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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgtattcactgacacttactttcgatcagcttccttggccttggtctccagtttactgtttattattcgactcgaagttacccttcgtgattatttgaata...

Basic information

species Physcomitrella patens
transcript PP1S47_46V6.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 4
TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgtattcactgacacttactttcgatcagcttccttggccttggtctcc-agtttactgtttattattc-gactcgaagttacccttcgtgattatttgaata------
 || || ||   ||| || ||| |||| ||  | ||||| |||||||| ||  | |||||||||||||||||||| || || || ||||| ||||| ||||||  |||  | |  |  ||     |   ||          ||||    || | | ||| || | ||| |||| ||  | |   | | || || ||| | |       
AGGTGGTCTGTCTGATCAGATTAGAGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAATCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaaatatatgtttagatcccaattatgcatatgaggtcaaagagataaatgtctaatgttccgactggatatcaatatgcttgtttgttttactcatccag

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA06G03230.1 (Glycine max), 5'ss of exon 4
TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgta---------ttcactgacacttactttcgatcagcttccttggccttggtctccagtttac-tgtttatta--ttcgactcgaagttacccttcgtgattatttgaata-----------------------------------------------------------------------
||| ||  ||  ||| || ||  | ||| |  | ||||| |||||  | ||  | ||||||||||| |||||||| |||||||| |||||||||||||||||          |||||||    ||    ||  | |  |   || |  ||  |||    ||||  | |||| ||  || |    ||  ||   | |    ||| ||| | |                                                                        
TGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGTCAATTGAACTACCTCTGATGAATCCTGAGCTCTTTCTTCGAGTTGGAATTAAACCTCCAAAGgtgatttaccctttcactgctctttctagtctctgacttctattagtgttaatctatgttttagatttttagtagctttgttatgacatttttcctacatatttttttagtggaagcttacttgtaatggctgtacttttgaattttacacttgatcaaaatcttttcaattctaattttcag

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA04G03180.1 (Glycine max), 5'ss of exon 4
TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgta---------ttcactgacacttactttcgatcagcttccttggccttggtctccagtttactgtttattattcgactcg--aagttacccttcgtgattatttgaata--------------------------------------------------------------------------
||| ||  ||  ||| || ||  | ||| |  | ||||| |||||  ||||  ||||||||||||| ||||| || |||||||| |||||||||||||||||          || ||||    ||    ||  | |  |   || |  ||  |||    ||||  | || ||| | |  | |  | || |   ||  |   |||||   ||                                                                          
TGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGTCAATTGAACTGCCTCTAATGAATCCTGAGCTCTTCCTTCGAGTTGGAATTAAACCTCCAAAGgtgatttacctttttactgctctttctagtctctgatttctattagtgttaatctatgtttta--gatttttagtagctttgttatgtcattttttctacatatttttttagtggaagcttatttgtaatggccgtacttttgaattttacatttaatcaaaatcttttcaattctaattttcag

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv18s0001g13090.t01 (Vitis vinifera), 5'ss of exon 4
TGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTCGATTGAGTTGCCGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgt-attcac---------tgacacttacttt--------cgatcagcttccttggccttggtctccagtttactgtttattattcgactcgaagttacccttcgtgattatttgaata--------------------------
 || ||  ||   || ||||| ||||||||  | || || |||||| | ||  ||||||||||||||||||||||  ||||||| ||||||||||| ||||| |||||          ||  | ||| | |         | || || |  |       | |  |||   || || |  | |   || | ||  |||   ||  |  ||| || || |                          
GGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAATCAATTGAGCTACCTCTAATGAATCCTGAACTCTTTCTTAGAGTTGGAATTAAACCTCCCAAGgtgattcatactttaatttgttagttattctgtatggtctgttctgcattgtcaattgagttagccatcctagtggtggtaacatgaatggattttatttttt-tccttaattaaaaagtctcttaaattttatttttttgcag

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|18338881|gb|BJ170907.1|BJ170907
EST:     TTGGCATT-AACCNTCCAAAG                         GGTGTGTTGTTATATGGGCNTCCTGGGACTGGTAAAACTCTTTTAGCACG
genomic: TTGGCATTAAACC-TCCAAAGgtattcactg ... ccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACG
EST: gi|208398538|gb|DC912383.1|DC912383
EST:     CGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAG                         GGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAA-CTCTTTTAGCACGA
genomic: CGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgtattcactg ... ccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGA
EST: gi|100405000|gb|BY991388.1|BY991388
EST:     TTAATGAATCCTGAAACTCTT-CTGCGAGTTGGCATAAAAC-TCCCAAAG                         G-TGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACG
genomic: TTAATGAATCCTGAA-CTCTTTCTGCGAGTTGGCATTAAACCTCC-AAAGgtattcactg ... ccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACG
EST: gi|162269527|gb|FC445083.1|FC445083
EST:     CGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAG                         GGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGA
genomic: CGTTAATGAATCCTGAACTCTTTCTGCGAGTTGGCATTAAACCTCCAAAGgtattcactg ... ccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGA