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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttgggttgaatcagattttagggtttagggttggttttaaacagagggttggagtttttgatgggttgttttgcgatgggatgcgaatcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCGTACTGGGGACTCACGGCGTTGGATATTATGGGACGCCTTGGTGATATGA

Basic information

species Physcomitrella patens
transcript PP1S34_430V6.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S34_430V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ06556 (Selaginella moellendorffii), 3'ss of exon 1
ttgttgggttgaatcagattttagggtttagggttggttttaaacagagggt-tggagtttttgatgggttgttttgcgatgggatgcgaatcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCGTACTGGGGACTCACGGCGTTGGATATTATGGGACGCCTTGGTGATATGA
                                    || | ||| | |        |   |   || | |   |   |||| |              | ||||   ||||||||| ||| |||||||||||||||| || |||||||| ||||| |||||| | || ||  ||||| | |||| | |    |  ||  |  
------------------------------------gtatgaaagaaatctcgcaaaagatagaatagatctctcctcgatcg-------------cgcagAAGAAGGATTTCGATTCAATGGTGATGGAGCACCTCCGGATGAACGGAGCGTATTGGGGATTGACCGCCCTGGATTTGATGGAATGTAGGGAAGACGTCG

upper sequence: PP1S34_430V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ31356 (Selaginella moellendorffii), 3'ss of exon 1
ttgttgggttgaatcagattttagggtttagggttggttttaaacagagggttggagtttttgatgggttgttttgcgatgggatgcgaatcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCGTACTGGGGACTCACGGCGTTGGATATTATGGGACGCCTTGGTGATATGA
                                      | | ||   |   | | |     | | |  | | | |    | |   |||          ||||   ||||||||| ||| |||||||||||||||| || |||||||| ||||| |||||  | || ||| ||||| | |||||| |    |  ||  |  
-------------------------------------gtatgaaagaaatctcgcaaaagatcaagaatagatctctcctcgatcgcg---------cagAAGAAGGATTTCGATTCAATGGTGATGGAGCACCTCCGGATGAACGGAGCGTATTGGGGGTTGACCGCGCTGGATTTGATGGGATGTAGGGAAGACGTCG
















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|18348984|gb|BJ181033.1|BJ181033
EST:     CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAG                         AAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
genomic: CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAGgtaggccttg ... tcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
EST: gi|22492619|gb|BU052542.1|BU052542
EST:     AGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAG                         AAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
genomic: AGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAGgtaggccttg ... tcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
EST: gi|100437122|gb|BY961362.1|BY961362
EST:     CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAG                         AAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
genomic: CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAGgtaggccttg ... tcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
EST: gi|100418156|gb|BY993361.1|BY993361
EST:     CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAG                         AAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
genomic: CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAGgtaggccttg ... tcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
EST: gi|100422700|gb|BY957957.1|BY957957
EST:     CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAG                         AAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
genomic: CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAGgtaggccttg ... tcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
EST: gi|100440809|gb|BY980629.1|BY980629
EST:     CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAG                         AAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
genomic: CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAGgtaggccttg ... tcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
EST: gi|208377833|gb|DC940945.1|DC940945
EST:     CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAG                         AAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
genomic: CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAGgtaggccttg ... tcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
EST: gi|100424688|gb|BY976765.1|BY976765
EST:     CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAG                         AAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
genomic: CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAGgtaggccttg ... tcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
EST: gi|100440735|gb|BY980555.1|BY980555
EST:     CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAG                         AAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG
genomic: CCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAGgtaggccttg ... tcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCG

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), 29 (downstream exon)
Score: 12

TCTGTTTTGTGAAGTTTTTCGGTGCAGAAGAAGAGAGGTTGTCATGGGGTCCGAGCTATATTTGGATAAGCATGTCGACTACATCAAGTCGCTTGACAAGgtaggccttg ... tcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCGTACTGGGGACTCACGGCGTTGGATATTATGGGACGCCTTGGTGATATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagggttggagtttttgatgggttgttttgcgatgggatgcgaatcttttgtagAAATCGGATTTCGACTCAGTGGTGATGGAGCACCTGCGCATGAACGGCGCGTACTGGGGACTCACGGCGTTGGATATTATGGGACGCCTTGGTGATATGA
             ttttgat  putative branch site (score: 12)
                                             tcttttgt  putative PPT
            tttttgat  TA-rich tract