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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcgagtagttctctgtcatgatcagtaaactggtgtctggaaagtaatgaagtgctggttgctctgaagtatattgagttgctcgacagctagacattttctgtatcggtttttaacattggtggcttgtactgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAATATCTGGTCATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGG

Basic information

species Physcomitrella patens
transcript PP1S130_248V6.2
intron # 8
splice site 3'
intron type U2

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|162255418|gb|FC431832.1|FC431832
EST:     ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAG                         GTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAGgcgagtagtt ... tgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162195248|gb|FC370821.1|FC370821
EST:     ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAG                         GTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAGgcgagtagtt ... tgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162160367|gb|FC337368.1|FC337368
EST:     ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAG                         GTTCTGTTNCA-CATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCA
genomic: ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAGgcgagtagtt ... tgtcctgcagGTTCTGTT-CAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCA
EST: gi|37850644|gb|BJ608652.1|BJ608652
EST:     GCTACAGACGTCGATTGGGATCCTACCGGCAG                         GTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: GCTACAGACGTCGATTGGGATCCTACCGGCAGgcgagtagtt ... tgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|208363001|gb|DC946898.1|DC946898
EST:     ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAG                         GTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAGgcgagtagtt ... tgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162169045|gb|FC345727.1|FC345727
EST:     ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAG                         GTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAGgcgagtagtt ... tgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162255419|gb|FC431833.1|FC431833
EST:     ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAG                         GTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAGgcgagtagtt ... tgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162265641|gb|FC441097.1|FC441097
EST:     ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAG                         GTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ACAGCTGAGCACTTCATGGCTACAGACGTCGATTGGGATCCTACCGGCAGgcgagtagtt ... tgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
EST: gi|162160006|gb|FC335668.1|FC335668
EST:     ATTGGGATCCTACCGGCAG                         GTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA
genomic: ATTGGGATCCTACCGGCAGgcgagtagtt ... tgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctagacattttctgtatcggtttttaacattggtggcttgtactgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAATATCTGGTCATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGG
                       ttttaac  putative branch site (score: 2)
                                            ctgtcct  putative PPT
                      tttttaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgagtagttctctgtcatgatcagtaaactggtgtctggaaagtaatgaagtgctggttgctctgaagtatattgagttgctcgacagctagacattttctgtatcggtttttaacattggtggcttgtactgtcctgcagGTTCTGTTCAACATCAGTAACATCTGTTCACCAGATGGAGAACGGTTTCAATATCTGGTCATTCCAAGGAAAATTGTTGTACCGCCTCCCTAGGGACAGG

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