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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgtgtacatcagccaaatcaaaacgtggtttggtctgttagcaatttcaatgtcttttgtaactgctgacgcgattccttttgctggtctctgtacagGTCGGTTTCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACTGTGGGATTTGGGTGGCCAACCCCGCTTTCGTAGTATGTGGGAGCGCTACT

Basic information

species Physcomitrella patens
transcript PP1S6_409V6.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ07633 (Selaginella moellendorffii), 3'ss of exon 3
cctgtgtacatcagccaaatcaaaacgtggtttggtctgttagcaatttcaatgtcttttgtaactgctgacgcgattccttttgctggtctctgtacagGTCGGTTTCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACTGTGGGATTTGGGTGGCCAACCCCGCTTTCGTAGTATGTGGGAGCGCTACT
                     |  |  |   | | ||  |   | ||     | || |   |  |||       |||  || |  |           ||||| || ||||| ||| | |||||| | || |||||||| || ||||| ||||||||| |||| || ||||| ||||| || ||||||||||||||||| |
-------------------gtaggaattctctcgatcgat---ccatccttgtctcctccatgcctgacctgaggatctctctctc----------gcagGTGGGATTCAACATGAGAAAAGTGACCAAAGGCAATGTGACGATCAAGCTGTGGGATCTGGGCGGACAACCACGCTTCCGGAGTATGTGGGAGCGCTATT

upper sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ11035 (Selaginella moellendorffii), 3'ss of exon 3
cctgtgtacatcagccaaatcaaaacgtggtttggtctgttagcaatttcaatgtcttttgtaactgctgacgcgattccttttgctggtctctgtacagGTCGGTTTCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACTGTGGGATTTGGGTGGCCAACCCCGCTTTCGTAGTATGTGGGAGCGCTACT
                               | ||  |  |  | ||       || |||    || |   |  ||       ||  | |||||   ||||| || ||||| ||| | |||||| | || |||||||| || ||||| ||||||||| |||| || ||||| ||||| || ||||||||||||||||| |
------------------------------gtaggaattctgtcgatcgatccatccttttctcctccatgcctga-----cctgaggatctct-cgcagGTGGGATTCAACATGAGAAAAGTGACCAAAGGCAATGTGACGATCAAGCTGTGGGATCTGGGCGGACAACCACGCTTCCGGAGTATGTGGGAGCGCTATT
















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|208364105|gb|DC950397.1|DC950397
EST:     ACTGGTGGTTATAGCGAAGATATGATTCCCACC                         GTCGGTTTCCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACT
genomic: ACTGGTGGTTATAGCGAAGATATGATTCCCACCgtaagtgctt ... ctctgtacagGTCGGTTT-CAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACT
EST: gi|208382259|gb|DC919247.1|DC919247
EST:     ACTGGTGGTTATAGCGAAGATATGATTCCCACC                         GTCGGTTTCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACTG
genomic: ACTGGTGGTTATAGCGAAGATATGATTCCCACCgtaagtgctt ... ctctgtacagGTCGGTTTCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACTG
EST: gi|208374248|gb|DC945294.1|DC945294
EST:     ACTGGTGGTTATAGCGAAGATATGATTCCCACC                         GTCGGTTTCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACTG
genomic: ACTGGTGGTTATAGCGAAGATATGATTCCCACCgtaagtgctt ... ctctgtacagGTCGGTTTCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACTG
EST: gi|67577659|gb|BJ949826.1|BJ949826
EST:     ACTGGTGGTTATAGCGAAGATATGATTCCCACC                         GTCGGTTTCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACTG
genomic: ACTGGTGGTTATAGCGAAGATATGATTCCCACCgtaagtgctt ... ctctgtacagGTCGGTTTCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcaatgtcttttgtaactgctgacgcgattccttttgctggtctctgtacagGTCGGTTTCAATATGCGTAAAGTGTCGAAGGGCAATGTTACTATCAAACTGTGGGATTTGGGTGGCCAACCCCGCTTTCGTAGTATGTGGGAGCGCTACT
                    tgctgac  putative branch site (score: 2)
                                            tctctgt  putative PPT
           ttttgtaa  TA-rich tract