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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacagtattgagagtgaaatcctcccttcttgaatggctgatatcatcatatcattcagaagtgtttctaggggaattttaacaaaaaagtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG

Basic information

species Physcomitrella patens
transcript PP1S47_23V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_23V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EDP00124 (Chlamydomonas reinhardtii), 3'ss of exon 5
----------atacagtattgagagtgaaatcctcccttcttgaatggctgatat---catcatatcattcagaagtgtttctaggggaa-------ttttaacaaaaaagtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCG---TGGCGGAGGCGAAGT----TCATAGAGGATCC--TGCG--AGGTTTGAGGGCCATATCAAGGCGCAG
           |   | |  | |||             ||| || |||  |  |    ||     |      |  |      | || |||       | |     | || |  ||| || || | | |       || |   || ||      |    |||    || | |     ||  || |||| |  | ||  | ||| | ||   |   |||    |  
gtgggcgcgggtgtgggagcgggaggtggggtaaggtgtct-gagtggtagggaagcgcactgggttgcgtgggggcacacgtcggcgaagcgatgctgtggggcacaacgggtcttcacgcccccccccttgtaatccctaattgccgacctgacccggcccgcgccagGCGCTGTCGAAGCGGATACACTACGGCAAGTTCGTGGCGGAGGCCAAATTCCT-
















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|208382438|gb|DC927972.1|DC927972
EST:     ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAG                         GCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
genomic: ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAGgtgcggaacc ... gtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
EST: gi|100414345|gb|BY992730.1|BY992730
EST:     TGATGGNCA-CTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAG                         GCTCTCTCTAA-CGTATACACTATGG
genomic: TGATGG-CAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAGgtgcggaacc ... gtttctgcagGCTCTCTCTAAACGTATACACTATGG
EST: gi|162223996|gb|FC400354.1|FC400354
EST:     ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAG                         GCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
genomic: ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAGgtgcggaacc ... gtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
EST: gi|208352569|gb|DC918278.1|DC918278
EST:     ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAG                         GCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
genomic: ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAGgtgcggaacc ... gtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
EST: gi|18335067|gb|BJ167085.1|BJ167085
EST:     ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAG                         GCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGNAGGCGAAGTTC
genomic: ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAGgtgcggaacc ... gtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
EST: gi|208354231|gb|DC957437.1|DC957437
EST:     ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAG                         GCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
genomic: ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAGgtgcggaacc ... gtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
EST: gi|18340006|gb|BJ172034.1|BJ172034
EST:     TTCTCTGCCTGCAG                         GCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
genomic: TTCTCTGCCTGCAGgtgcggaacc ... gtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
EST: gi|162223997|gb|FC400355.1|FC400355
EST:     ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAG                         GCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
genomic: ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAGgtgcggaacc ... gtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
EST: gi|208398077|gb|DC904382.1|DC904382
EST:     ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAG                         GCTCTCTCTAAACGTATACACTATGGCAAGTNCGTGGC
genomic: ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAGgtgcggaacc ... gtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGC
EST: gi|208351995|gb|DC925804.1|DC925804
EST:     ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAG                         GCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC
genomic: ATGATGGCAACTATGGCTCAGCTTCTGTGTGCGATGTTCTCTGCCTGCAGgtgcggaacc ... gtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcatatcattcagaagtgtttctaggggaattttaacaaaaaagtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG
                                ttttaac  putative branch site (score: 2)
                                              tttctgc  putative PPT
                              aattttaacaaaaaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacagtattgagagtgaaatcctcccttcttgaatggctgatatcatcatatcattcagaagtgtttctaggggaattttaacaaaaaagtttctgcagGCTCTCTCTAAACGTATACACTATGGCAAGTTCGTGGCGGAGGCGAAGTTCATAGAGGATCCTGCGAGGTTTGAGGGCCATATCAAGGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT