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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtttttaaacgcttgcagcagccaaccgagtagcctggtggcgtcgcatttgtcagtgcaactttgacagagaaggttttgatcacggttattgcagAGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAATGGACTTTGCTCAGATGGACCTTCAAGAGATTCGGGATAACATCACAAGG

Basic information

species Physcomitrella patens
transcript PP1S237_60V6.2
intron # 2
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|67571161|gb|BJ943985.1|BJ943985
EST:     GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGG                         AGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
genomic: GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGGgtatagtttt ... gttattgcagAGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
EST: gi|162150939|gb|FC327419.1|FC327419
EST:     GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGG                         AGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
genomic: GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGGgtatagtttt ... gttattgcagAGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
EST: gi|162215024|gb|FC391312.1|FC391312
EST:     GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGG                         AGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
genomic: GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGGgtatagtttt ... gttattgcagAGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
EST: gi|162229557|gb|FC404851.1|FC404851
EST:     GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGG                         AGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
genomic: GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGGgtatagtttt ... gttattgcagAGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
EST: gi|100360147|gb|BY966047.1|BY966047
EST:     GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGG                         AGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
genomic: GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGGgtatagtttt ... gttattgcagAGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
EST: gi|100355956|gb|BY946122.1|BY946122
EST:     GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGG                         AGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT
genomic: GCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGGgtatagtttt ... gttattgcagAGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAAT

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: 35 (upstream exon), 35 (downstream exon)
Score: 8

GAGGCAAGATGGAGTGGAAAGGTGTAGCGGGAAGCGACAAGGGTAAAAATGCCAAGAGCGTTGAAGGCGACGCTGTCAAAGTTTCGGCCATGTCATCCGGgtatagtttt ... gttattgcagAGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAATGGACTTTGCTCAGATGGACCTTCAAGAGATTCGGGATAACATCACAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgcatttgtcagtgcaactttgacagagaaggttttgatcacggttattgcagAGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAATGGACTTTGCTCAGATGGACCTTCAAGAGATTCGGGATAACATCACAAGG
                                  ttttgat  putative branch site (score: 8)
                                  ttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtttttaaacgcttgcagcagccaaccgagtagcctggtggcgtcgcatttgtcagtgcaactttgacagagaaggttttgatcacggttattgcagAGCGGAAGATGCAGATGCTTTTTGCATTATTGAAGGGCGTGATACGGTAATGGACTTTGCTCAGATGGACCTTCAAGAGATTCGGGATAACATCACAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - tgcagca