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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaatgtccgaagggctttcaacgccatttttcggtatttagtggtcaggacattcatcgaatttagttcgctgctgacatgtttgtgaggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAGAATCAGCTTCACCACTCATCAGCTTCTTACAGAACCCAGCTCTTGTTCA

Basic information

species Physcomitrella patens
transcript PP1S9_109V6.1
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|100398534|gb|BY972660.1|BY972660
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|208396897|gb|DC908189.1|DC908189
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|208354961|gb|DC914225.1|DC914225
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|67717505|gb|BJ967764.1|BJ967764
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|100414960|gb|BY956947.1|BY956947
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|18346098|gb|BJ178141.1|BJ178141
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|162171468|gb|FC346743.1|FC346743
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ATATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|208348620|gb|DC905857.1|DC905857
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|208368174|gb|DC931428.1|DC931428
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|100402664|gb|BY954948.1|BY954948
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|18363928|gb|BJ196000.1|BJ196000
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|100394165|gb|BY971971.1|BY971971
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
EST: gi|67508674|gb|BJ941535.1|BJ941535
EST:     TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAG                         ACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG
genomic: TGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAG

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: 28 (upstream exon), 34 (downstream exon)
Score: 10

ATCCTGAAAGCCAAAATCGAGTTGCTGGGCAAGACCAACATGGTGGACTATGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgc ... ggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAGAATCAGCTTCACCACTCATCAGCTTCTTACAGAACCCAGCTCTTGTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaggacattcatcgaatttagttcgctgctgacatgtttgtgaggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAGAATCAGCTTCACCACTCATCAGCTTCTTACAGAACCCAGCTCTTGTTCA
                            tgctgac  putative branch site (score: 10)
                aatttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaatgtccgaagggctttcaacgccatttttcggtatttagtggtcaggacattcatcgaatttagttcgctgctgacatgtttgtgaggtgatccagACATGGTGGACAGGAGGGTAGAGGTAGTCGGTCGGCTTAAGATGCTGGAAGAATCAGCTTCACCACTCATCAGCTTCTTACAGAACCCAGCTCTTGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC