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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatacaagtgcaacagcatgccgtttcttcactttacaattccctgtagacagaagtaacaaacatcagttcttggggtcttattaaattgttgtgttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATCCTAAACAATGCTGGTGGTGATTCGACAGAAGGATTTTTTGG

Basic information

species Oryza sativa
transcript LOC_Os08g29669.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29669.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G325026_T02 (Zea mays), 3'ss of exon 2
gttatacaagtgcaacagcatgccgtttcttcactttacaattccctgtagacagaagtaacaaacatcagttcttggggtcttattaaattgttgt-----gttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATCCTAAACAATGCTGGTGGTGATTCGACAGAAGGATTTTTTGG
||| ||||| ||      |||  |  ||  || | || |||| |||| |  |   || ||   |   |||  | ||  | |||| | || || |  |     |||||||||||| || ||||||||  ||||||| |||||||||||||| ||||||||||| ||||| |||||||| |||||||| || || || ||||||||
gttgtacaaatg------catttcagtttctcccatttcaatcccctatgcattaaaatagggagattcaaatattttgatcttctaaatttatctttggtggttgaaccagGTCTATGATGTCACTCCTTATGTAGAGGAACATCCAGGCGGAGATGCCATTCTAAATAATGCTGGGGGTGATTCCACGGAGGGCTTTTTTGG

upper sequence: LOC_Os08g29669.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ22166 (Selaginella moellendorffii), 3'ss of exon 1
gttatacaagtgcaacagcatgccgtttcttcactttacaattccctgtagacagaagtaacaaacatcagttcttggggtcttattaaattgttgtgttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATCCTAAACAATGCTGGTGGTGATTCGACAGAAGGATTTTTTGG
                                                     || | |   | |    ||    |    |||    | | | || | ||    |||||||||||||| || || || |||||||| ||||| || || |||  ||| |||||||| ||||||||| |||| || ||||||||||| ||
---------------------------------------------------gtagcattgg-agattctagagggtaaaatctgg--agaatttttttttaccgcagGTTTACGATGTGACTTCGTACGTGGAGGAGCATCCGGGAGGCGATAGCATTCTAAACAACGCTGGTGGTCATTCCACCGAAGGATTTTTCGG

upper sequence: LOC_Os08g29669.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ25784 (Selaginella moellendorffii), 3'ss of exon 1
gttatacaagtgcaacagcatgccgtttcttcactttacaattccctgtagacagaagtaacaaacatcagttcttggggtcttattaaattgttgtgttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATCCTAAACAATGCTGGTGGTGATTCGACAGAAGGATTTTTTGG
                                          |  |  | ||  ||  | | |      ||    |    |||    ||||| || |   |   |||||||||||||| || || || |||||||| ||||| || || |||  ||| |||||||| |||||||||||||| || ||||||||||| ||
-----------------------------------------gtagcattgga--gatttgaaagcttctagagggtaaaatctggagaaattttt-taccg---cagGTTTACGATGTGACTTCGTACGTGGAGGAGCATCCGGGAGGCGATAGCATTCTAAACAACGCTGGTGGTGATTCCACCGAAGGATTTTTCGG

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|88346208|gb|CI634081.1|CI634081
EST:     TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAG                         GTTTACGATGTCACCTCTTATGTGGAGGA
genomic: TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAGgttatacaag ... gttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGA
EST: gi|86255161|gb|CI062066.1|CI062066
EST:     TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAG                         GTNTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
genomic: TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAGgttatacaag ... gttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
EST: gi|55414457|gb|CV726833.1|CV726833
EST:     TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAG                         GTTTACGACGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
genomic: TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAGgttatacaag ... gttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
EST: gi|55430452|gb|CV728171.1|CV728171
EST:     CACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAG                         GTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
genomic: CACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAGgttatacaag ... gttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
EST: gi|88315535|gb|CI615407.1|CI615407
EST:     TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAG                         GTTTACGATGTCACCTCTTATGTGGAGGAACATC-AGGGGGAGATGCCATC
genomic: TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAGgttatacaag ... gttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
EST: gi|29684805|gb|CB681080.1|CB681080
EST:     TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAG                         GTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
genomic: TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAGgttatacaag ... gttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
EST: gi|88575459|gb|CI669604.1|CI669604
EST:     TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAG                         GTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
genomic: TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAGgttatacaag ... gttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATC
EST: gi|88313090|gb|CI592374.1|CI592374
EST:     TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAG                         GTTTACGATGTCACCTCTTATG
genomic: TCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAGgttatacaag ... gttgaaccagGTTTACGATGTCACCTCTTATG

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: 38 (upstream exon), 65 (downstream exon)
Score: 23

ACATTTAGGAGCTATACAAAAGAAGAGATCTCAGCACACAACACAAGGACGGATTGCTGGGTCATCATCAAGGATAAGgttatacaag ... gttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATCCTAAACAATGCTGGTGGTGATTCGACAGAAGGATTTTTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaagtaacaaacatcagttcttggggtcttattaaattgttgtgttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATCCTAAACAATGCTGGTGGTGATTCGACAGAAGGATTTTTTGG
   aagtaac  putative branch site (score: 23)
                            tcttattaaattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatacaagtgcaacagcatgccgtttcttcactttacaattccctgtagacagaagtaacaaacatcagttcttggggtcttattaaattgttgtgttgaaccagGTTTACGATGTCACCTCTTATGTGGAGGAACATCCAGGGGGAGATGCCATCCTAAACAATGCTGGTGGTGATTCGACAGAAGGATTTTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG