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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattagtcttgcaatacttgacagcaaacacttttttgacttttagatttattaggggaggattgcttaataacctatactggtgttcgattttattcagGTGTTGGAACTACTTACACCGATACTGCAAGATTCAAAGGTTGCAATCGATTTAGCAGGATTTGCCGCTGTAGCTTTGGGTCTCGTCTATGTGGGCTCTT

Basic information

species Physcomitrella patens
transcript PP1S3_553V6.1
intron # 16
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|162280079|gb|FC456473.1|FC456473
EST:     GAGCTGTTATGGGACTTGGGCTAGCCTATGCTGGTTCTCAGAAAGAGGAG                         GTGTTGGAACTACTTACACCGATACTGCAAGATTCAAAGGTTGCAATCGAT
genomic: GAGCTGTTATGGGACTTGGGCTAGCCTATGCTGGTTCTCAGAAAGAGGAGgttagaagta ... ttttattcagGTGTTGGAACTACTTACACCGATACTGCAAGATTCAAAGGTTGCAATCGAT
EST: gi|162186177|gb|FC362109.1|FC362109
EST:     GAGCTGTTATGGGACTTGGGCTAGCCTATGCTGGTTCTCAGAAAGAGGAG                         GTGTTGGAACTACTTACACCGATACTGCAAGATTCAAAGGTTGCAATCGAT
genomic: GAGCTGTTATGGGACTTGGGCTAGCCTATGCTGGTTCTCAGAAAGAGGAGgttagaagta ... ttttattcagGTGTTGGAACTACTTACACCGATACTGCAAGATTCAAAGGTTGCAATCGAT
EST: gi|162163327|gb|FC339653.1|FC339653
EST:     GAGCTGTTATGGGACTTGGGCTAGCCTATGCTGGTTCTCAGAAAGAGGAG                         GTGTTGGAACTACTTACACCGATACTGCAAGATTCAAA
genomic: GAGCTGTTATGGGACTTGGGCTAGCCTATGCTGGTTCTCAGAAAGAGGAGgttagaagta ... ttttattcagGTGTTGGAACTACTTACACCGATACTGCAAGATTCAAA

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), 31 (downstream exon)
Score: 10

TGCTCTTCTGTTTGACTCTGTCAACAAGAAAGACTTAACAGTCCGCATTGGAGCTGTTATGGGACTTGGGCTAGCCTATGCTGGTTCTCAGAAAGAGGAGgttagaagta ... ttttattcagGTGTTGGAACTACTTACACCGATACTGCAAGATTCAAAGGTTGCAATCGATTTAGCAGGATTTGCCGCTGTAGCTTTGGGTCTCGTCTATGTGGGCTCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttattaggggaggattgcttaataacctatactggtgttcgattttattcagGTGTTGGAACTACTTACACCGATACTGCAAGATTCAAAGGTTGCAATCGATTTAGCAGGATTTGCCGCTGTAGCTTTGGGTCTCGTCTATGTGGGCTCTT
                      taataac  putative branch site (score: 10)
                                             ttttattc  putative PPT
                                            attttattca  TA-rich tract