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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccatgaggttaatttggtacagcttggggaacagcctatattttgtaatccgctaactctttctcggctcgtaacacggatggcgtttactctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG

Basic information

species Physcomitrella patens
transcript PP1S397_39V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S397_39V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 2
-tccatgaggttaatttggtacagcttggggaacagcctatattttgtaatccgctaactctttctcgg-ctcgtaacacg-gatg-gcgtttactctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG
  ||   |    |||||   ||  | ||   |    | |  ||  | |||   | |  |  ||  | |  || | ||   | |||| |   |||    || ||||||||||||| ||||| || ||||| |||||||||||||| ||    ||||| ||||| |||   ||||| |  || |||  ||  || || |||
gaccgcaatagcaatttaaaac--catgcataggtacatgaataat-taagttgttttcaattcattgaacttggaaattgtgatgtgaaattaaaacga-cagTGCAGCACACCAGTGCTTCTCTTACCATCAATGAGAATTATGACTCAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG
















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|37835032|gb|BJ593044.1|BJ593044
EST:     GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTT                         TGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
genomic: GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTTgtgagtaaca ... ctctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
EST: gi|162267552|gb|FC444303.1|FC444303
EST:     GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTT                         TGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
genomic: GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTTgtgagtaaca ... ctctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
EST: gi|162267551|gb|FC444302.1|FC444302
EST:     GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTT                         TGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
genomic: GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTTgtgagtaaca ... ctctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
EST: gi|18336855|gb|BJ168878.1|BJ168878
EST:     GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTT                         TGCAGCACACTAAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGAT
genomic: GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTTgtgagtaaca ... ctctgatcagTGCAGCACACT-AGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatccgctaactctttctcggctcgtaacacggatggcgtttactctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG
                        tcgtaac  putative branch site (score: 2)
                                         tttactct  putative PPT