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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttcctggaagcttgccaaaggacatgaatggtgcagactatcagctacttattttatctacttattttctttggaacaaacgacatgaatggtgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG

Basic information

species Physcomitrella patens
transcript PP1S306_43V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 1
cttttcctggaagcttg--ccaaaggacatgaatggtgcagac--tatcagctacttattttatctacttattttctttggaacaaacgacatgaatgg----tgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG
         |||  |||    |||  | |||  ||     ||   || || | ||   ||| |  | ||| | |||||   ||       |  |||||     ||||||| ||||| ||   ||| ||||||||||||||||||||||||||||| ||||| ||||||
--------agaattttgaataaaattaaatgcttgagattgatgataacatccacgggtttcaatttcttctattcttcataaatttgtgctcgaatgccacttgcagACCATCAGTTACATGGCTGAACGTGTTGTTGGCACTGGATCATTCGGAATTGTTTTCCAG

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 2
---cttttcctggaagcttgccaaaggacatgaatggtgcagactatcagctacttattttatctacttattttctttggaacaaacgacatgaatggtgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG
   | ||       |   |       | |   ||      | | | |   || | ||  | |  || || || |  ||    | |  || |  |    ||||||| ||||| ||   |||||||||||||||||||||||||||||| ||  |||| || |||
atgcattaatatatattatctttggagtccaaaaaaaaataaaatttattcttcgtaaataacttatttgttatgattacttcca-tgataccacc--tgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAG

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 2
cttttcctggaagcttgccaaaggacatgaatggtgcagactatcagctacttattttatcta-cttattttctttggaacaaacgac-atgaatggtgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG
    | |   ||  ||   |  ||  ||      ||      || |  |  |  |  ||  || |||||||  | ||   |   |    ||      ||||||| ||||| ||   |||||||||||||||||||||||||||||| ||  |||| ||||||
--ggttcaataactttaaaattggtgatattgtctgagtttcattatttgttcttcgtaaataacttatttgttatgattccttccctgataccacctgcagACCATCAGTTACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTCCAG

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 2
cttttcctggaagcttgccaaaggacatgaatggtgcagactatcagctacttattttatctacttattttctttggaacaaacgacatgaatgg----tgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG
 ||||     ||  |  |      | ||  ||| ||  | |    | | ||   ||| |  | ||| | |||||   ||       |   ||||     ||||||| ||||| ||   ||| |||||||||||||||||||||||||| || ||||| ||||||
attttgaataaaattgactgcttaagattgatgatgatggc----atccacgggtttcaatttcttttattcttcataaatttgtgctctaatgcctcttgcagACCATCAGTTACATGGCCGAACGTGTTGTTGGCACTGGATCATTTGGCATTGTTTTCCAG

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 2
--cttttcctggaagcttgccaaaggacatgaatggtgcagactatcagctacttattttatctacttattttctttggaacaaacgacatgaatggtgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG
    |        || ||   | |     ||| |  |   | ||      | |  | | ||  | ||  | |    ||     | |    ||     | ||||| || || ||   ||| |||||||||||||| || ||||||||||| ||||| ||||||
caaataaataaataggtttttacatcttttgact--ttgtggctccttttttccaactctaagttctactctctaatgttttcatccctctggcctttacagACCATTAGTTACATGGCCGAACGTGTTGTTGGAACAGGATCATTCGGAATTGTATTCCAG

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|162196892|gb|FC373297.1|FC373297
EST:     GCCACATCATAGCTACTACTATTGGAGGGCGAAATGGACAACCTAAGCAG                         ACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATT
genomic: GCCACATCATAGCTACTACTATTGGAGGGCGAAATGGACAACCTAAGCAGgtatgccaat ... aatggtgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATT
EST: gi|100387363|gb|BY970507.1|BY970507
EST:     GCCACATCATAGCTACTACTATTGGAGGGCGAAATGGACAACCTAAGCAG                         ACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATT
genomic: GCCACATCATAGCTACTACTATTGGAGGGCGAAATGGACAACCTAAGCAGgtatgccaat ... aatggtgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctacttattttatctacttattttctttggaacaaacgacatgaatggtgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG
      ttattttatctactta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttcctggaagcttgccaaaggacatgaatggtgcagactatcagctacttattttatctacttattttctttggaacaaacgacatgaatggtgcagACGATCAGCTATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG

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