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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgccaagtttcattttactagaattgtctgccgaaccttgacgtctaatggatgtgatgatgtagttgtcaagtctcgctatcgaatgctgcgatttcttctaacaacccattgctctgtctttgacagGACATCAAATTTGCTGTGCATGCCCATCCGACCTTGTCTGAAGTGTTGGACGAGCTCTTCAAGTCAGCGAAG

Basic information

species Physcomitrella patens
transcript PP1S112_186V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
gtgagtgccaagtttcattttactagaattgtctgccgaaccttgacgtctaatggatgtgatgatgtagttgtcaag--tctcgctatcgaatgctgcgatttcttctaacaacccattgctctgtctttgacagGACATCAAATTTGCTGTGCATGCCCATCCGACCTTGTCTGAAGTGTTGGACGAGCTCTTCAAGTCAGCGAAG
                                                                  |||  || | ||  | |   | |  |    || |||| | | |    | |  |   |   ||     ||||||||||| |||||||| ||||| || || || |||||||| ||  |||| |||||||||||  | || |||
------------------------------------------------------------------gtaagtgacgagcattttattgtttatgaatg-gattgcatttgctcaacgctgtttacatcccc--cagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG

upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
gtgagtgccaagtttcattttactagaattgtctgccgaaccttgacgtctaatggatgtgatgatgtagttgtcaagtctcgctatc-gaatgctgc-gatttcttctaacaacccattgc--tctgtctttgacagGACATCAAATTTGCTGTGCATGCCCATCCGACCTTGTCTGAAGTGTTGGACGAGCTCTTCAAGTCAGCGAAG
                                  |        | | |  |  ||   |   ||  | | || |  | | | | | || | ||  |||  |   |||  |    | |||  |  | |||      ||||||||||| |||||||| ||||| || || || |||||||||||  |||| || ||||||||| | || |||
----------------------------------gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG

upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 13
gtgagtgccaagtttcattttactagaattgtctgccgaaccttgacgtctaat-ggatgtgatgatgtagttgtcaagtctcgctatcgaatgctgcgatttcttctaacaacccattgctctgtctttgacagGACATCAAATTTGCTGTGCATGCCCATCCGACCTTGTCTGAAGTGTTGGACGAGCTCTTCAAGTCAGCGAAG
                       |  || |  |   |    ||||   |||  | | | |||| | || |   |  |   || | |||     | || |   | || | |||   | ||  |       | ||||||||| ||||||||||| ||||| ||||| |||||||| |||||| |||| || ||||| || ||||| |||
-----------------------tcaaact--caatcatctcttggtttcttcttgaaagtgagggtggaaccggtag--cttgttat-----gatgag---tattttgacatttcttttttggacaccttacagGACATAAAATTTGCTGTTCATGCGCATCCAACCTTGTCAGAAGTGCTGGATGAACTCTTTAAATCAGCTAAG

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|208366234|gb|DC943808.1|DC943808
EST:     ACCTCATCCACGAAGCCTCCAACGCTATTGCTATGGGCAACACCATCAAA                         GACATCAAATTTGCTGTGCATGCCCATCCGACCTTGTCTGAAGTGTTGGAC
genomic: ACCTCATCCACGAAGCCTCCAACGCTATTGCTATGGGCAACACCATCAAAgtgagtgcca ... tctttgacagGACATCAAATTTGCTGTGCATGCCCATCCGACCTTGTCTGAAGTGTTGGAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgctatcgaatgctgcgatttcttctaacaacccattgctctgtctttgacagGACATCAAATTTGCTGTGCATGCCCATCCGACCTTGTCTGAAGTGTTGGACGAGCTCTTCAAGTCAGCGAAG
                        ttctaac  putative branch site (score: 1)
                                        ctctgtcttt  putative PPT
                   atttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgccaagtttcattttactagaattgtctgccgaaccttgacgtctaatggatgtgatgatgtagttgtcaagtctcgctatcgaatgctgcgatttcttctaacaacccattgctctgtctttgacagGACATCAAATTTGCTGTGCATGCCCATCCGACCTTGTCTGAAGTGTTGGACGAGCTCTTCAAGTCAGCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG