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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtctgactggggatgcacttttgtgctattcttgttcaacagttttctgttcttttgaattgatctgatgacatgctcttctgataagttttcctgattataccctttcattcgatggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG

Basic information

species Physcomitrella patens
transcript PP1S22_76V6.1
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|162262297|gb|FC437624.1|FC437624
EST:     ACATGGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: ACATGGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|67694098|gb|BJ954331.1|BJ954331
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162270731|gb|FC446344.1|FC446344
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162224836|gb|FC400836.1|FC400836
EST:     ACATGGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: ACATGGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162227758|gb|FC402686.1|FC402686
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|18350710|gb|BJ182761.1|BJ182761
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162262298|gb|FC437625.1|FC437625
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|19781574|gb|BQ039741.1|BQ039741
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162273803|gb|FC449734.1|FC449734
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|18365111|gb|BJ197185.1|BJ197185
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|18363914|gb|BJ195986.1|BJ195986
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|18361968|gb|BJ194035.1|BJ194035
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|37834576|gb|BJ592588.1|BJ592588
EST:     GACATGGTCAAGTACGCGAGGGACCCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GACATGGTCAAGTACGCGAGGGA-CCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162224837|gb|FC400837.1|FC400837
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|18364653|gb|BJ196726.1|BJ196726
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|67692927|gb|BJ953160.1|BJ953160
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162205889|gb|FC381335.1|FC381335
EST:     TTCGACATGGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: TTCGACATGGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162270730|gb|FC446343.1|FC446343
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162272796|gb|FC447978.1|FC447978
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|67570800|gb|BJ943624.1|BJ943624
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162205890|gb|FC381336.1|FC381336
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|18365599|gb|BJ197676.1|BJ197676
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|18345004|gb|BJ177045.1|BJ177045
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|18352797|gb|BJ184852.1|BJ184852
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|67571863|gb|BJ944687.1|BJ944687
EST:     TCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: TCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|67569660|gb|BJ942484.1|BJ942484
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|18346488|gb|BJ178531.1|BJ178531
EST:     GAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162273804|gb|FC449735.1|FC449735
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
EST: gi|162227744|gb|FC402685.1|FC402685
EST:     GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG                         CCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
genomic: GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG

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), 34 (downstream exon)
Score: 19

GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGGgtaggtctga ... atggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacatgctcttctgataagttttcctgattataccctttcattcgatggatgcagCCTGCAAGGCCAGAGGTTCCGATTTGCGAGTGCACTTCAAG
                      tcctgat  putative branch site (score: 19)
              ataagtttt  TA-rich tract