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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCGGGTGTACACCGAACGTCGGCGCGCTTTGGAGGCGACAAACTTAGAAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAGgtacgcgtttccttactgttggtgttacaactattgtttgtatcgaaaaaaaattattcctcagtaatccaaagtgtctctggatagttctctgctgggaagttgtaaggtaatgaatgatgtgatgatgcag

Basic information

species Physcomitrella patens
transcript PP1S9_141V6.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_141V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 5'ss of exon 17
TGACCGGGTGTACACCGAACGTCGGCGCGCTTTGGAGGCGACAAACTTAGAAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAGgtacgcgtttccttactgttggtgttacaactattgtttgtatcgaaaaaaaattattcctcagtaatccaaagtgtctctggatagttctctgctgggaagttgtaaggtaatgaatgatgtgatgatgcag
 ||||| || ||  | ||  |  |||| ||  | ||  | |  ||| |  || | |   | ||||||||||| ||| ||||||||||||| ||| ||||||||      ||||   | ||             ||||| |      |      || || | ||   ||   ||||    |     |||||  ||   |  | |   |   |  || ||    ||||| |  ||
GGACCGTGTATATGCAGAGAGAAGGCGAGCCCTTGAATCTAACAACCTCCAATCTCTTCTTATTGAATATGCTGAACTGACAATGGATGACATCTTGGAGgtaaaatcatcctgggtttt-------------ttgttcgc--tagacttcccttttttcccatctattgcaagttatacacaccagttccttg--agatattaacagattgttgtatttaatgatg-tatag
















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|162180613|gb|FC356970.1|FC356970
EST:     AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAG                         GCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
genomic: AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAGgtacgcgttt ... gatgatgcagGCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
EST: gi|162261062|gb|FC436936.1|FC436936
EST:     AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAG                         GCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
genomic: AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAGgtacgcgttt ... gatgatgcagGCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
EST: gi|162262117|gb|FC436872.1|FC436872
EST:     AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAG                         GCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
genomic: AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAGgtacgcgttt ... gatgatgcagGCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
EST: gi|162159762|gb|FC336343.1|FC336343
EST:     AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAG                         GCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
genomic: AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAGgtacgcgttt ... gatgatgcagGCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
EST: gi|162180612|gb|FC356969.1|FC356969
EST:     AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAG                         GCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
genomic: AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAGgtacgcgttt ... gatgatgcagGCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
EST: gi|162262116|gb|FC436871.1|FC436871
EST:     AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAG                         GCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA
genomic: AAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAGgtacgcgttt ... gatgatgcagGCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTA

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: 29 (upstream exon), 32 (downstream exon)
Score: 3

TGACCGGGTGTACACCGAACGTCGGCGCGCTTTGGAGGCGACAAACTTAGAAGCACAAATGATTGAATATGCAGAATTGACAATGGATGATATCCTGGAGgtacgcgttt ... gatgatgcagGCAAACGTGGACTCATCCCTTCCTCAGGAAGAATGGAATTTAGAAGCTTTATGTGCAAAAGTCAAGCA




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