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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacaattgcactggtcttaataatataggggtaggacatgctcatatacttcaaattaaattcccatgacctgaagcacatttgattgctctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAGAAGATGTTTGAAAAGCAATGTAAATCCAGCACACAGAGTGTGCAGGATC

Basic information

species Oryza sativa
transcript LOC_Os03g21240.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21240.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G006477_T01 (Zea mays), 3'ss of exon 7
ctacaattgcactggtcttaataatataggggtaggac--atgctcatatacttcaaattaaattc-ccatgacctgaagcacatttg-attgctctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAGAAGATGTTTGAAAAGCAATGTAAATCCAGCACACAGAGTGTGCAGGATC
    ||  | || || | |||     |  |   |  |   ||  | ||     | ||  |   ||   | | ||   |   | || |  ||| || |||||||||||||| | ||||||||| | || |||||||| ||||| || |||||||||| |||||||||||||||  || |||| |||||  |||  || |||||||
----aaacgaacgggccctaagtgattttgcccaacattaatattaatgccaatgaagcttgctttatcctaacactatatatatatatattcctatattgcagATTCAGCGAAAATTGCAGTTGCGGATTGAAGAGCAAGGAAAGTATCTGCAGATGATGTTTGAAAAGCAGAGTCAATCGAGCACGGAGAAAGTCCAGGATC

upper sequence: LOC_Os03g21240.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0005g04120.t01 (Vitis vinifera), 3'ss of exon 7
-ctacaattgcactggtcttaataatataggggtaggacatgctcatatacttcaaattaaattcccatgacctgaa-gcacatttgattgctct----attgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAGAAGATGTTTGAAAAGCAATGTAAATCCAGCACACAGAGTGTGCAGGATC
   ||||    ||  |  |  ||| |||| |  ||    |   |   ||| |    | |  ||  ||||||  |  | | |   ||| |  || |     | |||||| || || || || ||||| ||||| ||||||||||||| ||| || || | ||||||||| |||||||| |||||  | |   | |   || ||    
tacacaaagagacatgcatatata-tataagcataaag-agaattgcatatt----agttcatatccatgatttttatgtaatattggtaactttcatggtcgcagATACAAAGAAATTTACAGCTGCGAATAGAAGAACAAGGGAGATACCTCCAAATGATGTTTGAGAAGCAATGCAAATCAGGAATTGACAAGCTGAAGACAT
















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|86436761|gb|CI118483.1|CI118483
EST:     CACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAG                         ATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
genomic: CACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAGgtactaattc ... tctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
EST: gi|86502166|gb|CI144799.1|CI144799
EST:     TTCATGAACAACTCGAG                         ATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
genomic: TTCATGAACAACTCGAGgtactaattc ... tctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
EST: gi|29624851|gb|CB629862.1|CB629862
EST:     CACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAG                         ATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
genomic: CACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAGgtactaattc ... tctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
EST: gi|29672928|gb|CB669203.1|CB669203
EST:     CACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAG                         ATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
genomic: CACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAGgtactaattc ... tctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
EST: gi|88828554|gb|CI073424.1|CI073424
EST:     CACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAG                         ATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
genomic: CACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAGgtactaattc ... tctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
EST: gi|86597934|gb|CI276720.1|CI276720
EST:     CACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAG                         ATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG
genomic: CACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAGgtactaattc ... tctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAG

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: 70 (upstream exon), 66 (downstream exon)
Score: 43

GAGCATGGATCTTACTGAAGCACTGCGCCTTCAGATGGAAGTTCAGAAGCGCCTTCATGAACAACTCGAGgtactaattc ... tctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAGAAGATGTTTGAAAAGCAATGTAAATCCAGCACACAGAGTGTGCAGGATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacttcaaattaaattcccatgacctgaagcacatttgattgctctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAGAAGATGTTTGAAAAGCAATGTAAATCCAGCACACAGAGTGTGCAGGATC
                                   atttgat  putative branch site (score: 43)
                                         ttgctct  CT-rich tract
     ttcaaattaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacaattgcactggtcttaataatataggggtaggacatgctcatatacttcaaattaaattcccatgacctgaagcacatttgattgctctattgcagATTCAGAGGAAATTGCAGCTTCGAATTGAAGAACAAGGGAAATATCTGCAGAAGATGTTTGAAAAGCAATGTAAATCCAGCACACAGAGTGTGCAGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - -tgcactg
- - - - - - - - - - - - - - - - - - -catgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgc