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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaatgacttgtttcaagtgtatctaatggtttagtgtggatttttttctccgtctttatggctcttgttgatatttgttcattgttttgtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAACATGTGCATCCAGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g29409.1
intron # 6
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|86260139|gb|CI066012.1|CI066012
EST:     AGTACCTTGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAG                         GTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
genomic: AGTACCTTGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAGgtagttccaa ... gtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
EST: gi|88199516|gb|CI199366.1|CI199366
EST:     CATTGTTCTTAACAAGCTCGAGAGAAAAATCGAG                         GTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
genomic: CATTGTTCTTAACAAGCTCGAGAGAAAAATCGAGgtagttccaa ... gtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
EST: gi|29617638|gb|CB622650.1|CB622650
EST:     AGTACCTTGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAG                         GTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
genomic: AGTACCTTGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAGgtagttccaa ... gtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
EST: gi|29618956|gb|CB623968.1|CB623968
EST:     AGTACCTTGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAG                         GTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
genomic: AGTACCTTGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAGgtagttccaa ... gtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
EST: gi|86882808|gb|CI327409.1|CI327409
EST:     ACAAGCTCGAGAGAAAAATCGAG                         GTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
genomic: ACAAGCTCGAGAGAAAAATCGAGgtagttccaa ... gtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
EST: gi|86890133|gb|CI321310.1|CI321310
EST:     AGTACC-TGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAG                         GTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
genomic: AGTACCTTGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAGgtagttccaa ... gtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
EST: gi|29689147|gb|CB685422.1|CB685422
EST:     AGTACCTTGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAG                         GTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA
genomic: AGTACCTTGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAGgtagttccaa ... gtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAA

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: 64 (upstream exon), 49 (downstream exon)
Score: 13

AAGAAAGGTCAAATATGTCTATGCGAATGACCTAAACCCCACTGCAGTGGAGTACCTTGAGAGAAACATTGTTCTTAACAAGCTCGAGAGAAAAATCGAGgtagttccaa ... gtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAACATGTGCATCCAGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctccgtctttatggctcttgttgatatttgttcattgttttgtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAACATGTGCATCCAGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTG
                      tgttgat  putative branch site (score: 13)
                                         ttttgtc  putative PPT
                        ttgatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatgacttgtttcaagtgtatctaatggtttagtgtggatttttttctccgtctttatggctcttgttgatatttgttcattgttttgtcgaaccagGTTTTTAACATGGACGCTAGAAGGTTTATCAGTTCAATATACTCAAGCCAACATGTGCATCCAGTCACACAAGTAGTAATGAATTTGCCCAATGATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - tgtttca
- - - - - - - - - gtgtatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttg