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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcatggttttccttgtccaattgatttacattcgctgaattcacgtgaatggtgtgatgtgccttgagtatcagcacgaaacatgaagtcttttatcaaaagggattgataatcactttcttaagtcacatcctgtgtttggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACTGGAGCCGGTGATGCGTTTTGTGCTGGTCTTCTGAGCCAGATTGCTAAGT

Basic information

species Physcomitrella patens
transcript PP1S276_108V6.1
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|162251022|gb|FC426351.1|FC426351
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
EST: gi|162232338|gb|FC408681.1|FC408681
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
EST: gi|208365170|gb|DC947350.1|DC947350
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
EST: gi|67694142|gb|BJ954375.1|BJ954375
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
EST: gi|162160373|gb|FC337374.1|FC337374
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
EST: gi|162155160|gb|FC331669.1|FC331669
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
EST: gi|162232339|gb|FC408682.1|FC408682
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
EST: gi|208360527|gb|DC950073.1|DC950073
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
EST: gi|37850493|gb|BJ608501.1|BJ608501
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
EST: gi|162263876|gb|FC438664.1|FC438664
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
EST: gi|162257881|gb|FC434079.1|FC434079
EST:     AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCG                         AAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT
genomic: AGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACT

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: 29 (upstream exon), 35 (downstream exon)
Score: 17

AGATCCCAAGGATGATGCCCTCAACCTAAAGATGATGCATCCTGGCTGCAAGTTGATGCTAGTGACTGAGGGTGGAGAGGGCTGTCGTTATTACACCCCGgtaattcatg ... ggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACTGGAGCCGGTGATGCGTTTTGTGCTGGTCTTCTGAGCCAGATTGCTAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaaagggattgataatcactttcttaagtcacatcctgtgtttggaaatgcagAAATTTCATGGCCACGTGAGTGGTCTCAAGGTTCAACCAGTTGATACCACTGGAGCCGGTGATGCGTTTTGTGCTGGTCTTCTGAGCCAGATTGCTAAGT
        gattgat  putative branch site (score: 17)
         attgataat  TA-rich tract