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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttatttatttctttatttattggaaagcttcaggtggtttatgcatgatgtatcatctcagcctgagtacaatcttgaacggttgtttggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCCTTTCGGGAATGCCGGATCTGAAACTTGGACTCAACGACAAAATAGGACT

Basic information

species Physcomitrella patens
transcript PP1S54_156V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 6
---acttatttatttcttta--tttattggaaagct-tcaggtggtttatgcatgatgtatcatctcagcctgagtacaatcttgaacggttgtttggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCCTTTCGGGAATGCCGGATCTGAAACTTGGACTCAACGACAAAATAGGACT
     | ||  ||| || |   ||||||| |  ||| | | ||  ||  ||       | |    |   |    ||  ||| | |||   |||  |  |  |||||| | |  | | || ||||| |||||||| |||||| | ||||||||||||||||| |||||||| ||||||||| | ||| | || ||||| || || ||
gtatttcatggattactatgattttattgtactgctctgatgtttttgttgtccttaatgttgctttgactgatgtttaatgtggaa--attgccttct-ctgcagGGAGTGTTCTACGATGTGATGTGACTGGGAAGATTCTTATGAAGTGCTTCCTTTCTGGAATGCCTGATCTGAAATTGGGATTAAATGACAAGATCGGGCT

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 6
acttatttatttctttatttattggaaagcttca-ggtggtttatgcatgatgtatcatctcagcctgagtacaatcttgaacggttgtttggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCCTTTCGGGAATGCCGGATCTGAAACTTGGACTCAACGACAAAATAGGACT
  |  | |||      |  || |      || ||  || || | | | |  ||||| |  | |   |   |     | | || |  |||    |  |||||| | |  | |  | ||||| ||||| || |||||| | ||||| ||||||||||| |||||||| |||||||| || ||| | || ||||| || |||||
-gtactctatggaccaacctaattttggactgcacagttgtctttacct--tgtattaattgatgttccttgtgtacataaatg--tgtc-attcctgcagGGAGTGTTCTAAGATGTGATGTGACGGGAAAGATTCTTATGAAATGCTTCCTTTCTGGAATGCCTGATCTGAAGCTGGGATTAAATGACAAGATTGGACT

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 6
acttatttatttctttatttattggaaagcttcaggtggt-ttatgcatgatgtatcatctcagcctgagtacaatcttgaacggttgtttggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCCTTTCGGGAATGCCGGATCTGAAACTTGGACTCAACGACAAAATAGGACT
                        |   |||   |||  | || | |   || | | || |  ||  |  | |   | ||     | ||||||   |  ||| | |  | |||||||||| || ||||| |||||| | ||||||||||| ||||| |||||||| ||| | ||  | ||  | || ||||| || || ||
------------------------gtgggctgtgggttttatttttctccatat-tgatatttgctaggttgcctgcctgctaactggtttgggaatttagGTAGTGTTCTGCGTTGTGATGTCACTGGGAAGATTCTCATGAAGTGCTTTCTTTCTGGAATGCCTGATTTAAAGTTGGGTTTGAATGACAAGATTGGTCT

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA17G16630.3 (Glycine max), 3'ss of exon 6
acttatttatttctttatttattggaaagcttcaggtggt-ttatgcatgatgtatcatctcagcctgagtacaatcttgaacggttgtttggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCCTTTCGGGAATGCCGGATCTGAAACTTGGACTCAACGACAAAATAGGACT
                        |   |||   | |    || | |   || | | || |  ||  |  | |   | ||     | |||||    |  ||| | |  | |||||||||| || ||||| |||||| | ||||||||||| ||||| |||||||| ||| | ||  | || || || ||||| || || ||
------------------------gtgggctgtggatttcatttttctccatat-taatatttgctaggttgcccgcatgctaactagtttgtgaatttagGTAGTGTTCTGCGTTGTGATGTCACTGGGAAGATTCTTATGAAGTGCTTTCTTTCTGGAATGCCTGATTTAAAGTTGGGTCTGAATGACAAGATTGGTCT

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 6
acttatttatttctttatttattggaaagcttcaggtggtttatgcatgatgtatcatctcagcctgagtacaatcttgaacggttgtttggtgttg--cagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCCTTTCGGGAATGCCGGATCTGAAACTTGGACTCAACGACAAAATAGGACT
  | | | ||| | ||  ||||        || | || || | | | || || ||   ||  |  ||| |    | ||| |   || | |||    |   ||| | |  | | || ||||| ||||| || ||| |||||||||| || ||||||||||||||||| ||| ||||  | ||  | || || ||||| || ||
-gtaaataattgcctt--ttatgaagttttttgaagttgtcttt-cttgttg-atttgctgtgtatgactg--gttttgca---ttttatggaaacggttagGCAATGTTCTTCGGTGTGATGTGACGGGGAAGGTTTTAATGAAATGTTTCCTTTCGGGAATGCCTGATTTGAAGTTGGGGTTGAATGATAAAATTGGTCT

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 6
acttatttatttctttatttattggaaagcttcaggtggtttatgcatgatgtatcatctcagcctgagtacaatcttgaacggttgtttggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCCTTTCGGGAATGCCGGATCTGAAACTTGGACTCAACGACAAAATAGGACT
                               | ||| | ||    |    || |   ||   |  ||   | | ||||      || |||     || ||| || |   |  | || ||||| || || |||||| | ||||||||||| || ||||| ||||| ||| | || || || ||||||||||||||||||||
------------------------------gtaaggcgcttgccac----tgaaaagtccttgt-tggaaatattcttcc----ttcttta----tgtagGGACAATCCTCAGATGCGACGTAACAGGGAAGATTCTCATGAAGTGCTTTCTATCGGGCATGCCTGATTTAAAGCTCGGGCTCAACGACAAAATAGGACT

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 6
acttatttatttctttatttattggaaagcttcaggtggtttatgcatgatgtatcatctcagcctgagtacaatcttgaacggttgtttggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCCTTTCGGGAATGCCGGATCTGAAACTTGGACTCAACGACAAAATAGGACT
                               | ||| | ||    |    || |   ||   |  ||   | | ||||      || |||     || ||| || |   |  | || ||||| || || |||||| | ||||||||||| || ||||| ||||| ||||| || || || ||||||||||||||||||||
------------------------------gtaaggcgcttgccac----tgaaaagtccttgt-tggaaatattcttcc----ttcttta----tgtagGGACAATCCTCAGATGCGACGTAACAGGGAAGATTCTCATGAAGTGCTTTCTATCGGGCATGCCTGATCTAAAGCTCGGGCTCAACGACAAAATAGGACT

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|100401870|gb|BY954751.1|BY954751
EST:     GTCTTTCTCGATATTGTGGAAAGTGTCAATCTCCTCATGTCTCAGAAAG                         GAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCC
genomic: GTCTTTCTCGATATTGTGGAAAGTGTCAATCTCCTCATGTCTCAGAAAGgtgagtcttt ... ggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCC
EST: gi|162233608|gb|FC409367.1|FC409367
EST:     GTCTTTCTCGATATTGTGGAAAGTGTCAATCTCCTCATGTCTCAGAAAG                         GAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCC
genomic: GTCTTTCTCGATATTGTGGAAAGTGTCAATCTCCTCATGTCTCAGAAAGgtgagtcttt ... ggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCC
EST: gi|208385555|gb|DC937100.1|DC937100
EST:     GTCTTTCTCGATATTGTGGAAAGTGTCAATCTCCTCATGTCTCANAAAG                         GAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCC
genomic: GTCTTTCTCGATATTGTGGAAAGTGTCAATCTCCTCATGTCTCAGAAAGgtgagtcttt ... ggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCC
EST: gi|162178167|gb|FC354885.1|FC354885
EST:     GTCTTTCTCGATATTGTGGAAAGTGTCAATCTCCTCATGTCTCAGAAAG                         GAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCC
genomic: GTCTTTCTCGATATTGTGGAAAGTGTCAATCTCCTCATGTCTCAGAAAGgtgagtcttt ... ggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCC
EST: gi|67578518|gb|BJ950685.1|BJ950685
EST:     GTCTTTCTCGATATTGTGGAAAGTGTCAATCTCCTCATGTCTCAGAAAG                         GAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCC
genomic: GTCTTTCTCGATATTGTGGAAAGTGTCAATCTCCTCATGTCTCAGAAAGgtgagtcttt ... ggtgttgcagGAACTACTTTGCGTTGTGACGTGACTGGCAAGATTTTAATGAAGTGCTTCC