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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtggcaatggcaatggtggagacggagtgaaacatggattccgtttttattatttattatttattattttaattggaatagtgtctaaacagttctgtgtgcttatttatatcgtttggagttttttagGGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGGCTATTGCCAAAGCCCTGTCAGCAGCTGGAGCTGAAATCCTTGTCGGAAC

Basic information

species Physcomitrella patens
transcript PP1S99_59V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S99_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 2
gtgtgtggcaatggcaatggtggagacggagtgaaacatggattccgtttttattatttattatttattattttaattggaatagtgtctaaacagttctgtgtgcttatttat--atcgtttggagttttttagGGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGGCTATTGCCAAAGCCCTGTCAGCAGCTGGAGCTGAAATCCTTGTCGGAAC
                                    |||  |||  ||| ||   |  | | | || || | ||| |     |  | | |      |||  ||||    |  |   |  |||  | | | |  ||| || || || |||||||||||||||||||||||  | || | ||||||||| || || ||| | ||  ||||||| ||||||||||| |||||||| ||
---------------------------------tctcataaattt-gttattgccaagtgtaacttttt-tcttactaccttttttatatctttgattcgttgtggcattccactgaatgttatgtgatgtgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTTGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC

upper sequence: PP1S99_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
gtgtgtggcaatggcaatggtggagacggagtgaaacatggattccgtttttattatttattatttattattttaattggaatagtgtctaaacagttctgtgtgcttatttatatcgtttggagttttttagGGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGGCTATTGCCAAAGCCCTGTCAGCAGCTGGAGCTGAAATCCTTGTCGGAAC
                 |  |  |   |   |    || |  | || ||||| |||  | |  ||| |||| |   || || |  |||     || | |  ||     || ||| |  |  |         ||| || || || |||||||||||||||||||||||  | || | ||||||||| || || ||| | ||  ||||||| ||||||||||| |||||||| ||
----------------ctcataaatttgttattgc-caagtgtaccttttttcttaactgtccttttttatatc--tttgatt--tgttgtggcattccactga----atgtatgtgatgcg--------cagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC
















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|162157331|gb|FC333459.1|FC333459
EST:     TTCCAACGGGGGTGCATTGCCGCCCAGCGGTCTTCCCATTGATCTGCGAG                         GGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGG
genomic: TTCCAACGGGGGTGCATTGCCGCCCAGCGGTCTTCCCATTGATCTGCGAGgtgtgtggca ... agttttttagGGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGG
EST: gi|18373999|gb|BJ205577.1|BJ205577
EST:     TTCCAACGGGGGTGCATTGCCGCCCAGCGGTCTTCCCATTGATCTGCGAG                         GGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGG
genomic: TTCCAACGGGGGTGCATTGCCGCCCAGCGGTCTTCCCATTGATCTGCGAGgtgtgtggca ... agttttttagGGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGG
EST: gi|208357946|gb|DC943058.1|DC943058
EST:     TTCCAACGGGGGTGCATTGCCGCCCAGCGGTCTTCCCATTGATCTGCGAG                         GGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGG
genomic: TTCCAACGGGGGTGCATTGCCGCCCAGCGGTCTTCCCATTGATCTGCGAGgtgtgtggca ... agttttttagGGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatagtgtctaaacagttctgtgtgcttatttatatcgtttggagttttttagGGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGGCTATTGCCAAAGCCCTGTCAGCAGCTGGAGCTGAAATCCTTGTCGGAAC
        gtctaaa  putative branch site (score: 3)
                                               tttttt  putative PPT
                            ttatttatatcgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtggcaatggcaatggtggagacggagtgaaacatggattccgtttttattatttattatttattattttaattggaatagtgtctaaacagttctgtgtgcttatttatatcgtttggagttttttagGGAAGAGAGCGTTCATTGCTGGTGTGGCTGATGATCAAGGTTTTGGCTGGGCTATTGCCAAAGCCCTGTCAGCAGCTGGAGCTGAAATCCTTGTCGGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA