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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATCGCTGGTTTAGTTCGCGGTGCGAACGAAGGGCAGGGTCTGGGCAATGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagttttattaaaagtctgaccaaccataaatatgcaatatctgtattatctactttggttgtttgtcataccatggcatgaagcaattggctgattgtttcattcaaagagtaatcctctttggattccgacgggttttaaactaaaagaaattatgtttctgcag

Basic information

species Physcomitrella patens
transcript PP1S207_28V6.1
intron # 3
splice site 5'
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|18361521|gb|BJ193587.1|BJ193587
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|162272681|gb|FC448307.1|FC448307
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|208383342|gb|DC907517.1|DC907517
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|67573864|gb|BJ946688.1|BJ946688
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|18363393|gb|BJ195465.1|BJ195465
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTC
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTC
EST: gi|100415938|gb|BY956998.1|BY956998
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|208370398|gb|DC931810.1|DC931810
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|208394358|gb|DC904178.1|DC904178
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|100451884|gb|CJ974990.1|CJ974990
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTTGAGGATNCAGTTGACCCN
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTT-GAGGATTCAGTTGACCCC
EST: gi|100395348|gb|BY953692.1|BY953692
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|162263698|gb|FC439623.1|FC439623
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|18358448|gb|BJ190507.1|BJ190507
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|162202372|gb|FC379991.1|FC379991
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|100387386|gb|BY988257.1|BY988257
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|208399872|gb|DC904954.1|DC904954
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|162264593|gb|FC440889.1|FC440889
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|18361750|gb|BJ193817.1|BJ193817
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGGATTCAGTTGACCCC
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGG-ATTCAGTTGACCCC
EST: gi|18347703|gb|BJ179750.1|BJ179750
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|208397168|gb|DC911777.1|DC911777
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|100352204|gb|BY983091.1|BY983091
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|208391589|gb|DC933838.1|DC933838
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|162278437|gb|FC454523.1|FC454523
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|18351948|gb|BJ184000.1|BJ184000
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAG
EST: gi|18363198|gb|BJ195270.1|BJ195270
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAG
EST: gi|18347772|gb|BJ179819.1|BJ179819
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|208393061|gb|DC929556.1|DC929556
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|18345717|gb|BJ177760.1|BJ177760
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCC
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCC
EST: gi|162175835|gb|FC352137.1|FC352137
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|18371439|gb|BJ203041.1|BJ203041
EST:     TGCCTTTTTGTCACATATTCGAGCAGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|18347497|gb|BJ179543.1|BJ179543
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATC
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATC
EST: gi|208359117|gb|DC930449.1|DC930449
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
EST: gi|18349457|gb|BJ181506.1|BJ181506
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGAT
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGAT
EST: gi|100386335|gb|BY988002.1|BY988002
EST:     TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGA                         GGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG
genomic: TGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCG

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: 34 (upstream exon), 21 (downstream exon)
Score: 28

GACATCGCTGGTTTAGTTCGCGGTGCGAACGAAGGGCAGGGTCTGGGCAATGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagtttta ... gtttctgcagGGGCTTTTGATGATCCAGAGGTCACACATGTTGAGGATTCAGTTGACCCCGTTAGAGATCTGGAAATCATTTCTCAAGAATTGCGTTTAAAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACATCGCTGGTTTAGTTCGCGGTGCGAACGAAGGGCAGGGTCTGGGCAATGCCTTTTTGTCACATATTCGAGCGGTGGATGGCATCTTTCATGTCTTGAgtaagttttattaaaagtctgaccaaccataaatatgcaatatctgtattatctactttggttgtttgtcataccatggcatgaagcaattggctgattgtttcattcaaagagtaatcctctttggattccgacgggttttaaactaaaagaaattatgtttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA