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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatttccttcgcacccgatcgcgttatatccaaacttgtgtgattctgtattgaccgaatcgtaatacatatactgtacatgataagcgctgatgttggagttattcttttttaatcgaattagctcatcctgtcttgcaattttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGCGAGTACCTTGCCGCTAAGGGTCCCAAG

Basic information

species Physcomitrella patens
transcript PP1S165_105V6.1
intron # 3
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|162157574|gb|FC333832.1|FC333832
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|100411604|gb|BY992247.1|BY992247
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|100422280|gb|BY976296.1|BY976296
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|208352513|gb|DC910213.1|DC910213
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|162232093|gb|FC407695.1|FC407695
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|100409366|gb|BY991976.1|BY991976
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|100448582|gb|CJ972881.1|CJ972881
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|100390506|gb|BY952914.1|BY952914
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATNTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|208358223|gb|DC939391.1|DC939391
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|162216664|gb|FC392730.1|FC392730
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|208368598|gb|DC940019.1|DC940019
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|208365412|gb|DC950879.1|DC950879
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|100375067|gb|BY949170.1|BY949170
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATNTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGNAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|100384199|gb|BY950585.1|BY950585
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|208391805|gb|DC942339.1|DC942339
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|100390026|gb|BY989106.1|BY989106
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|162222464|gb|FC397198.1|FC397198
EST:     CCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|208378861|gb|DC927563.1|DC927563
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|208374639|gb|DC931978.1|DC931978
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
EST: gi|208357969|gb|DC938840.1|DC938840
EST:     CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAG                         GTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC
genomic: CCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGC

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: 23 (upstream exon), 34 (downstream exon)
Score: 7

GGGCTTTGATTCCGAAGGTACTGAAGTCGTTAGGCCGTATACCCCCACCACCCTCGATTCCGACCTTGGTTATTTTGAGCTTGTTGTCAAGgtgagatttc ... attttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGCGAGTACCTTGCCGCTAAGGGTCCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggagttattcttttttaatcgaattagctcatcctgtcttgcaattttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGCGAGTACCTTGCCGCTAAGGGTCCCAAG
              ttttaat  putative branch site (score: 7)
                                              ttttttc  putative PPT
      ttattcttttttaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatttccttcgcacccgatcgcgttatatccaaacttgtgtgattctgtattgaccgaatcgtaatacatatactgtacatgataagcgctgatgttggagttattcttttttaatcgaattagctcatcctgtcttgcaattttttcagGTTTACAAGGAAGGGAAAGTGTCGTCTTACTTCGGTCGCATGAAGGAGGGCGAGTACCTTGCCGCTAAGGGTCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG