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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcctcgaagaagaaatattcaatatggttttgattggtggagaaacaattgttatgtgcaaatgtaatgtttatttagttgcggatgtgacggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTGTGGAACTCTGCCGTAGATAGGACTTTCGGACCCCTCATCGCTGTAATAA

Basic information

species Physcomitrella patens
transcript PP1S42_179V6.1
intron # 2
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|67699611|gb|BJ959844.1|BJ959844
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|67700202|gb|BJ960435.1|BJ960435
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|67573858|gb|BJ946682.1|BJ946682
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|37840142|gb|BJ598150.1|BJ598150
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|18362927|gb|BJ194999.1|BJ194999
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|67697245|gb|BJ957478.1|BJ957478
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|67576669|gb|BJ949493.1|BJ949493
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|67570787|gb|BJ943611.1|BJ943611
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|162229865|gb|FC404318.1|FC404318
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|67694084|gb|BJ954317.1|BJ954317
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|162259072|gb|FC435157.1|FC435157
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|13251314|gb|BG362217.1|BG362217
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAACTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
EST: gi|67576120|gb|BJ948944.1|BJ948944
EST:     TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCG                         AGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG
genomic: TTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTG

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), 33 (downstream exon)
Score: 9

GGGGGTTTCCATGTACGACCAACGAGAGATTTGGAAGTCGACTGCAGGTCTTGCCGAGATGTTGTCCCGAGGGACTCTCCCAGCTGCCCGTGGTATTTCGgtatggagct ... acggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTGTGGAACTCTGCCGTAGATAGGACTTTCGGACCCCTCATCGCTGTAATAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaattgttatgtgcaaatgtaatgtttatttagttgcggatgtgacggttgcagAGTCCGCCTCCAATTTTGGGAAGAGAAGCGCGGGCCGATCTAGCTCATTTGTGGAACTCTGCCGTAGATAGGACTTTCGGACCCCTCATCGCTGTAATAA
               aaatgtaatgtttatt  TA-rich tract