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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcttctatcgtaacttaagcaggttggttttcacaggttgatgttttatcacggttgagatttctagtgtctgacatgaatttttttatgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAATATTCAAGATCTCACACCAGAAGAGCCGTTACATTTATGATCTATTTTA

Basic information

species Physcomitrella patens
transcript PP1S22_313V6.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_313V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA05G28440.2 (Glycine max), 3'ss of exon 3
atgcttctatcgtaacttaagcaggttggttttcacaggttgatgttttatcacggttgagatttctagtgtc--tgacatgaatttttttatgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAATATTCAAGATCTCACACCAGAAGAGCCGTTACATTTATGATCTATTTTA
         | | || || | ||   ||   ||   || ||  | || | |      ||| ||   |    |   |    | |  |  |||||| |  |||||||| |||||  | ||||| ||||| || ||||||||| | || ||||||||||| |||||  |||||||||||||||| ||||| | ||| || |   |
--------gttggaatttta-catcatgtgcttagtagattt-tattatgttctttctgaaatcaatgaaattaatagttttatatcctttatgtg--gcagCTGAGAATGATCCACATGATGGCAAAAGAAAATGTGAGACATTATGGCCAATATTTAAGATTGCACACCAGAAGAGCCGCTACATATTTGACCTCTACCA

upper sequence: PP1S22_313V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G11450.1 (Glycine max), 3'ss of exon 3
atgcttctatcgtaacttaagcaggttggttttcacaggttgatgttttatcacggttgagatt--tctagtgtctgacatgaatttttttatgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAATATTCAAGATCTCACACCAGAAGAGCCGTTACATTTATGATCTATTTTA
         | | || || | ||   || | ||   |||||  | || | |      ||| ||   |  | ||  |    | |  |  |||||| |  |||||||| |||||  | ||||| ||||| || ||||||||| | || ||||| ||||| |||||  |||||||||||||||| ||||| | ||||||||   |
--------gttggaaattta-catcatgttcttagtaggttt-tattatgttctttctgaaatcaatgaaatgaatagttttatatcctttatgtg--gcagCTGAGAATGATCCGCATGATGGCAAAAGAAAATGTGAGACCTTATGGCCTATATTTAAGATTGCACACCAGAAGAGCCGCTACATATTTGATCTATACCA

upper sequence: PP1S22_313V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G15700.1 (Glycine max), 3'ss of exon 2
atgcttctatcgtaacttaagcaggttggttttcacaggttgatgttttatcacggttgagatttctagtgtctgacatgaatttttttatgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAATATTCAAGATCTCACACCAGAAGAGCCGTTACATTTATGATCTATTTTA
    ||  |   | |  |  |    |||  ||||  || ||  | || | |      ||| |    |    |      |      ||   |  |  |||||||| || ||  | ||||| |||||||| || |||||| | || ||||| ||||| |||||  |||||||||||||||| ||||| | ||| || | | |
---gttggaattttatatgtgatacttgcctttc-tagattt-tattgtgttctttctgaaacccttgaacttaattgttttgcattccttatgtggcagCTGAGAACGATCCACATGATGGCAAGAGAAACTGTGAGACATTATGGCCTATATTTAAGATTGCACACCAGAAGAGCCGCTACATATTTGACCTCTATCA

upper sequence: PP1S22_313V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv05s0020g01520.t01 (Vitis vinifera), 3'ss of exon 2
---atgcttctatcgtaacttaagcaggttggttttcacaggttgatgttttatcac--ggttgagatttctagtgtctgacatgaatttttttatgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAATATTCAAGATCTCACACCAGAAGAGCCGTTACATTTATGATCTATTTTA
   || ||  | |  | |   |  ||| |  |  |       |||  | ||  |  |     | | |   |||     |||||    | | | | |      |||||||||||||  | ||||| || ||||| |||||||||||  | ||||| || ||||| ||  |||| |||||||||||||| |||| |||||| |   |
gttattctctttttctcatgcatacagctctgaatgttgtctttgtcgcttgtttgctgaacttataaaactaacaa-tgacaccgttctatgtcttttgaacagCTGAAAATGACCCACATGATGGTAAGAGAAAATGTGAGGCACTATGGCCGATTTTCAAAATAGCACATCAGAAGAGCCGTTATATTTTTGATCTTTACCA

