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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctactcacacgcgatccttcaattcatcggaacaatcgatgtagacgtctagaaatagtactcacgtgattggagactccgttgctgtacaaattttgttgtgctatctcgagattattacgtgtggcctaaatttaggaagttgtatattggtgacaattctgcagAGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACAGGAAGTATCCAACGGGGATACGAACCAACAGAGCCACTGAGAAGGGGTA

Basic information

species Physcomitrella patens
transcript PP1S259_58V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S259_58V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g42630.1 (Oryza sativa), 3'ss of exon 1
gtacgctactcacacgcgatccttcaattcatcggaacaatcgatgtagacgtctagaaatagtactcacgtgattggagactccgttgctgtacaaattttgttgtgctatctcgagattattacgtgtggcctaaatttaggaagttgtatattggtgacaattctgcagAGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACAGGAAGTATCCAACGGGGATACGAACCAACAGAGCCACTGAGAAGGGGTA
                                                               || |||| ||  || | || |      || |||  |     ||    |  |   ||| | |   | |  |  |        | |||| ||    |||| |    |||||  || || |   | ||||||||||| ||||| ||||||||| |||| ||| | ||||| || |||||||| || |||||| | ||||| ||    || ||
--------------------------------------------------------------ata-tcac-tgcatgcatacactacaaatgcacacgtacaaatgaatgaatt---gatcaatcgttcttacacatgaacgcaatgttg-atggatgtgata----tgcagGCAAGGCAAGCATGGGGGAGAAGGAGTGGTACTTCTTCAGCATGCGCGACCGCAAGTACCCGACGGGGATCCGCACCAACCGCGCCACGGACTCCGGCTA

upper sequence: PP1S259_58V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G04610.1 (Glycine max), 3'ss of exon 1
gtacgctactcacacgcgatccttcaattcatcggaacaatcgatgtagacgtctagaaatagtactcacgtgattggagactccgttgctgtacaaattttgttgtgctatctcgagattattacgtgtggc-ctaaatttaggaagttgta--tattggtgacaatt--ctgcagAGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACAGGAAGTATCCAACGGGGATACGAACCAACAGAGCCACTGAGAAGGGGTA
                                                                          ||||| |||       |  |||||||   | ||  | | |  |   | ||| |||      |||||  |  || || |   ||||| |||    |      ||  || ||     | || |||||||||||||||||||||||| ||  |||  |||| |||||||| ||| | ||||||||| ||||||||||    |||||
--------------------------------------------------------------------------ttggacact--aaccgtagacaaattgattcgta-tgtatatatgcttttaagtgaaaaattaaataaactaaattatgactattgatgatgtgtggtaatagGTAAGGCATCGATGGGCGAGAAGGAATGGTATTTCTTCAGCTTGAAAGATCGGAAATATCCAACTGGGCTTCGAACCAACCGAGCCACTGAATCAGGGTA

upper sequence: PP1S259_58V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA05G35090.1 (Glycine max), 3'ss of exon 1
gtacgctactcacacgcgatccttcaattcatcggaacaatcgatgtagacgtctagaaatagtactcacgtgattggagactccgttgctgtacaaattttgttgtgctatctcgagattattacgtgtggcctaaatttaggaagttgtatattg-gtgacaattctgcagAGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACAGGAAGTATCCAACGGGGATACGAACCAACAGAGCCACTGAGAAGGGGTA
                                                         |||||      |  | |||  ||       |  | || | ||  | ||  |       || |  || |    |   |||||||  |    ||| || ||| |||  |||     ||  || ||     | || |||||||||||||||||||||||| ||  |||  |||| |||||||| ||| | ||||||||| ||||||||||    |||||
---------------------------------------------------------aaatatgcgctatat-attatagcgcgtagtattatatatatgcttttaagt------gaaaaaataa---ataaactaaattaggattattg-atgttgtgtggtaat-----agGTAAGGCTTCGATGGGCGAGAAGGAATGGTATTTCTTCAGCTTGAAAGATCGGAAATATCCAACTGGGCTTCGAACCAACCGAGCCACTGAATCAGGGTA

upper sequence: PP1S259_58V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT3G15170.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacgctactcacacgcgatccttcaattcatcggaacaatcgatgtagacgtctagaaatagtactcacgtgattggagactccgttgctgtacaaattttgttgtgctatctcgagattattacgtgtggcctaaatttaggaagttgtatattggtgacaattctgcagAGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACAGGAAGTATCCAACGGGGATACGAACCAACAGAGCCACTGAGAAGGGGTA
                                                    | || |   |    |||| ||| ||   | |||     ||| |   | |      |    |||    ||| |  || ||   ||| |||            | |  |  || ||  ||||||||||||||| | ||||||||||| ||||| |||||||  ||  ||||| | || || ||||||||  |  |||| |||||||| || ||    || ||
---------------------------------------------------ctttatatcaacccttcacatgagtgaccagtcc----ttgttcggttctaaaacagagtcctcc---ttactctgtttg---taacttt-----------cacttataccatttgagcagAGAAAGCGAAAATGGGGGAGAAGGAGTGGTACTTCTTCACACTAAGAGACCGTAAATACCCAACGGGACTGAGAACGAACAGAGCAACAGAAGCTGGTTA

upper sequence: PP1S259_58V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
gtacgctactcacacgcgatccttcaattcatcggaacaatcgatgtagacgtctagaaatagtactcacgtgattggagactccgttgctgtacaaattttgttg--tgctatctcgagattattacgtgtggcctaaatttaggaagttgtatattggtgacaattc-tgcagAGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACAGGAAGTATCCAACGGGGATACGAACCAACAGAGCCACTGAGAAGGGGTA
                                                                          ||  |  |  |||| ||  | ||  || | |   ||||||||     ||       |||  |   | | |     | || | | | |     | |   |||| || || ||  | || |||||||||||||| |||||||  ||||||||| | |||||||| ||||| || || || ||| ||||||| |||   || ||
--------------------------------------------------------------------------ttctatgcatcgtttct-cataatcttggctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA

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|162155137|gb|FC330931.1|FC330931
EST:     GTCGATTCCGAACGTGAGCCTCAACAAATGCGAGCCCTGGGATCTTCCTG                         AGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACA
genomic: GTCGATTCCGAACGTGAGCCTCAACAAATGCGAGCCCTGGGATCTTCCTGgtacgctact ... aattctgcagAGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattattacgtgtggcctaaatttaggaagttgtatattggtgacaattctgcagAGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACAGGAAGTATCCAACGGGGATACGAACCAACAGAGCCACTGAGAAGGGGTA
              gcctaaa  putative branch site (score: 3)
                 taaattta  TA-rich tract