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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaccttttgacccaaatacaaatttgccttgaaattcatattgtactctatgggttaattggattttctttgtgaatacagAAACCTTAATCATAACCAATTACAAGGAAATATGACAGATGTCTTTTCCAACCTTCCAAGTTTATCAACACT

Basic information

species Oryza sativa
transcript LOC_Os10g25090.1
intron # 5
splice site 3'
intron type U2

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|88385785|gb|CI566647.1|CI566647
EST:     GCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAAGTTAAGTATTT                         AAAACTTAATCATAAGCAATTA
genomic: GCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCTgtgagtacct ... gtgaatacagAAACCTTAATCATAACCAATTA
EST: gi|6507597|gb|AU064258.2|AU064258
EST:     GCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCT                         AAACCTTAATCANAACCAATTACAAGGAAATATGACAGATGTCTTTTCCAA
genomic: GCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCTgtgagtacct ... gtgaatacagAAACCTTAATCATAACCAATTACAAGGAAATATGACAGATGTCTTTTCCAA
EST: gi|88425544|gb|CI569268.1|CI569268
EST:     GCTGGAAATGTGCCATACTCAATTTCCACACTGC-TAAACTTA-GTATCT                         AATCCTTA-TCATACCCAATTA
genomic: GCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCTgtgagtacct ... gtgaatacagAAACCTTAATCATAACCAATTA
EST: gi|88385459|gb|CI564119.1|CI564119
EST:     GCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCT                         AAACCTTAATCATAACCAATTACAAGGGAAATATGACAGATGTCTTTTCCA
genomic: GCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCTgtgagtacct ... gtgaatacagAAACCTTAATCATAACCAATTACAAGG-AAATATGACAGATGTCTTTTCCA
EST: gi|29631005|gb|CB636014.1|CB636014
EST:     GCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCT                         AAACCTTAATCATAACCAATTA
genomic: GCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCTgtgagtacct ... gtgaatacagAAACCTTAATCATAACCAATTA

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: 47 (upstream exon), 73 (downstream exon)
Score: 13

CAATCTTGCTGGGAACCAGTTTGCTGGAAATGTGCCATACTCAATTTCCACAATGCCTAAACTTAAGTATCTgtgagtacct ... gtgaatacagAAACCTTAATCATAACCAATTACAAGGAAATATGACAGATGTCTTTTCCAACCTTCCAAGTTTATCAACACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgaaattcatattgtactctatgggttaattggattttctttgtgaatacagAAACCTTAATCATAACCAATTACAAGGAAATATGACAGATGTCTTTTCCAACCTTCCAAGTTTATCAACACT
                          ggttaat  putative branch site (score: 13)
                                     ttttctttgt  putative PPT
     aaattcatattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaccttttgacccaaatacaaatttgccttgaaattcatattgtactctatgggttaattggattttctttgtgaatacagAAACCTTAATCATAACCAATTACAAGGAAATATGACAGATGTCTTTTCCAACCTTCCAAGTTTATCAACACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG