCTCAACGACGGCGCCACCGCCGGCgtacggacca ... ggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
EST: gi|58670346|gb|CK059032.1|CK059032
EST:     GCCTCCGCTGGCGCCGTGACTCCGCCCTCAACGACGGCGCCACCGCCGGC                         GTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGTGACTCCGCCCTCAACGACGGCGCCACCGCCGGCgtacggacca ... ggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
EST: gi|58656909|gb|CK045589.1|CK045589
EST:     GCCTCCGCTGGCGCCGTGACTCCGCCCTCAACGACGGCGCCACCGCCGGC                         GTGGACCTGACGGCAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: GCCTCCGCTGGCGCCGTGACTCCGCCCTCAACGACGGCGCCACCGCCGGCgtacggacca ... ggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
EST: gi|58652631|gb|CK041311.1|CK041311
EST:     CCTCCGCTGTGCGCCGTGACTCCGCCCTCAACGACGGCGCCACCGCCGGC                         GTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG
genomic: CCTCCGCTG-GCGCCGTGACTCCGCCCTCAACGACGGCGCCACCGCCGGCgtacggacca ... ggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
            cgctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT