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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggattcatcttgcctttgttgtccttataaaacttcatgtgaccccatttctttcatagaatactgttttccgaaacttcggcagggctgaaaactttttttaaagtagggccttaactggtgttcctatgggagcagGTGCCATGCAGAACTGCCAACAAAGGCTCTTTTCCTTTGAATGGAACATATTTTCAAGTTAATGAG

Basic information

species Physcomitrella patens
transcript PP1S226_20V6.1
intron # 18
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|22133008|gb|BQ827486.1|BQ827486
EST:     CCCATTTGCTAGTTGCAACTCAGGGCAAGAAGTCCCTGTTTTTAATTCTT                         GTGCCATGCAGAACTGCCAACAAAGGCTCTTTTCCTTTGAATGGAACATAT
genomic: CCCATTTGCTAGTTGCAACTCAGGGCAAGAAGTCCC-GGGAACAATTCTTgtaggattca ... atgggagcagGTGCCATGCAGAACTGCCAACAAAGGCTCTTTTCCTTTGAATGGAACATAT
EST: gi|162193628|gb|FC371233.1|FC371233
EST:     ACCCATTTGCTAGTTGCAACTCAGGGCAAGAAGTCCCGGGAACAATTCTT                         GTGCCATGCAGAACTGCCAACAAAGGCTCTTTTCCTTTGAATGGAACATAT
genomic: ACCCATTTGCTAGTTGCAACTCAGGGCAAGAAGTCCCGGGAACAATTCTTgtaggattca ... atgggagcagGTGCCATGCAGAACTGCCAACAAAGGCTCTTTTCCTTTGAATGGAACATAT

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), 27 (downstream exon)
Score: 28

ATGAGGTGCCAGCGGCTATGCCCAAAATTAGCGATGATGATGCAAGCAACCCATTTGCTAGTTGCAACTCAGGGCAAGAAGTCCCGGGAACAATTCTTgtaggattca ... atgggagcagGTGCCATGCAGAACTGCCAACAAAGGCTCTTTTCCTTTGAATGGAACATATTTTCAAGTTAATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggctgaaaactttttttaaagtagggccttaactggtgttcctatgggagcagGTGCCATGCAGAACTGCCAACAAAGGCTCTTTTCCTTTGAATGGAACATATTTTCAAGTTAATGAG
                            ccttaac  putative branch site (score: 28)
                                        ttcctat  putative PPT
       aaaactttttttaaag  TA-rich tract