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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaattagagtcactgttccgtcagtgaaggttagtgtcgccgaaagccacgatgaatttgcaaaattaacttctagttttctgtccatcttgtgaacagGAAGATTTTAGGCCCGTTTTACGAGAATTGTTGTTGACGCATCGCGGTTTGGAATTTCTCCATGACACCCCGGAGTTTCAAGACAGATATG

Basic information

species Physcomitrella patens
transcript PP1S7_163V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 5
gtaattagagtcactgttccgtcagtgaaggttagtgtcgccgaaagccacgatgaatttgcaaaattaacttctagttttctgtccatcttgtgaacagGAAGATTTTAGGCCCGTTTTACGAGAATTGTTGTTGACGCATCGCGGTTTGGAATTTCTCCATGACACCCCGGAGTTTCAAGACAGATATG
                                  ||  |      |||  ||||    ||| ||   ||| |               ||| | |   ||||| ||||| |  ||  | ||    ||  | ||| |||| || ||||||||||||||||| |||||||| || ||||||||||| |||||||
----------------------------------gtaactttagcagc--cgatattcttgaaagcataattgt-------------atcgtatctccagGAGGATTTCAAACCAATCTTGAAGGAGCTTTTGATGACTCACCGCGGTTTGGAATTTCTTCATGACACTCCTGAGTTTCAAGAAAGATATG

upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 5
gtaattagagtcactgttccgtcagtgaaggttagtgtcgccgaaagccacgatgaatttgcaaaattaacttctagttttctgtccatcttgtgaacagGAAGATTTTAGGCCCGTTTTACGAGAATTGTTGTTGACGCATCGCGGTTTGGAATTTCTCCATGACACCCCGGAGTTTCAAGACAGATATG
                                  ||  |      |||  ||||    ||| ||   ||| |               ||| | |   ||||| ||||| |  ||  | ||    ||  | ||| |||| || ||||||||||||||||| |||||||| || ||||||||||| |||||||
----------------------------------gtaactttagcagc--cgatatccttgaaagcataattgt-------------atcgtatctccagGAGGATTTCAAACCAATCTTGAAGGAGCTTTTGATGACTCACCGCGGTTTGGAATTTCTTCATGACACTCCTGAGTTTCAAGAAAGATATG
















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|162155853|gb|FC332402.1|FC332402
EST:     CTCGCGTCTTCACTGTGTTGAAGCAACCCGACAAGAATTTTCTGAGACAG                         GAAGATTTTAGGCCCGTTTTACGAGAATTGTTGTTGACGCATCGCGGTTTG
genomic: CTCGCGTCTTCACTGTGTTGAAGCAACCCGACAAGAATTTTCTGAGACAGgttagtttct ... ttgtgaacagGAAGATTTTAGGCCCGTTTTACGAGAATTGTTGTTGACGCATCGCGGTTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccacgatgaatttgcaaaattaacttctagttttctgtccatcttgtgaacagGAAGATTTTAGGCCCGTTTTACGAGAATTGTTGTTGACGCATCGCGGTTTGGAATTTCTCCATGACACCCCGGAGTTTCAAGACAGATATG
                   aattaac  putative branch site (score: 2)
                                ttttctgtccatctt  putative PPT
          aatttgcaaaattaa  TA-rich tract