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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTAATTGCCTTTAGCATCACTGATCACATGAAGAAGCTCTTTTATTCTGAACAAGGGGTTAATTCTAGgtactgcaaactcccgtttacatacttatagtttctttcatccttcagagttttggaataactccatttgattttctttccacag

Basic information

species Oryza sativa
transcript LOC_Os01g06270.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06270.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G102196_T01 (Zea mays), 5'ss of exon 13
ATTGTAATTGCCTTTAGCATCACTGATCACATGAAGAAGCTCTTTTATTCTGAACAAGGGGTTAATTCTAGgtactg-caaactcccgtt-----tacatacttatagtttctttcatccttcagagttttggaataactccatttgattttctttccacag-------
|| || |||||||| |||||    |||| |||||||||| | ||||||||||| |||| || ||||||||||||||  |  ||||   |      ||| |||| |   | | |||  | |    ||    || | | |  | |      || |  ||   |        
ATCGTGATTGCCTTCAGCATTGTAGATCGCATGAAGAAGATGTTTTATTCTGAGCAAGCGGCTAATTCTAGgtactctctgactcttctcatctctacttactgaatctcttttttgtacccatgatccctgcagttagacaaaccaccttaccctctctatttttcag
















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|9864923|gb|AU100673.1|AU100673
EST:     ACTGATCACATGAAGAAGCTCTTTTATTCTGAACAAGGGNTTAATTCTAG                         GAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
genomic: ACTGATCACATGAAGAAGCTCTTTTATTCTGAACAAGGGGTTAATTCTAGgtactgcaaa ... ctttccacagGAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
EST: gi|88563880|gb|CI494597.1|CI494597
EST:     TGATCACATGAAGAAGCTCTTTTATTCTGAACAAGGGGTTAATTCTAG                         GAGGGATGATGAGGACGTCAGGGAACTTATTTTCTGAGATAGAGAAACTTA
genomic: TGATCACATGAAGAAGCTCTTTTATTCTGAACAAGGGGTTAATTCTAGgtactgcaaa ... ctttccacagGAGGGATGATGAGGACGTCA-GGAACTTATTTTCTGAGATAGAGAAACTTA
EST: gi|88461547|gb|CI504674.1|CI504674
EST:     CAAGGGGTTAATTCTAG                         GAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
genomic: CAAGGGGTTAATTCTAGgtactgcaaa ... ctttccacagGAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
EST: gi|88562561|gb|CI493278.1|CI493278
EST:     TATTCTGAACAAGGGGTTAATTCTAG                         GAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
genomic: TATTCTGAACAAGGGGTTAATTCTAGgtactgcaaa ... ctttccacagGAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
EST: gi|88563510|gb|CI494227.1|CI494227
EST:     GGGGTTAATTCTAG                         GAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
genomic: GGGGTTAATTCTAGgtactgcaaa ... ctttccacagGAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
EST: gi|88285839|gb|CI512496.1|CI512496
EST:     ATTCTGAACAAGGGGTTAATTCTAG                         GAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
genomic: ATTCTGAACAAGGGGTTAATTCTAGgtactgcaaa ... ctttccacagGAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
EST: gi|27547499|gb|CA765726.2|CA765726
EST:     ACAAGGGGTTAATTCTAG                         GAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
genomic: ACAAGGGGTTAATTCTAGgtactgcaaa ... ctttccacagGAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
EST: gi|88568935|gb|CI499652.1|CI499652
EST:     CATGAAGAAGCTCTTTTATTCTGAACAAGGGGTTAATTCTAG                         GAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG
genomic: CATGAAGAAGCTCTTTTATTCTGAACAAGGGGTTAATTCTAGgtactgcaaa ... ctttccacagGAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAG

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: 53 (upstream exon), 65 (downstream exon)
Score: 15

ATTGTAATTGCCTTTAGCATCACTGATCACATGAAGAAGCTCTTTTATTCTGAACAAGGGGTTAATTCTAGgtactgcaaa ... ctttccacagGAGGGATGATGAGGACGTCAGGAACTTATTTTCTGAGATAGAGAAACTTAGAGAGAGATTCGAGTCTGTAGAACGACCGACGTTAGACATTGAAGTCCGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTAATTGCCTTTAGCATCACTGATCACATGAAGAAGCTCTTTTATTCTGAACAAGGGGTTAATTCTAGgtactgcaaactcccgtttacatacttatagtttctttcatccttcagagttttggaataactccatttgattttctttccacag

- - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - AGAAGC