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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgacttcgttacaaattctgcacatgatctatgcactgatcctgtaaagacttcaatggtatttttgaatgctagcatgattagattttcaacttgagtaatgcatcctgattctttgtactccaatgaaatgctgtgttggtggacagCTGAAACTGTGATCTACAGAATATTCTACCATGTAAATAAATCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAACGGAGTAACTTAATTACTGCTCT

Basic information

species Physcomitrella patens
transcript PP1S147_62V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacgacttcgttacaaattctgcacatgatctatgcactgatcctgtaaagacttcaatggtatttttgaatgctagcatgattagattttcaacttgagtaatgcatcctgattctttgtactccaatgaaatgctgtgttggtgga-cagCTGAAACTGTGATCTACAGAATATTCTACCATGTAAATAAATCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAACGGAGTAACTTAATTACTGCTCT
                                        ||      ||| |  |  |   | ||| |||||     ||||     ||||| |  |  |  |    || || || ||   | ||   |  |  |||  | ||| || | ||||||||||||| | |||||||||||| ||| |  |||||| |||||| ||||||||  |   | |||| ||| | |||||| | |||||||||  |||| |
----------------------------------------gaaaaaaaaaaaatctggagcttgtttatgaat-----catgt----attttga--tgaaacagctgatgct-atgctacatgctgatacaatttgc-attttgatgaaacagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 6
gtacgacttcgttacaaattctgcacatgatctatgcactgatcctgtaaagacttcaatggtatttttgaatgctagcatgattagattttcaacttgagtaatgcatcctgattctttgtactccaatgaaatgctgtgttggtggacagCTGAAACTGTGATCTACAGAATATTCTACCATGTAAATAAATCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAACGGAGTAACTTAATTACTGCTCT
                                                       |   | |  ||||| | || |     | ||   || ||  ||    | || | |  |  || ||||   |         || | | || ||   |||| || || || || ||||| ||||||||||||||||||| |||||| |||||  |||||   || |||||||| | | | || ||| |  || | || ||
------------------------------------------------------gttggttgatttttttagtgtt-----gtttttgttgtcg-ctcagatcattctttttctttgtttgcttt---------tgttctttttgttcgcagCCGAGACAGTAATGTACAGGATATTCTACCATGTAAATAGATCTGGAAATGGAAGGCTATTGCTAAGAGAGTTGAGAAGAAGCAACCTTGTTGCAGCACT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 6
gtacgacttcgttacaaattctgcacatgatctatgcactgatcctgtaaagacttcaatggtatttttgaatgctagcatgattagattttcaacttga-gtaatgcatcctgattctttgtactccaatgaaat-gctgtgttggtggacagCTGAAACTGTGATCTACAGAATATTCTACCATGTAAATAAATCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAACGGAGTAACTTAATTACTGCTCT
                                                                     |   |||    || |||| ||||    |||  ||    ||     ||||||| |  |    ||   | | | | || ||   |||| || || || || ||||| ||||||||||||||||||| |||||| |||||  |||||   || |||||||| | | | || ||| |  || | || ||
---------------------------------------------------------------------gttggctgatttgtttagtttttttttttgttgtcgctcaaatc-attctttttctttgtttgcttttgttctttttgttcgcagCCGAGACAGTAATGTACAGGATATTCTACCATGTAAATAGATCTGGAAATGGAAGGCTATTGCTAAGAGAGTTGAGAAGAAGCAACCTTGTTGCAGCACT

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|162193203|gb|FC369963.1|FC369963
EST:     TCGCGGTTTGGAATTTCTTCATGATACCCCAGAGTTTCAAGACAGATATG                         CTGAAACTGTGATCTACAGAATATTCTACCATGTAAATAAATCTGGGAATG
genomic: TCGCGGTTTGGAATTTCTTCATGATACCCCAGAGTTTCAAGACAGATATGgtacgacttc ... tggtggacagCTGAAACTGTGATCTACAGAATATTCTACCATGTAAATAAATCTGGGAATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtaatgcatcctgattctttgtactccaatgaaatgctgtgttggtggacagCTGAAACTGTGATCTACAGAATATTCTACCATGTAAATAAATCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAACGGAGTAACTTAATTACTGCTCT
           tcctgat  putative branch site (score: 3)
                              aatgaaat  TA-rich tract