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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacataacatattatttgctttagttcgtagtttcccaactggatattttattcacgtgtaatcagtgtgagagtttagtgcatatgacactagcacttaatgtattggaattttgtcatgtatagGTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTCATGCTTACGGAATTACTAGACATCGTCATG

Basic information

species Physcomitrella patens
transcript PP1S101_184V6.1
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|162168514|gb|FC344451.1|FC344451
EST:     TGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAG                         GTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
genomic: TGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAGgtacataaca ... tcatgtatagGTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
EST: gi|162234960|gb|FC411747.1|FC411747
EST:     GAGTCAGTGGTGCAG                         GTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
genomic: GAGTCAGTGGTGCAGgtacataaca ... tcatgtatagGTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
EST: gi|162226448|gb|FC403546.1|FC403546
EST:     TGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAG                         GTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
genomic: TGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAGgtacataaca ... tcatgtatagGTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
EST: gi|162234961|gb|FC411748.1|FC411748
EST:     TGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAG                         GTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
genomic: TGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAGgtacataaca ... tcatgtatagGTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
EST: gi|162261823|gb|FC438347.1|FC438347
EST:     TGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAG                         GTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
genomic: TGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAGgtacataaca ... tcatgtatagGTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
EST: gi|162265710|gb|FC443116.1|FC443116
EST:     TGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAG                         GTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC
genomic: TGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAGgtacataaca ... tcatgtatagGTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTC

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), 34 (downstream exon)
Score: 10

GCCGGATTAATTGAGAAGGATAACATTATCATTAATGCGAACTCTGGAGTCAGTGGTGCAGgtacataaca ... tcatgtatagGTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTCATGCTTACGGAATTACTAGACATCGTCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtttagtgcatatgacactagcacttaatgtattggaattttgtcatgtatagGTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTCATGCTTACGGAATTACTAGACATCGTCATG
                        acttaat  putative branch site (score: 10)
                                        ttttgtc  putative PPT
                          ttaatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacataacatattatttgctttagttcgtagtttcccaactggatattttattcacgtgtaatcagtgtgagagtttagtgcatatgacactagcacttaatgtattggaattttgtcatgtatagGTCGGTCTGCGAAGGAAGCAAATTTATATACGGAGATTTGTGAGGGCATTCATGCTTACGGAATTACTAGACATCGTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT