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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctaatttgtcacacgcatcctgtccatttccctgccttactggtgaccaagctttcatactccaggattgttaatatcatggtatttctcacctgcagATACAGTCGCCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACACTTACATGATGCGCACCTAAATCTGAGCACTGATATGGCTTTGCATATA

Basic information

species Oryza sativa
transcript LOC_Os05g05260.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G097605_T01 (Zea mays), 3'ss of exon 9
-ttctaatttgtcacacgcatcctgtccat-ttccctgccttactggtgaccaagctt-tcatactccaggattgttaatatcatggtatttctcacctgcagATACAGTCGCCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACACTTACATGATGCGCACCTAAATCTGAGCACTGATATGGCTTTGCATATA
 |  | ||||       || |  |||  || |||  ||      || | |       | | |  |  ||   || ||  ||  ||    ||  |    | |||||||||||| |||||||||||||| ||  |||||||||||||||| || || || |||||||||||||||||||||||||||||||||||| | ||||||
gtgttcattttcttggtgcgt--tgttaatgttctatgtgaagttgttaattttctatgtgaagcgtcacatttcttggtaa-attcctttctttctttacagATACAGTCGGCATGATAAACGGTCCAAGTTGCCTGGGTGGATACTCTCGCATTTGCATGATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATA

upper sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 10
ttctaatttgtcacacgcatcctgtccatttccctgccttactggtgaccaagctttcatactccaggattgttaat-----atcatggtatttctcacctgcagATACAGTCGCCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACACTTACATGATGCGCACCTAAATCTGAGCACTGATATGGCTTTGCATATA
   | |||  || ||   ||  | |    |||      |  ||  ||||   | | | | | |  |   |  |  ||      | ||    | |     |||||| || ||||||||||| ||||| || ||| ||||| | |||||||| || |||||||||||||| ||||| ||  ||||||| || |||||||||||||||
---tgattgctc-catttatggttttggcttctacttttctcta-tgacagtgttctgacagtaaatagtaatacattgttggttataacttctgcactctgcagGTATAGTCGCCATGACAAACGTTCAAAATTGCCTAGTTGGATACTATCTCACTTACATGATGCCCACCTGAACTTGAGCACAGACATGGCTTTGCATATA

upper sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 10
-----ttctaatttgtcacacgcatcctgtccatttccctgccttactggtgaccaagctttcatactccaggattgttaatatcatggtatttctcacctgcagATACAGTCGCCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACACTTACATGATGCGCACCTAAATCTGAGCACTGATATGGCTTTGCATATA
       |  |   |  ||||  ||  | | | ||    ||  ||| |  ||  ||   ||  ||  || |  | |   | |   || |    |   || ||||||||||| || |||||||| ||||| ||||| ||||| |||||||| || ||  | | |||||| ||| | ||||| ||||||||||||||| | || || 
cgtaggacagaagagagacacagata-tatgc-ttatgttggttta-taatg-tcacatttctatggtctaacaatac-actgcaattgatggtaaaacttgcagATACAGCCGTCATGATAAGCGGTCCAAACTACCTGGTTGGATACTTTCGCATCTGCGTGATGCACACTTGAATCTAAGCACTGATATGGCTATTCACATT

upper sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 10
--ttctaatttgtcacacgcatcctgtccatttccctgccttactggtgaccaagctttcatactccaggattgttaatatcatggt--atttctcacctgcagATACAGTCGCCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACACTTACATGATGCGCACCTAAATCTGAGCACTGATATGGCTTTGCATATA
    || |   |  | |     |   |   ||     |   || |  | |     ||||  |||||    | |  | || | |||||  | |   |   ||||| |||||||| ||||||||||| |||||| ||||||||||||| |||||||| |||| |||||| ||||| ||| |||||||||| |||||||||||||| 
agccctgagacgagatatttcccaaatgtgttatttggagataatt-tcattcgtcttttttactc--ataatacttatgt-atggtcaactgaacttgtgcagGTACAGTCGTCATGATAAACGCTCTAAATTGCCTGGGTGGATTCTGTCACATTTACGTGATGCACACCTGAATTTGAGCACTGACATGGCTTTGCATATT

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|25799157|gb|CA755118.1|CA755118
EST:     GTGATCCGTTCTAAAGCAGATTATGGAATGATGATATTTGCTGACAAGAG                         ATACAGTCGCCATGATAAACGGTCTAAACTGCCTGNGTGGATACTGTCACA
genomic: GTGATCCGTTCTAAAGCAGATTATGGAATGATGATATTTGCTGACAAGAGgtacttgatc ... tcacctgcagATACAGTCGCCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACA
EST: gi|218486391|gb|FG950822.1|FG950822
EST:     GTGATCCGTTCTAAAGCAGATTATGGAATGATGATATTTGCTGACCAGAG                         ATACAGTCGCCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACA
genomic: GTGATCCGTTCTAAAGCAGATTATGGAATGATGATATTTGCTGACAAGAGgtacttgatc ... tcacctgcagATACAGTCGCCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaccaagctttcatactccaggattgttaatatcatggtatttctcacctgcagATACAGTCGCCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACACTTACATGATGCGCACCTAAATCTGAGCACTGATATGGCTTTGCATATA
                                          ttctcac  putative branch site (score: 2)
                                         tttctcacct  CT-rich tract
                       attgttaatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctaatttgtcacacgcatcctgtccatttccctgccttactggtgaccaagctttcatactccaggattgttaatatcatggtatttctcacctgcagATACAGTCGCCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACACTTACATGATGCGCACCTAAATCTGAGCACTGATATGGCTTTGCATATA

- - - - - - - - gcatcct
- - - - - - - - - - - - - - - -ccctgcc
- - - - - - - - - - - - - - - - - - - - -ctggtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccagg