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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgttttccacttttctattcttcttcgatcatgttttacctttcgcaatttttaccgggttcgtgagctgatttaaaaaattagggttttggtgggagtctcaattgttttgtgttattttggggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGCTTCGCCATCGCCAGTGACCGCCGTCTGGGTGTAAATTTCCAGACGATTG

Basic information

species Physcomitrella patens
transcript PP1S130_217V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S130_217V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacgtgttttccacttttctattcttcttcgatcatgttttacctttcgcaatttttaccgggttcgtgagctgatttaaaaaattagggttttggtgggagtctcaattgttttgtgttattttggggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGCTTCGCCATCGCCAGTGACCGCCGTCTGGGTGTAAATTTCCAGACGATTG
                  | |  |  |   |  | |  |||||  ||  |  |  |   |    || ||     |  | ||    |||    |    ||   |    ||||| ||  | ||    || ||      ||||       ||||||||||||||  |  |||| ||||| || |||||||| ||||||||||||||||| ||  | || |||||  |  | ||||| || |
-------------gtaagtttgataattcccagtta-attttaatttcggagacctcagctctattagtcttacgcatcaatggtttaatagtg-actgaacgataaaattgattgatatt----tgtggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGTTTCGCCATCGCCAGTGATCGGAGACTCGGTGTTCAGCTACAGACAATCG

upper sequence: PP1S130_217V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ32896 (Selaginella moellendorffii), 3'ss of exon 1
gtacgtgttttccacttttctattcttcttcgatcatgttttacctttcgcaatttttaccgggttcgtgagctgatttaaaaaattagggttttggtgggagtc--tcaattgttttg--tgttattttggggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGCTTCGCCATCGCCAGTGACCGCCGTCTGGGTGTAAATTTCCAGACGATTG
                                                                                      || | | || |   | | |  || |||  |     ||  |  ||  |   ||  |||||   | ||||||||| || ||  || |||| ||||| || ||| ||||||| |||||||||||||| ||||| || ||||| |||||||||||||| |
-------------------------------------------------------------------------------------gtaagatgtttgctagcgccgatcgattcctggagctgagagcttccgccttggcagATTTTCACCTACAATGGCAGCGCCTTGGTTGCGATGGTCGGAAAGGATTGCTTTGCCATCGCCAGTGATCGCCGGCTTGGTGTGAATTTCCAGACGATAG

upper sequence: PP1S130_217V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ05723 (Selaginella moellendorffii), 3'ss of exon 1
gtacgtgttttccacttttctattcttcttcgatcatgttttacctttcgcaatttttaccgggttcgtgagctgatttaaaaaattagggttttggtgggagtc--tcaattgttttg--tgttattttggggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGCTTCGCCATCGCCAGTGACCGCCGTCTGGGTGTAAATTTCCAGACGATTG
                                                                                      || |||||| |   | | |  || |||  |     ||  |  ||  |   ||  |||||   | ||||||||| || ||  || |||| ||||| || ||| ||||||| ||||| |||||||| ||||| || ||||| |||||||||||||| |
-------------------------------------------------------------------------------------gtaaggtttttgctagcgccgatcgattcctggagctgagagcttccgccttggcagATTTTCACCTACAATGGCAGCGCCTTGGTTGCGATGGTCGGAAAGGATTGCTTTGCCATAGCCAGTGATCGCCGGCTTGGTGTGAATTTCCAGACGATAG

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|162247133|gb|FC421358.1|FC421358
EST:     CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCG                         ATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
genomic: CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCGgtacgtgttt ... ggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
EST: gi|100359970|gb|BY965963.1|BY965963
EST:     CGCTGCTTGTTGAAGTTTGTGGATCATCGAGTGGGCTTCTCCTGATGTCG                         ATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
genomic: CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCGgtacgtgttt ... ggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
EST: gi|67576219|gb|BJ949043.1|BJ949043
EST:     CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCG                         ATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
genomic: CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCGgtacgtgttt ... ggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
EST: gi|162213862|gb|FC389853.1|FC389853
EST:     CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCG                         ATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
genomic: CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCGgtacgtgttt ... ggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
EST: gi|162206028|gb|FC382813.1|FC382813
EST:     CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCG                         ATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
genomic: CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCGgtacgtgttt ... ggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
EST: gi|18332387|gb|BJ164400.1|BJ164400
EST:     CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCG                         ATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
genomic: CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCGgtacgtgttt ... ggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
EST: gi|18350731|gb|BJ182782.1|BJ182782
EST:     CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCG                         ATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
genomic: CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCGgtacgtgttt ... ggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
EST: gi|162220663|gb|FC396875.1|FC396875
EST:     CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCG                         ATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC
genomic: CGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCGgtacgtgttt ... ggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGC

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: 27 (upstream exon), 34 (downstream exon)
Score: 5

GTTTAGGGTTCGAATTAGGTTTTACAGTTTGGTTTCTGAGGATCTCGCTGCTTGTTGAAGTTTGTGGGTCATCGAGTGGGCTTCTCCTGATGTCGgtacgtgttt ... ggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGCTTCGCCATCGCCAGTGACCGCCGTCTGGGTGTAAATTTCCAGACGATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattagggttttggtgggagtctcaattgttttgtgttattttggggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGCTTCGCCATCGCCAGTGACCGCCGTCTGGGTGTAAATTTCCAGACGATTG
                             ttttgtgttatttt  TA-rich tract