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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcttcttcatcttcaagtgttaaggtcaacgaatagcatttcatgatttatttgtcttctttttgataactttttgttgtgttatcaaaccctcatgcctttcaaccttcgtttcttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCGAGGAAACAAACTGATCGACGCCGCCATTACTTCATCTTTGCTTGAGACG

Basic information

species Physcomitrella patens
transcript PP1S98_222V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA10G32040.1 (Glycine max), 3'ss of exon 7
gtaggcttcttcatcttcaagtgttaaggtcaacgaatagcatttcatgatttatttgtcttctttttgataactttttgttgtgttatcaaaccctcatgcctttcaaccttcgtttcttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCGAGGAAACAAACTGATCGACGCCGCCATTACTTCATCTTTGCTTGAGACG
             | ||    | ||    |  | ||||    |||||  | |  | ||  |||||  |  |      | | | | | ||||||   | ||           || ||    |    |||    |||||||| ||||||||||||||||||||||| ||| |||||||| |||       | | |   | || ||  | || |||||||| |||||| ||
------------gtattttttttttgtcttgtaagaatgttttttcacaaatgttctgcattcttggttttg----ctagatttttcatcaaattttgat---------tatttgtgaaataaaccagACGACAAGATTCTTCAATTGGTTTTGGAGCACCTGTCCGTTCCAATATGAGAGCTGGTGGAATTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 10
gtaggcttcttcatcttcaagtgttaaggtcaacgaatagcatttcatgatttatttgtcttctttttgataactttttgttgtgttatcaaaccctcatgcctttcaaccttcgtttcttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCGAGGAAACAAACTGATCGACGCCGCCATTACTTCATCTTTGCTTGAGACG
   |   | ||   |||    |   ||    |     |   |  |||   ||  |||   |     ||| |    || || |||  || |      | || |  || |       |    |    |||    |||||||| || ||||||||||||||||| ||||||||||||||| |||       | | |  ||  | ||  | || |||||||| |||||| | 
---gtaatgttggcctttgtcttgcaaaaatatttgctcataaatcacagttggtttacatatgacttggt----ttctgctgtactaac------ttatacgattta-------tcaaataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaggcttcttcatcttcaagtgttaaggtcaacgaatagcatttcatgatttatttgtcttctttttgataactttttgttgtgttatcaaaccctcatgcctttcaacct-tcgtttcttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCGAGGAAACAAACTGATCGACGCCGCCATTACTTCATCTTTGCTTGAGACG
                                       | | ||||| |||  |   | || |||||   ||    ||   | ||| |       | |      ||| | | ||   |  | |  |||    ||||| |||||||||||||||||||| |||||||||||||| |||      |    | ||| |   |  || || |||||||||||||| ||  ||
---------------------------------------gtaattcattattcgtccttttttttttttgcaatagattaggg-gttct---gttttgacattgatcagcatctctaatgctctgccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG

upper sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
-gtaggcttcttcatcttcaagtgttaaggtcaacgaatagcatttcatgatttatttgtcttctttttgataactttttgttgtgttatcaaaccctcatgcctttcaaccttcgtttcttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCGAGGAAACAAACTGATCGACGCCGCCATTACTTCATCTTTGCTTGAGACG
 ||  |  | |   | |    |||| || |  |  ||      |      || ||||||           ||||     | | |  |    ||||  |    || | ||      | || || |  |||   ||||||||| ||||||||||||||||||||||||||||| || ||| ||          | | | | || |   | || ||||| || || ||  ||
tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggt-----aatatatttg----------aataa-----tatggcct----aaactttggaaccctaca-----tggtttttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG

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|162179889|gb|FC355960.1|FC355960
EST:     TTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAG                         GAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCG
genomic: TTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAGgtaggcttct ... cttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCG
EST: gi|162247501|gb|FC425067.1|FC425067
EST:     TTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAG                         GAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCG
genomic: TTCATATGTGGAGGTGCTTTCGTTGAATTGGAGAAGAGCATTGCAGAAAGgtaggcttct ... cttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttgttgtgttatcaaaccctcatgcctttcaaccttcgtttcttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCGAGGAAACAAACTGATCGACGCCGCCATTACTTCATCTTTGCTTGAGACG
                                    ccttcgtttcttgttt  CT-rich tract
            ttatcaaa  TA-rich tract