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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgctctcaccatgtcctcgtttctctcctttgtatcttaaatttagacattttgatgatgtcacattatgcagtgcctaggatgtggacatgattggggctgttgggtagcaaggttgctgttgctaacctttctcttccttcggcagATTTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACATTGGTGTTCCATATCCCGACTCAAAGGCCGTGGGGATCTACAGCACTATT

Basic information

species Physcomitrella patens
transcript PP1S309_38V6.2
intron # 4
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|208394669|gb|DC928829.1|DC928829
EST:     ACGGCAGAGTTCCATTCCTACTCCGTTTTGTGGAATAAACAACAGATCAT                         ATTTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACAT
genomic: ACGGCAGAGTTCCATTCCTACTCCGTTTTGTGGAATAAACAACAGATCATgtgcgctctc ... ccttcggcagATTTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACAT
EST: gi|208347946|gb|DC917625.1|DC917625
EST:     AACAACAGATCAT                         A-TTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACAT
genomic: AACAACAGATCATgtgcgctctc ... ccttcggcagATTTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACAT
EST: gi|208385498|gb|DC953103.1|DC953103
EST:     ACNGCAGAGTTCCA-TCCTACTCCG-TTTGNGGAATAAACAACAGATCAT                         ATTTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACAT
genomic: ACGGCAGAGTTCCATTCCTACTCCGTTTTGTGGAATAAACAACAGATCATgtgcgctctc ... ccttcggcagATTTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACAT
EST: gi|208366551|gb|DC954859.1|DC954859
EST:     AACAACAGATCAT                         ATTTTATGTGGACANCACGCCTATCCGTGTTTACAAGAATAATAAGGACAT
genomic: AACAACAGATCATgtgcgctctc ... ccttcggcagATTTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACAT
EST: gi|208364136|gb|DC947268.1|DC947268
EST:     GGAATAANCAACAGATCAT                         A-TTTATG-GGACAACACGCCTATCCGTG-TTACCAGAATAATAAGGACA-
genomic: GGAATAAACAACAGATCATgtgcgctctc ... ccttcggcagATTTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACAT

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: 26 (upstream exon), 18 (downstream exon)
Score: 3

CGAATGGCGAAGGAAAGCGTGAGCAGCGAATATACCTTTGGTTTGACCCAACGGCAGAGTTCCATTCCTACTCCGTTTTGTGGAATAAACAACAGATCATgtgcgctctc ... ccttcggcagATTTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACATTGGTGTTCCATATCCCGACTCAAAGGCCGTGGGGATCTACAGCACTATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggggctgttgggtagcaaggttgctgttgctaacctttctcttccttcggcagATTTTATGTGGACAACACGCCTATCCGTGTTTACAAGAATAATAAGGACATTGGTGTTCCATATCCCGACTCAAAGGCCGTGGGGATCTACAGCACTATT
                             tgctaac  putative branch site (score: 3)
                            ttgctaacctttctct  CT-rich tract