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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACATGGGAGAAATCATGTTCGAGACTTTCAACGTGCCAGGATTGTATATCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAGgtagagtttggctattttgggttctttctggtgctcccgtgaatcattgataatggagtcttttgattcgtgaattgataagtgtattgaagtagccctg...

Basic information

species Physcomitrella patens
transcript PP1S85_160V6.1
intron # 3
splice site 5'
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|100404540|gb|BY973629.1|BY973629
EST:     TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAG                         CTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTT
genomic: TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAGgtagagtttg ... ctgaatgcagCTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTT
EST: gi|18351206|gb|BJ183257.1|BJ183257
EST:     TCGCAACTCAAGCAGTGTTAGTTCTAGCAGCTGGCTACACGACCTCCAAG                         CTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTC
genomic: TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAGgtagagtttg ... ctgaatgcagCTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTC
EST: gi|100397452|gb|BY972506.1|BY972506
EST:     TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAG                         CTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTT
genomic: TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAGgtagagtttg ... ctgaatgcagCTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTT
EST: gi|67570355|gb|BJ943179.1|BJ943179
EST:     TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAG                         CTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTT
genomic: TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAGgtagagtttg ... ctgaatgcagCTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTT
EST: gi|100448162|gb|CJ972461.1|CJ972461
EST:     TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAG                         CTGGAAATGACGGGCTTGGTGGTGGATGCCNGGGGATGGAATGACTCANGT
genomic: TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAGgtagagtttg ... ctgaatgcagCTGGAAATGACGGGCTTGGTGGTGGATGCC-GGGGATGGAATGACTCATGT
EST: gi|208359135|gb|DC930467.1|DC930467
EST:     TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAG                         CTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTT
genomic: TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAGgtagagtttg ... ctgaatgcagCTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTT
EST: gi|100440187|gb|BY980439.1|BY980439
EST:     CGCAACTCAAGCAGTGTTAGCTCTAGGCAGCTGGGTACACGACCTCCAAG                         CTGGAAATGACGGG
genomic: CGCAACTCAAGCAGTGTTAGCTCTAG-CAGCTGGCTACACGACCTCCAAGgtagagtttg ... ctgaatgcagCTGGAAATGACGGG
EST: gi|100365851|gb|BY967178.1|BY967178
EST:     TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAG                         CTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTT
genomic: TCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAGgtagagtttg ... ctgaatgcagCTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTT

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: 33 (upstream exon), 34 (downstream exon)
Score: 9

ATACATGGGAGAAATCATGTTCGAGACTTTCAACGTGCCAGGATTGTATATCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAGgtagagtttg ... ctgaatgcagCTGGAAATGACGGGCTTGGTGGTGGATGCCGGGGATGGAATGACTCATGTTGTTCCAGTGGCGGATGGTTACATCATTGGTAGCAGCATCAAGTCAATTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACATGGGAGAAATCATGTTCGAGACTTTCAACGTGCCAGGATTGTATATCGCAACTCAAGCAGTGTTAGCTCTAGCAGCTGGCTACACGACCTCCAAGgtagagtttggctattttgggttctttctggtgctcccgtgaatcattgataatggagtcttttgattcgtgaattgataagtgtattgaagtagccctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG