Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcaccaatttgaggactaggctccttaaagattgtaagctacaccgtttctgtacaggttcggcatttgatgttttcagtgaaaatgtgccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACAATACTTTGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAA

Basic information

species Physcomitrella patens
transcript PP1S97_166V6.1
intron # 1
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|100381423|gb|BY950104.1|BY950104
EST:     GGGGCTCATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTANCA-TATGATCCCAAAGAATGCAGCTAC
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTA-CAATATGATCCCAAAGAATGCAGCTAC
EST: gi|162236116|gb|FC411118.1|FC411118
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162247221|gb|FC423045.1|FC423045
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|208349651|gb|DC917829.1|DC917829
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|67693837|gb|BJ954070.1|BJ954070
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|208394315|gb|DC904135.1|DC904135
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCANCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|100365610|gb|BY966682.1|BY966682
EST:     GGGGCACATAGATTACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTAC
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTAC
EST: gi|208359302|gb|DC954197.1|DC954197
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162236117|gb|FC411119.1|FC411119
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162223584|gb|FC399409.1|FC399409
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|208397380|gb|DC908256.1|DC908256
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCANCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|208351470|gb|DC921775.1|DC921775
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|100385117|gb|BY987580.1|BY987580
EST:     GGGGCACATAGATTACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGGACAATATGATCCCAA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAA
EST: gi|162204709|gb|FC381118.1|FC381118
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162265427|gb|FC440753.1|FC440753
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|208398630|gb|DC920525.1|DC920525
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|67698661|gb|BJ958894.1|BJ958894
EST:     CGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: CGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|19782856|gb|BQ039927.1|BQ039927
EST:     GCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162204708|gb|FC381117.1|FC381117
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|22133285|gb|BQ827650.1|BQ827650
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|208374469|gb|DC941198.1|DC941198
EST:     GGGGCACATANATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAANAATGCANCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162227818|gb|FC403968.1|FC403968
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162181923|gb|FC357730.1|FC357730
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|100362334|gb|BY947307.1|BY947307
EST:     GGGGCACATAGATNACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|100411853|gb|BY992373.1|BY992373
EST:     GGGGCACATAGATNACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAACGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162233114|gb|FC408937.1|FC408937
EST:     GGGGCACATGGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACN
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162227819|gb|FC403969.1|FC403969
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|208349313|gb|DC918035.1|DC918035
EST:     GGGGCACATAGATAACCCTGANTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162233113|gb|FC408936.1|FC408936
EST:     CTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: CTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162265428|gb|FC440754.1|FC440754
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|67575202|gb|BJ948026.1|BJ948026
EST:     GGGCACATAGAATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGCACATAG-ATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162208098|gb|FC384254.1|FC384254
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|22132784|gb|BQ827354.1|BQ827354
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162247220|gb|FC423044.1|FC423044
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162223598|gb|FC399410.1|FC399410
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|208353708|gb|DC922140.1|DC922140
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
EST: gi|162208097|gb|FC384253.1|FC384253
EST:     GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAG                         GTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA
genomic: GGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACA

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), 31 (downstream exon)
Score: 22

GCGTTCCAGCGCGTCCATGGTGTGTCACACACCGAGGTGGGATACACACAGGGGCACATAGATAACCCTGACTACTATGCCGTCTGCTCCGGGGACACAGgtactgagaa ... gccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACAATACTTTGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtttctgtacaggttcggcatttgatgttttcagtgaaaatgtgccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACAATACTTTGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAA
                     atttgat  putative branch site (score: 22)
                     atttgat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcaccaatttgaggactaggctccttaaagattgtaagctacaccgtttctgtacaggttcggcatttgatgttttcagtgaaaatgtgccggaacagGTCACTCTGAGGTTGTGAGGGTACAATATGATCCCAAAGAATGCAGCTACAATACTTTGCTGGATGTTTTCTGGAAGCGCCACGATCCAACCACGCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG