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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actatataatacctgaattggtaattctggagaactgattttgtacttgtttaatttctattcctttccatttttttttttttgtattttctttctgcagGTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAAGGAGTCGTAAATGATGCTACTTCTGTGGTTCTGTTTCGAGCTGTTCAAA

Basic information

species Physcomitrella patens
transcript PP1S169_48V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 6
actatataatacctgaattggtaattctggagaactgattttgtacttgtttaatttctattcctttccatttttttttttttgtattttctttctgcagGTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAAGGAGTCGTAAATGATGCTACTTCTGTGGTTCTGTTTCGAGCTGTTCAAA
                 ||  |   | |   || ||| | ||    |  | |||  |  |   |    ||   ||   | |     |||  |   |||||||||| |||||||| ||||| || ||||| || ||| |||| ||||| ||||| || || ||||||||||| ||||| || || |||   ||  || || 
----------------gtttttccatttaatgacctgttgttaatgtcttgtaaaatgaaa--cagcacaccattaaatatgcaattttgttacttgcagGTGCTTAACCAAGACGAAACACCCCTACTCTATAGTCTGGTTTTTGGTGAAGGGGTTGTCAATGATGCTACATCTGTTGTGCTCTTTAATGCAATTGAAG

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 5
actatataatacctgaattggtaattctggagaactgattttgtacttgtttaatttcta---ttcctttccatttttttttttttgtattttctttctgcagGTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAAGGAGTCGTAAATGATGCTACTTCTGTGGTTCTGTTTCGAGCTGTTCAAA
                 || | ||   |      ||  ||  | |    |  |    | |   |  |  | | |  |  |    || ||  |  | | |||||||||| ||||| ||||| || ||| |||| |||||| | || ||||| || || || || ||||||||||| |||||||| || ||    ||  |  |||
----------------gtttggaacaatatgtgcctttttccgcaacgttgcagcaaccaaggtgtcaatgcttagtactgaacttataaatgatgt-tgcagGTGCTAAACCAGGATGAGACACCTTTACTGTACAGTCTTGTATTTGGCGAGGGTGTTGTGAATGATGCTACATCTGTGGTGCTTTTCAATGCAATCAAAA

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 5
actatataatacctgaattggtaattctggagaactgattttg-tacttgtttaatttctattcctttccatttttttttttttgtattttctttctgcagGTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAAGGAGTCGTAAATGATGCTACTTCTGTGGTTCTGTTTCGAGCTGTTCAAA
    |||  | | | |    || ||    |  |    |   || |||      |||   | |     |  |  ||||  || |  |  |        ||||||||| ||||| ||||| || ||| ||||||| ||  ||||||||||||| || || |||||||||||  | || || ||||| ||    ||  | || |
---gtatggtgcattacaaagttatagcagccagacaacaatggtacc-----aatagttgtgaaactaaaccttttccttctgatgat--------gcagGTGCTTAACCAGGATGAGACGCCTTTACTTTATAGCCTGGTCTTTGGGGAGGGGGTTGTAAATGATGCAGCATCAGTTGTTCTTTTCAATGCAATCCAGA

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 5
actatataatacctgaattggtaattctggagaactgattttgtacttgtttaatttctattcctttccatttttttttt---tttgtattttctttctgcagGTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAAGGAGTCGTAAATGATGCTACTTCTGTGGTTCTGTTTCGAGCTGTTCAAA
              | || | ||  |    |   |||   || | |||   ||||    |        ||||| |   |    |||| || |  | |  ||||||||| || || ||||| || ||| | || |||||| | |||||||||||||| || ||||||||||| || ||||||                      
--------------gtatagatatcttctcaaggctgtgattctgcttccataatggggacaatagaacatttctgactaaagtttgcatctgatatg-gcagGTGCTCAATCAGGATGAGACACCTTTGCTATACAGTCTAGTCTTTGGGGAAGGTGTGGTAAATGATGCCACATCTGTG----------------------

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|162195589|gb|FC371890.1|FC371890
EST:     CTATTGGAGTCATCTTTTCTGCTACCGATTCCGTCTGCACGTTGCAG                         GTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAA
genomic: CTATTGGAGTCATCTTTTCTGCTACCGATTCCGTCTGCACGTTGCAGgtacgttgga ... ctttctgcagGTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAA
EST: gi|162255349|gb|FC432075.1|FC432075
EST:     CTATTGGAGTCATCTTTTCTGCTACCGATTCCGTCTGCACGTTGCAG                         GTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAA
genomic: CTATTGGAGTCATCTTTTCTGCTACCGATTCCGTCTGCACGTTGCAGgtacgttgga ... ctttctgcagGTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttaatttctattcctttccatttttttttttttgtattttctttctgcagGTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAAGGAGTCGTAAATGATGCTACTTCTGTGGTTCTGTTTCGAGCTGTTCAAA
   gtttaat  putative branch site (score: 4)
         tttctattcctttcca  CT-rich tract
                   tttccatttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actatataatacctgaattggtaattctggagaactgattttgtacttgtttaatttctattcctttccatttttttttttttgtattttctttctgcagGTGCTGAACCAAGATGAAACCCCTCTACTTTACAGTTTGGTCTTTGGGGAAGGAGTCGTAAATGATGCTACTTCTGTGGTTCTGTTTCGAGCTGTTCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT