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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaaccttcccactaaacttctggaaagttaagttttttggatttattgagttattagaaggccttaagcttattagatttcacacagcctggtcaagttatgttcccgactaataagtaccttgttctggagcagGTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAAATTCCTAAGCCGGGTCTTGTGTTCAGTCGACTGACTTGCCTTGCAAAAT

Basic information

species Physcomitrella patens
transcript PP1S35_276V6.1
intron # 24
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|162257287|gb|FC433370.1|FC433370
EST:     AGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAA                         GTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA
genomic: AGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAAgtaattaacc ... tctggagcagGTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA
EST: gi|162257286|gb|FC433369.1|FC433369
EST:     AGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAA                         GTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA
genomic: AGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAAgtaattaacc ... tctggagcagGTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA
EST: gi|37831373|gb|BJ589385.1|BJ589385
EST:     AGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAA                         GTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA
genomic: AGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAAgtaattaacc ... tctggagcagGTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA
EST: gi|162184258|gb|FC360499.1|FC360499
EST:     AGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAA                         GTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA
genomic: AGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAAgtaattaacc ... tctggagcagGTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA
EST: gi|162198920|gb|FC372947.1|FC372947
EST:     AGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAA                         GTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA
genomic: AGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAAgtaattaacc ... tctggagcagGTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA
EST: gi|100412907|gb|BY992494.1|BY992494
EST:     GAAGCTGGTAGCACTGCGAGATGATATCCCAAAAGAA-GACGCCAAAGAA                         GTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGGA
genomic: GAAGCTGGTAGCACTGCGAGATGATATCCCAAA-GAAAGACGCCAAAGAAgtaattaacc ... tctggagcagGTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAA

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: 35 (upstream exon), 35 (downstream exon)
Score: 15

CCGGAAGTAGTGGAGAAGCTGGTAGCACTGCGAGATGATATCCCAAAGAAAGACGCCAAAGAAgtaattaacc ... tctggagcagGTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAAATTCCTAAGCCGGGTCTTGTGTTCAGTCGACTGACTTGCCTTGCAAAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacagcctggtcaagttatgttcccgactaataagtaccttgttctggagcagGTGGTTGGAGAGTGCAAATCTCTTCACAACGACAAGTTAAAGGAAGGGGAAATTCCTAAGCCGGGTCTTGTGTTCAGTCGACTGACTTGCCTTGCAAAAT
                           gactaat  putative branch site (score: 15)
                                       ccttgttct  putative PPT
                              taataagta  TA-rich tract