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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaagtttaaacatggacgatagttttgttttggggtgagatgtagtggaagatgtcatgggtgtcgtctcactgggtggttgcggttgatgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCC

Basic information

species Physcomitrella patens
transcript PP1S69_31V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ11261 (Selaginella moellendorffii), 3'ss of exon 1
gcaagtttaaacatggacgatagttttgttttggggtgagatgtagtggaagatgtcatgggtgtcgtctcactgggtggttgcggttgatgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCC
    ||        |  ||||  |   | ||   ||    ||||  |||||       |||      ||||            | |||  | |    |||||||||| || || ||||||||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || || || ||||| || || ||||||||
----gtaagcggccgatcgatgttcgcgattctagggtttatgtgatggaa-------tggaaaatttctc------------ctgttcttctctcccagGGCCTGTCGCGGAGGATATGTTCCACTGGCAAGCGACGATCATGGGACCTCCCGATAGTCCCTACGCGGGTGGGGTTTTCCTGGTGACCATCCACTTCCC

upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ27529 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------gcaagtttaaacatggacgatagttttgttttggggtgagatgtagtggaagatgtcatgggt--gtcg-tctcactgggtggttgcggttgatgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCC
                            |||  |  | |  |||  |  |  ||||   |||  | |||  || ||| || | | |   ||| ||||||||  | |  ||| ||         |||| || ||||| ||||||||||| |||||||| || ||||||||||| || || ||||| || || ||||| || ||||| |||||||||||||| |||||
gtgagcgcgcgccacaaaatccatgggattttgatgtcgg-gattttccttctttgccttgatttctagctgacgatctcgtcgatctatcgatctcactgctttgc-gcgattcg-------cagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGCCCGATAGCCCCTACGCGGGCGGTGTGTTCCTGGTCACTATTCATTTCCC

upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ15547 (Selaginella moellendorffii), 3'ss of exon 1
gcaagtttaaacatggacgatagttttgttttggggtgagatgtagtggaagatgtcatgggtgtcgtctcactgggtggttgcggttgatgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCC
          |   ||||||| | |    || | | |   | |   |    ||||   |||      ||||            | |||  | |    |||||||||| || || ||||||||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || || || ||||| || || ||||||||
--------gtaagcggacgatcgat---cttcgcgattctagggtttatgtgatggagtggaaaatttctc------------ctgttcttctctcccagGGCCTGTCGCGGAGGATATGTTCCACTGGCAAGCGACGATCATGGGACCTCCCGATAGTCCCTACGCGGGTGGGGTTTTCCTGGTGACCATCCACTTCCC

upper sequence: PP1S69_31V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ35297 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------gcaagtttaaacatggacgatagttttgttttggggtgagatgtagtggaagatgtcatgggt--gtcg-tctcactgggtggttgcggttgatgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCC
                            |||     | |  |||  |  |  ||||   |||  | |||  || ||| || | | |   ||| ||||||||  | |  ||| ||         |||| || ||||| ||||||||||| |||||||| || ||||||||||| || || ||||| || || ||||| || ||||| |||||||||||||| |||||
gtgagcgcgcgccacaaaatccatgggattttggtgtcgg-gattttccttctttgccttgatttctagctgacgatctcgtcgatctatcgatctcactgctttgc-gcgattcg-------cagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGCCCGATAGCCCCTACGCGGGCGGTGTGTTCCTGGTCACTATTCATTTCCC

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|162193815|gb|FC369223.1|FC369223
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTG                         GGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
EST: gi|208392917|gb|DC928603.1|DC928603
EST:     GGAGTTGAAAGA-TTGCAGAAGGACCCCCCGACATCATGCAGCGCT-                         GGCCTGTGGCCGAAGATATGTTCCATTGCCAGGCTACGATAATGGGACCTC
genomic: GGAGTTGAAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCT-
EST: gi|100444703|gb|BY982532.1|BY982532
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTG                         GGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
EST: gi|208368971|gb|DC955056.1|DC955056
EST:     GACATCATGCAGCGCTN                         GGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
genomic: GACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
EST: gi|208354417|gb|DC953823.1|DC953823
EST:     AAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTG                         GGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
genomic: AAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
EST: gi|100380283|gb|BY968931.1|BY968931
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTG                         GGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
EST: gi|208353619|gb|DC946357.1|DC946357
EST:     AAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTG                         GGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
genomic: AAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
EST: gi|208366616|gb|DC955650.1|DC955650
EST:     CGACATCATGCAGCGCTG                         GGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAAT-GGACCTC
genomic: CGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
EST: gi|208370020|gb|DC948115.1|DC948115
EST:     TCATGCAGCGCTG                         GGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
genomic: TCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
EST: gi|208390085|gb|DC942386.1|DC942386
EST:     GAAGGAGTTGAAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTG                         GGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
genomic: GAAGGAGTTGAAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
EST: gi|162193814|gb|FC369222.1|FC369222
EST:     GACATCATGCAGCGCTG                         GGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC
genomic: GACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 131

TAGTGGTGTGCCGGTGAGTGGCTGCGCCTGATGGCCTCCAAGCGTATTCTGAAGGAGTTGAAAGATTTGCAGAAGGACCCCCCGACATCATGCAGCGCTGgtgagactgc ... tgtacgacagGGCCTGTGGCCGAAGATATGTTCCATTGGCAGGCTACGATAATGGGACCTCCAGATAGTCCGTATGCGGGAGGCGTGTTTCTGGTCACTATTCACTTCCC




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