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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGACTTACGCTCAAATCAGGCAGCTTTTGGAGGGCCTAGCAGACCGGTTTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccgcaactccttggcaacgtttcatttcagcttgtagcggtatcaaccattccgcagtaattagggtttggttagagtttctgcatttgagagagagcgaaccgtagagagcgatcgaggattttgatttcgttctggtgatatttatag

Basic information

species Physcomitrella patens
transcript PP1S479_14V6.1
intron # 2
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|162182552|gb|FC357527.1|FC357527
EST:     TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTT                         GATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
genomic: TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
EST: gi|100435994|gb|BY979327.1|BY979327
EST:     TTGAGTGGGAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTT                         GATGGTCAAAGTGTATCTTTGGGACCCCGGCG-CCAGTTTGAATTGAGTGG
genomic: TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCC-GGCGGCCAGTTTGAATTGAGTGG
EST: gi|162186779|gb|FC362815.1|FC362815
EST:     TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTT                         GATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
genomic: TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
EST: gi|67716872|gb|BJ967131.1|BJ967131
EST:     TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTT                         GATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
genomic: TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
EST: gi|100413370|gb|BY956638.1|BY956638
EST:     TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTT                         GATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
genomic: TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
EST: gi|67704735|gb|BJ964968.1|BJ964968
EST:     TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTT                         GATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
genomic: TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
EST: gi|208384006|gb|DC907397.1|DC907397
EST:     TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTT                         GATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
genomic: TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
EST: gi|67717406|gb|BJ967665.1|BJ967665
EST:     TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTT                         GATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
genomic: TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
EST: gi|18324874|gb|BJ156869.1|BJ156869
EST:     TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTT                         GATGGTCAAAGTGTATCTTTGGAACCCGGCGG
genomic: TTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGG
EST: gi|162239290|gb|FC415389.1|FC415389
EST:     GGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTT                         GATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA
genomic: GGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGA

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: 34 (upstream exon), 32 (downstream exon)
Score: 16

CATGACTTACGCTCAAATCAGGCAGCTTTTGGAGGGCCTAGCAGACCGGTTTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccg ... atatttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGAGCGCCTCTGGAGACACTTCATCAAACATGCGCCGAGGTCAATTCACATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGACTTACGCTCAAATCAGGCAGCTTTTGGAGGGCCTAGCAGACCGGTTTGAGTGGAAGAAAGTGATGGAGGGAGACAACATAATTGGACTGACATTTgtgagctccgcaactccttggcaacgtttcatttcagcttgtagcggtatcaaccattccgcagtaattagggtttggttagagtttctgcatttgagagagagcgaaccgtagagagcgatcgaggattttgatttcgttctggtgatatttatag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG