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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgtacgcaggctttagcattcttctaagtatttcgcttttactttgcaattgtggacgtgagggaaatttgttgtag

Basic information

species Oryza sativa
transcript LOC_Os03g18310.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 19
ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgtacgcaggctttagcattcttctaagtatttcgctttt---actttgcaattgtggacg--tgagggaaatttgttgtag--
| |||||||||| || ||||| |||||||| ||||||||||||||||| |||||| |||||||||||   | |   ||||||| |  |   | | |  |||||   ||   || ||||  || |  ||||   ||| |  ||||   
ACTAGAACCTGTGATAATTGAACTTGAACGACAGCGTGCTCCAGTTGTAGTCATAGCTCACCAGgta-ataaggactagcattgtcattcttctgttccttttgataccaagccattgcagatgcctgagaagaatattctgtatag

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA14G37520.1 (Glycine max), 5'ss of exon 32
ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgta--cgcaggctttag---------cattcttctaagtatttcgcttttactttgcaattgtggacgtgagggaaatttgttgtag
 |||||||||||||||||||||||||| || || || || || |||||||| ||||||||||||||   | || |   |||             ||| ||  |      ||     |      || |     |   |    ||  ||  ||
GTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAGgttttcacatgaactagatgtaaacttgcccttttatatgccctcctacggttgacttgttctaattcttgagtttgttcattacag

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 22
ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgt---acgcaggct-ttagcattcttctaagtatttc--gcttttactttgc-aattgtggacgtgagggaaatttgtt-gtag--------------
|||||||||||||||||| |||||||| || || || || || |||||||| ||||||||||||||   | ||| |   |||   | | |  | |  | |   |  ||||  | |   | |||     |  | ||  ||| |   ||               
ATTAGAACCTGTAATTATAGAGCTTGAGCGCCAACGAGCACCTGTTGTTGTGATATCTCACCAGgttgtatgcaagtcattaagctacattcatgcttgtaaagactttatatggttgactgttctaatccgtgaggtttttccatacgtttcacattgcag

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 21
ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgta--cgcaggctttag---------cattcttctaagtatttcgcttttactttgcaattgtggacgtgagggaaatttgttgtag
 |||||||||||||||||||| ||||| || || || || || |||||||| ||||||||||||||   | || |  ||||             ||| ||         || |   |      || |     |   |    ||  ||  ||
GTTAGAACCTGTAATTATTGAACTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAGgttttcacatgacttagatgtaaacttgcccttgtataggccctactatggttgatttgttttaattcttgagtttgttcattacag

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 28
ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgt---acgcaggct-ttagcattcttctaagtatttc--gcttttactttgc-aattgtggacgtgagggaaatttgtt-gtag--------------
|||||||||||||||||| |||||| | || || || || || |||||||| ||||||||||||||   | ||| |   |||   | | |  | |  | |   |  ||||  | |   | |||     |  | ||  ||| |   ||               
ATTAGAACCTGTAATTATAGAGCTTAAGCGCCAACGAGCACCTGTTGTTGTGATATCTCACCAGgttgtatgcaagtcattaagctacattcatgcttgtaaagactttatatggttgactgttctaatccgtgaggtttttccatacgtttcacattgcag

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 23
ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgt---acgcaggc--tttagc---attcttctaagtatttcgcttttac--tttgcaattgtgga-cgtgaggga----aatttgttgtag--------
 ||||||||||||||||| |||||||| || || || || || |||||||| ||||||||||||||   ||||| |   || |||   |||| |    |||      || ||   ||  |  || |    |||||||       |||||||            
-TTAGAACCTGTAATTATAGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAGGttgtacgcaagtcgttaagctaaattcatgcttgtaaagaatttatatggttgactgttctaattcgtgaggtttttcgatttgtttcgcattgcagg

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 20
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 21
ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgt---acgcaggctttagc----attcttctaagtatttcgcttt-tactttgcaattgtggacgtgagggaaatttgttgtag
  | || |||||||| ||||||||||||||||| || || || ||||| || ||||||||||||||   |    |  || | |     ||||| | ||| | | |  || |  || | ||   |  | |||       ||||||||||
GCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAGgttatatattgaattaaacttgtgttcttttcagtttctggtgttgtggttagaaaccttaaaagtgtcattgctttgttgtag

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|25044722|gb|AJ420705.1|AJ420705
EST:     TTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG                         GCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAA
genomic: TTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgtacgcaggc ... tttgttgtagGCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAA
EST: gi|86436870|gb|CI118592.1|CI118592
EST:     TTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG                         GCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAA
genomic: TTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgtacgcaggc ... tttgttgtagGCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAA
EST: gi|58672416|gb|CK061102.1|CK061102
EST:     TTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG                         GCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAA
genomic: TTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgtacgcaggc ... tttgttgtagGCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAA
EST: gi|88269203|gb|CI380501.1|CI380501
EST:     TTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG                         GCTGTGCTAAGAGCACTGTATGCATATTTTGCGGATAAACCACTGGAGGAA
genomic: TTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgtacgcaggc ... tttgttgtagGCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAA
EST: gi|58679011|gb|CK067698.1|CK067698
EST:     TTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG                         GCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAA
genomic: TTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgtacgcaggc ... tttgttgtagGCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 43 (upstream exon), 66 (downstream exon)
Score: 6

ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgtacgcaggc ... tttgttgtagGCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAGgtacgcaggctttagcattcttctaagtatttcgcttttactttgcaattgtggacgtgagggaaatttgttgtag

- - - - - - - - -  GAGCTT