upper sequence: PP1S22_313V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ34999 (Selaginella moellendorffii), 3'ss of exon 1
atgcttctatcgtaacttaagcaggttggttttcacaggttgatgttttatcacggt--tgagatttctagtgtctgacatgaatttttttatgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAATATTCAAGATCTCACACCAGAAGAGCCGTTACATTTATGATCTATTTTA
           ||||   ||||     |    | | |  | |          | | |  ||| | |  ||     ||   ||   | | ||  |     ||||||  |||||  |  | || ||||||||||  || ||||| | |||||| || ||||||||| | |||||||||||||| ||||| || ||||| |  ||
-----------gtaagc-aagctaagcgccgctgagatttcggctccccgcgaggatgatgaaaatattatcccttgttgtgctctctcttgcg-----cagCTGTGAATGAATCCGACGACGGCAAGAGGATTTGCGAGGCGTCGTGGCCGATTTTCAAGATCGCGCACCAGAAGAGCCGCTACATATACGATCTCTACTA

upper sequence: PP1S22_313V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ09355 (Selaginella moellendorffii), 3'ss of exon 1
atgcttctatcgtaacttaagcaggttggttttcac-aggttgatgttttatcacggttgagatttctagtgtctgacatgaatttttttatgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAATATTCAAGATCTCACACCAGAAGAGCCGTTACATTTATGATCTATTTTA
                 |||||| | |      | | | | |   |  |   | ||     |||    |   | |  | ||   |  | | |     |||||||  |||||  |  | || ||||||||||  || ||||| | |||||| || ||||||||| | |||||||||||||| ||||| || ||||| |  ||
----------------gtaagcaagctaagcgccgctaagatttcggctccccgcgaggatgatgaaaatattatcccttgttgtgctctctcttgcgcagCTGTGAATGAATCCGACGACGGCAAGAGGATTTGCGAGGCGTCGTGGCCGATTTTCAAGATCGCGCACCAGAAGAGCCGCTACATATACGATCTCTACTA

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|67717622|gb|BJ967881.1|BJ967881
EST:     GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAG                         CTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
genomic: GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAGgtgtgctcaa ... tgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
EST: gi|162222516|gb|FC398667.1|FC398667
EST:     GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAG                         CTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
genomic: GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAGgtgtgctcaa ... tgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
EST: gi|162222515|gb|FC398666.1|FC398666
EST:     GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAG                         CTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
genomic: GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAGgtgtgctcaa ... tgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
EST: gi|162224109|gb|FC400675.1|FC400675
EST:     GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAG                         CTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
genomic: GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAGgtgtgctcaa ... tgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
EST: gi|162224108|gb|FC400674.1|FC400674
EST:     GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAG                         CTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
genomic: GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAGgtgtgctcaa ... tgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
EST: gi|67726135|gb|BJ976394.1|BJ976394
EST:     TCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAG                         CTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
genomic: TCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAGgtgtgctcaa ... tgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
EST: gi|19787471|gb|BQ040629.1|BQ040629
EST:     GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAG                         CTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
genomic: GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAGgtgtgctcaa ... tgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
EST: gi|18341950|gb|BJ173985.1|BJ173985
EST:     GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAG                         CTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA
genomic: GGAGCTCATCGAGCCTACTCTGCGCGAACTGGAAACTAAGATGCGTGAAGgtgtgctcaa ... tgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatcacggttgagatttctagtgtctgacatgaatttttttatgggatgcagCTGAAAATGAGACTCATGAGGGCAAGAGGAAATGTGAGGCTTTGTGGCCAATATTCAAGATCTCACACCAGAAGAGCCGTTACATTTATGATCTATTTTA
                         gtctgac  putative branch site (score: 3)
                                     tttttttat  putative PPT
                              acatgaatttttttat  TA-rich tract