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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actcttacatagttttattcacatatgcatactctctgaaatcagtgttaaatattcgaaataaattgtttcatgggttgcttgtattgttattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG

Basic information

species Physcomitrella patens
transcript PP1S83_162V6.1
intron # 4
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|18329713|gb|BJ161719.1|BJ161719
EST:     AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAG                         GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
genomic: AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAGgttgcccttc ... tattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
EST: gi|208347445|gb|DC909752.1|DC909752
EST:     AACCGCAGGGGTGTGC-TTTACACTGACAGTTCCAGCAGGAGAACCAGAG                         GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
genomic: AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAGgttgcccttc ... tattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
EST: gi|162240627|gb|FC419365.1|FC419365
EST:     AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAG                         GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
genomic: AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAGgttgcccttc ... tattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
EST: gi|18372591|gb|BJ204193.1|BJ204193
EST:     AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAG                         GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
genomic: AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAGgttgcccttc ... tattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
EST: gi|18356123|gb|BJ188182.1|BJ188182
EST:     AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAG                         GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
genomic: AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAGgttgcccttc ... tattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
EST: gi|18349502|gb|BJ181551.1|BJ181551
EST:     AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAG                         GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
genomic: AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAGgttgcccttc ... tattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
EST: gi|162150536|gb|FC326392.1|FC326392
EST:     AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAG                         GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
genomic: AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAGgttgcccttc ... tattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
EST: gi|18349065|gb|BJ181114.1|BJ181114
EST:     AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAG                         GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGGTGCC
genomic: AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAGgttgcccttc ... tattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGGTGCC
EST: gi|18345693|gb|BJ177736.1|BJ177736
EST:     AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAG                         GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
genomic: AACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAGgttgcccttc ... tattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG

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: 30 (upstream exon), 33 (downstream exon)
Score: 5

GAATAACGAAGTTCAGTTCGCTGGCCAATTGCAACCGCAGGGGTGTGCTTTTACACTGACAGTTCCAGCAGGAGAACCAGAGgttgcccttc ... tattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaaatattcgaaataaattgtttcatgggttgcttgtattgttattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG
     aatattcgaaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actcttacatagttttattcacatatgcatactctctgaaatcagtgttaaatattcgaaataaattgtttcatgggttgcttgtattgttattgtgcagGTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG

- - - - - - - - - - -catatgc