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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgagatgaatggtagcgaatgggagattgctgggattgcagtgtcggaggaacagtagacgggggaagtctcaccagtacggacacgcgtggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAGGAGCAGCTGGAGCAGCGCATGGCAGCGGTACGAGAGGATCCGACCCTGA

Basic information

species Physcomitrella patens
transcript PP1S8_3V6.1
intron # 3
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|162203208|gb|FC379305.1|FC379305
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|100399907|gb|BY990681.1|BY990681
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|208383022|gb|DC927772.1|DC927772
EST:     TCGGCAACGCCCTGATGCAG                         GACCCCGCAATNTCNGNCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: TCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162156693|gb|FC333549.1|FC333549
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|208360463|gb|DC930816.1|DC930816
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162174547|gb|FC350202.1|FC350202
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162210973|gb|FC387071.1|FC387071
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162155861|gb|FC332410.1|FC332410
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162209197|gb|FC385416.1|FC385416
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162151736|gb|FC328593.1|FC328593
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162192827|gb|FC369652.1|FC369652
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|208386947|gb|DC956930.1|DC956930
EST:     TCGGCAACGCCCTGATGCAG                         GACCCCGCNATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: TCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162187054|gb|FC362836.1|FC362836
EST:     AGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: AGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162277694|gb|FC453533.1|FC453533
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162153901|gb|FC329408.1|FC329408
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162182198|gb|FC358213.1|FC358213
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162176549|gb|FC353018.1|FC353018
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162247198|gb|FC420240.1|FC420240
EST:     AACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: AACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|100388693|gb|BY970841.1|BY970841
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162189806|gb|FC366055.1|FC366055
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|100390591|gb|BY971346.1|BY971346
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162152256|gb|FC328235.1|FC328235
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
EST: gi|162157916|gb|FC334902.1|FC334902
EST:     ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAG                         GACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG
genomic: ATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAG

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: 79

CCAGTTGGACCCGAACCAGTACATCAACGCGATGCAACAAGTGATGCAAAATCCTCAGTTCATGACCATGGCAGAACGGCTCGGCAACGCCCTGATGCAGgtgcggtagc ... tggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAGGAGCAGCTGGAGCAGCGCATGGCAGCGGTACGAGAGGATCCGACCCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggaggaacagtagacgggggaagtctcaccagtacggacacgcgtggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAGGAGCAGCTGGAGCAGCGCATGGCAGCGGTACGAGAGGATCCGACCCTGA
                       gtctcac  putative branch site (score: 79)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatgaatggtagcgaatgggagattgctgggattgcagtgtcggaggaacagtagacgggggaagtctcaccagtacggacacgcgtggattgcagGACCCCGCAATGTCGGGCATGCTGTCGAACCTGACGAACCCCGCGCACAAGGAGCAGCTGGAGCAGCGCATGGCAGCGGTACGAGAGGATCCGACCCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT