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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgattcgatcagtcattcctctaatctagagttcctcatgttcagctttgtaacccaatcgcatagccgttgtatactttgcacgtccgttagtgaaggtacttactttttagttaatagttagtaggttttctctggggatgtacttatgtctgacgtttctgttctgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAATTTCAACTGACTGTCAATGTTACGGCTCTTACCATCAATTTTGTCGCAT

Basic information

species Physcomitrella patens
transcript PP1S8_288V6.1
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 27
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 27
gttcgattcgatcagtcattcctctaatctagagttcctcatgttc-----agctttgtaacccaatcgcatagccgttgta-------tactttgcacgtccgt---tagtgaaggta--cttactttttagttaatagttagtaggttttctctggggatgtacttatgtctgacgtttctgt----tctgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAATTTCAACTGACTGTCAATGTTACGGCTCTTACCATCAATTTTGTCGCAT
|||  |||| |     | ||  |||| | || || | |   ||||      || | || ||  ||     ||  |   |  |       |  ||||    ||| |   || |    |||     |    |   ||  | || | |   |||  |      | ||| |     || |  ||   ||    | |  |   |||||||| || ||||| ||||| || ||||||||||||||||||||||| |||||||| || || ||||||||  | |||||    || ||| |||| ||  
gttt-attcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG

upper sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 27
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 25
gttcgattcgatcagtcattcctctaatctagagttcctcatgttcagctttgtaacccaatcgcatagccgttgtatactttgcacgtccgttagtgaaggtacttactttttagttaatagttagtaggttttctctggggatgtacttatgtctgacgtttctgttctgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAATTTCAACTGACTGTCAATGTTACGGCTCTTACCATCAATTTTGTCGCAT
                                                                          ||     |   || ||   ||  |||     | |  || ||  | ||  ||  |   | | || |    ||  | | |  ||||     | |  |||     | ||||||| || ||||| || || || ||||| ||||||||||| ||||||||||| || || ||||| |||||| | || ||||  |||||| |||| ||| 
--------------------------------------------------------------------------gttagtctactacatcaaatatagaaacatgtgatcttctacattatccttcatctttatgcttttctaat-caataaactctg-----tttactctt----ccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG

upper sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 27
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
gttcgattcgatcagtcattcctctaatctagagttcctcatgttcagctttgtaacccaatcgcatagccgttgtatactttgcacgtccgttagtgaaggtacttactttttagttaatagttagtaggttttctctggggatgtacttatgtctgacgtttctgttctgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAATTTCAACTGACTGTCAATGTTACGGCTCTTACCATCAATTTTGTCGCAT
                                                                                                                         || ||  || ||||    | |   ||    | |   ||  ||  ||           ||||||| |||||||| || ||||| |||||||| ||||||||||| || || || || |||||||| ||||||   || ||     ||||  | || ||  
----------------------------------------------------------------------------------------------------------------------gtaagataacagcttttg---gtgcgagtctgaaggatcgaaattcttgc----------agGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG

upper sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 27
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 23
gttcgattcgatcagtcattcctctaatctagagttcctcatgttcagctttgtaacccaatcgcatagccgttgtatactttgcacgtccgttagtgaaggtacttactttttagttaatagttagtaggttttctctggggatgtacttatgtctgacgtttctgttctgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAATTTCAACTGACTGTCAATGTTACGGCTCTTACCATCAATTTTGTCGCAT
                                                                                                                         || ||  || ||||    | |   ||    | |   ||  ||  ||           ||||||| |||||||| || ||||| |||||||| ||||||||||| || || || || |||||||| |||||    || ||     ||||  | || ||  
----------------------------------------------------------------------------------------------------------------------gtaagataacagcttttg---gtgcgagtctgaaggatcgaaattcttgc----------agGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTAGTTGCGCTGGTTCTCAACGTCGTGGCCG

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|162259197|gb|FC435217.1|FC435217
EST:     AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAG                         GTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
genomic: AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcg ... tgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
EST: gi|162153113|gb|FC329519.1|FC329519
EST:     AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAG                         GTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
genomic: AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcg ... tgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
EST: gi|162155067|gb|FC330861.1|FC330861
EST:     AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAG                         GTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
genomic: AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcg ... tgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
EST: gi|100367439|gb|BY984706.1|BY984706
EST:     AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAG                         GTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
genomic: AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcg ... tgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
EST: gi|162208804|gb|FC384940.1|FC384940
EST:     AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAG                         GTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
genomic: AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcg ... tgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
EST: gi|162191836|gb|FC367985.1|FC367985
EST:     AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAG                         GTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
genomic: AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcg ... tgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
EST: gi|162175273|gb|FC351471.1|FC351471
EST:     AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAG                         GTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
genomic: AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcg ... tgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
EST: gi|162186821|gb|FC363065.1|FC363065
EST:     AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAG                         GTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
genomic: AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcg ... tgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA
EST: gi|100443051|gb|BY981677.1|BY981677
EST:     AA-GTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAA                         GTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACNA
genomic: AAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcg ... tgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAA

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), 33 (downstream exon)
Score: 6

GCCGACATTGGTCTTTCAATGGGTATAGCAGGAACGGAAGTCGCGAAAGAAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcg ... tgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAATTTCAACTGACTGTCAATGTTACGGCTCTTACCATCAATTTTGTCGCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaggttttctctggggatgtacttatgtctgacgtttctgttctgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAATTTCAACTGACTGTCAATGTTACGGCTCTTACCATCAATTTTGTCGCAT
                                          ttctgat  putative branch site (score: 6)
                                    tttctgttct  CT-rich tract
                     tacttat  TA-rich tract