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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttgattggtccatctctggaaatcagattgcggactattttgctgtccaaattattttctgctgtgatattatttactgagtttcttccattctccagTACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAAAAAGGCTCCATGTACCCGTTCCGAAATATGGATGATCGAGAAAGGTTCC

Basic information

species Oryza sativa
transcript LOC_Os01g67250.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67250.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G093119_T01 (Zea mays), 3'ss of exon 9
-agttgattggtccatctctggaaatcagattgcggactattt-tgctgtccaaattattttctgctgtgatattatttactgagtttcttccattctccagTACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAAAAAGGCTCCATGTACCCGTTCCGAAATATGGATGATCGAGAAAGGTTCC
    ||  ||     |   ||    || |    |     |||  |||| ||||||  |  || || | ||| | |   |    | | |||| | ||||||||||| |||||||| |||||||||| ||||||||||||| |||||||||||||||| |||||||| || |||||||||||||||||||| ||||||||||| 
tgtgtgtgtgcctgctgaatgagtctctgcacacaattaattaatgctttccaaaacaagttttg-tatgacacttggtgacca-tctctttccttctccagTACTATACGGCAACAGTTGATCAACACTGAGGATATACGGCGCATTCGTAAAAAAGCTCCATGCACTCGTTCCGAAATATGGATGATTGAGAAAGGTTCA

upper sequence: LOC_Os01g67250.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G421829_T01 (Zea mays), 3'ss of exon 9
------agttgattggtccatctctggaaatcagattgcggactattttgctgtccaaattattttctgctgtgatattatttactgagtttcttc-cattctccagTACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAAAAAGGCTCCATGTACCCGTTCCGAAATATGGATGATCGAGAAAGGTTCC
      || || |   | | |||||| ||  ||  |   | |      |||| |||||| ||  ||||| |||||   || || ||||   ||||  | ||||||||||| |||||||| ||||||||||  |||||||||||| ||||||||||||||||||||||||| || |||||||||||||||||||| ||||||||||| 
atgtagagatgctgaatgcgtctctgcaag-caattaatgaa------tgctttccaaaataacttctggtgtgagtatacttgctgaccgtcttttctttctccagTACTATACGGCAACAGTTGATCAATACTGAGGATATACGGCGCATTCGTAAAAAGGCTCCATGCACTCGTTCCGAAATATGGATGATTGAGAAAGGTTCA
















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|58610682|gb|CK038394.1|CK038394
EST:     ACACCGAAGAGAAAAGTGCAAATGGATGATGCCATGGTTATACATGCTGA                         TACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAA
genomic: ACACCGAAGAGAAAAGTGCAAATGGATGATGCCATGGTTATACATGCTGAgtatgtatac ... cattctccagTACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAA
EST: gi|58656617|gb|CK045297.1|CK045297
EST:     ACACCGAAGAGAAGGGTGCAAATGGATGATGCCATGGTTATACATGCTGA                         TACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAA
genomic: ACACCGAAGAGAAAAGTGCAAATGGATGATGCCATGGTTATACATGCTGAgtatgtatac ... cattctccagTACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAA
EST: gi|58590475|gb|CF988783.1|CF988783
EST:     ACACCGAAGAGAAAAGTGCAAATGGATGAGGCCATGGTTATACATGCTGA                         TACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAA
genomic: ACACCGAAGAGAAAAGTGCAAATGGATGATGCCATGGTTATACATGCTGAgtatgtatac ... cattctccagTACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAA
EST: gi|29625771|gb|CB630782.1|CB630782
EST:     GAAAAGTGCAAATGGATGATGCCATGGTTATACATGCTGA                         TACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAA
genomic: GAAAAGTGCAAATGGATGATGCCATGGTTATACATGCTGAgtatgtatac ... cattctccagTACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAA

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: 75 (upstream exon), 72 (downstream exon)
Score: 26

CACCTAAGACGTCATCTTTGAAACGTCCAAGGTTGACGTCAAAGAGTACCACACCGAAGAGAAAAGTGCAAATGGATGATGCCATGGTTATACATGCTGAgtatgtatac ... cattctccagTACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAAAAAGGCTCCATGTACCCGTTCCGAAATATGGATGATCGAGAAAGGTTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtccaaattattttctgctgtgatattatttactgagtttcttccattctccagTACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAAAAAGGCTCCATGTACCCGTTCCGAAATATGGATGATCGAGAAAGGTTCC
                                      tttcttccattctcc  CT-rich tract
                   tgtgatattattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttgattggtccatctctggaaatcagattgcggactattttgctgtccaaattattttctgctgtgatattatttactgagtttcttccattctccagTACCATACGGCAGCAGTTGATCAGCACTGAGGATATAAGGCGCATTCGTAAAAAGGCTCCATGTACCCGTTCCGAAATATGGATGATCGAGAAAGGTTCC

- ttgattg
- - - - -gtccatc
- - - - - - - - - - - - - - - - - - - - - tgctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactga