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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcatcatttttctagtgaatagtataaacctgggagtagttttttttctgtttttaaggctttcaatcatttagcgacgttcgtcttaaatgtttcagTGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGGCAGCAGTATCATGCCG

Basic information

species Physcomitrella patens
transcript PP1S49_154V6.1
intron # 10
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|162199788|gb|FC375861.1|FC375861
EST:     GTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAG                         TGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGG
genomic: GTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAGgtacgattac ... aatgtttcagTGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGG
EST: gi|162169177|gb|FC345144.1|FC345144
EST:     GTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAG                         TGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGG
genomic: GTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAGgtacgattac ... aatgtttcagTGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGG
EST: gi|67569924|gb|BJ942748.1|BJ942748
EST:     GTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAG                         TGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGANTGAACCTGG
genomic: GTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAGgtacgattac ... aatgtttcagTGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGG
EST: gi|208369492|gb|DC955905.1|DC955905
EST:     AGATTNCC-ATGACATTCGTTTGTTGGGAAG                         TGGACCTCGATGCGGGCTGCATGAGTTGA-TTTACCGGAGAATGAACCTGG
genomic: AGATTGCCAATGACATTCGTTTGTTGGGAAGgtacgattac ... aatgtttcagTGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGG
EST: gi|162170412|gb|FC347610.1|FC347610
EST:     GTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAG                         TGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGG
genomic: GTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAGgtacgattac ... aatgtttcagTGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGG
EST: gi|162193053|gb|FC371477.1|FC371477
EST:     GTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAG                         TGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGG
genomic: GTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAGgtacgattac ... aatgtttcagTGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGG

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: 13 (upstream exon), 34 (downstream exon)
Score: 4

GCAGCTCATGACGCTATTGTAGAATGTAGTGGTGCACTCAACACTGTAGCTGTTTCTCTTATGAAGATTGCCAATGACATTCGTTTGTTGGGAAGgtacgattac ... aatgtttcagTGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGGCAGCAGTATCATGCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctgtttttaaggctttcaatcatttagcgacgttcgtcttaaatgtttcagTGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGGCAGCAGTATCATGCCG
                                          ttaaatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcatcatttttctagtgaatagtataaacctgggagtagttttttttctgtttttaaggctttcaatcatttagcgacgttcgtcttaaatgtttcagTGGACCTCGATGCGGGCTGCATGAGTTGATTTTACCGGAGAATGAACCTGGCAGCAGTATCATGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA