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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttcttacggaggagcgatgacttgccactagtgtggtcagggttctaaactatttgttgactttctgtagttcaaaccggaatgtctgttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGCAAGTAGAGCATTGGCTAAAATGTCTTTTGAGGAGAAGGATCTGACAGGT

Basic information

species Physcomitrella patens
transcript PP1S97_92V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S97_92V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA20G29660.1 (Glycine max), 3'ss of exon 1
-tatttcttacggaggagcgatgacttgccactagtgtggtcagggttctaaactatttgttgactttctgtagttcaaaccggaatgtctgttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGCAAGTAGAGCATTGGCTAAAATGTCTTTTGAGGAGAAGGATCTGACAGGT
  ||    || |         |   |      |  | || |     |  ||   |  |      | || | |   |||    | | ||| |  |    ||||   ||||| ||| |||| |||||||||||||| || ||||| || || || || ||||| || || || ||||||||||| ||||| |||||||| || 
gaatgaaatatgtgctgattttatttgtttctttatatgttttatttgatagggtgctaacaccccttatttttatcatgtggaattgtgtccttcc-cagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCAAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG

upper sequence: PP1S97_92V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G38150.1 (Glycine max), 3'ss of exon 1
tatttcttacggaggagcgatgacttgccactagtgtggtcagggttctaaactatt--tgttgac-----tttctgtagttcaaaccggaatgtctgttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGCAAGTAGAGCATTGGCTAAAATGTCTTTTGAGGAGAAGGATCTGACAGGT
       ||  | |  |       || |   |  | |  | |    | | || |  |  || | ||     ||  | |  ||   ||  | |  | |||     ||||   ||||| ||| |||| |||||||||||||| || ||||| || || || || ||||| || || || ||||||||||| ||||| |||||||| || 
-------tattgtgctgatgcttttttctttttttttcattacatattttaattgatagtgctaacactgcttcttatttttatcacgtggaattgtgtccctccagGATGTTTTATGGACCTGGTGGACCTTATGCCCTATTTGCTGGCAAGGATGCTAGCAGAGCCTTAGCGAAGATGTCTTTTGAAGAGAAAGATCTGACTGGG
















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|18368956|gb|BJ201041.1|BJ201041
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|37850244|gb|BJ608252.1|BJ608252
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|18328263|gb|BJ160267.1|BJ160267
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|162268785|gb|FC444710.1|FC444710
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|208385441|gb|DC953074.1|DC953074
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|37840608|gb|BJ598616.1|BJ598616
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|208355810|gb|DC929991.1|DC929991
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|67693759|gb|BJ953992.1|BJ953992
EST:     TATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: TATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|208359380|gb|DC954233.1|DC954233
EST:     AAGGACNAATTTATGATGT-TCTCAATCAAG                         GGCA-TTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: AAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|37838677|gb|BJ596685.1|BJ596685
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|37837193|gb|BJ595201.1|BJ595201
EST:     CCTTTGCTGATGGTTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
EST: gi|18363477|gb|BJ195549.1|BJ195549
EST:     CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAG                         GGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC
genomic: CCTTTGCTGATGGCTATTAAAGGACAAATTTATGATGTATCTCAATCAAGgtatgtgaac ... gttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaaactatttgttgactttctgtagttcaaaccggaatgtctgttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGCAAGTAGAGCATTGGCTAAAATGTCTTTTGAGGAGAAGGATCTGACAGGT
     aactattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttcttacggaggagcgatgacttgccactagtgtggtcagggttctaaactatttgttgactttctgtagttcaaaccggaatgtctgttgaaacagGGCATTTTACGGAACTGGAGGACCTTATGCCCTCTTCGCTGGAAAAGACGCAAGTAGAGCATTGGCTAAAATGTCTTTTGAGGAGAAGGATCTGACAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA