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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtgtgggaattgctaagttttaaagcaacagacttgttctagctgcgtacgttttaaattggtacgagtacatgaagcgacttatattttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAAAACTCCCTCAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGG

Basic information

species Physcomitrella patens
transcript PP1S209_135V6.1
intron # 1
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|18350329|gb|BJ182380.1|BJ182380
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|18351887|gb|BJ183939.1|BJ183939
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|18373193|gb|BJ204795.1|BJ204795
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|18325961|gb|BJ157960.1|BJ157960
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|100360816|gb|BY965915.1|BY965915
EST:     GGGAGTATAAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|18360367|gb|BJ192429.1|BJ192429
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|18369571|gb|BJ201659.1|BJ201659
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|18363051|gb|BJ195123.1|BJ195123
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|18348401|gb|BJ180449.1|BJ180449
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|208368222|gb|DC931448.1|DC931448
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|67508066|gb|BJ940937.1|BJ940937
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|208353659|gb|DC929702.1|DC929702
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCANCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTANCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|18329866|gb|BJ161872.1|BJ161872
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|18361973|gb|BJ194040.1|BJ194040
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
EST: gi|18329732|gb|BJ161738.1|BJ161738
EST:     GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCG                         GTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA
genomic: GGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 20 (downstream exon)
Score: 10

GGCGCAGTTCGATTTGCAGGCCATGAAGGTCTACTTGGCGGGAGGCCAGCGGGAGTATGAGATCTCGACCAAGATGGCGCAGCTTGTGGCTAACGACCCGgtatgattgt ... tttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAAAACTCCCTCAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcgtacgttttaaattggtacgagtacatgaagcgacttatattttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAAAACTCCCTCAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGG
                                      cttatattttctttc  CT-rich tract
                                     acttatattttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgtgtgggaattgctaagttttaaagcaacagacttgttctagctgcgtacgttttaaattggtacgagtacatgaagcgacttatattttctttcagGTCTTTTCTAAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAAAACTCCCTCAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA