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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcccgtttcagctttcacactggggatttatctcttgcattccatcctctactttgacatttaagcatgttgttgagctcattaaattcacgtgcgttttgagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGACGGACAG

Basic information

species Physcomitrella patens
transcript PP1S51_241V6.1
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|162269245|gb|FC445802.1|FC445802
EST:     TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
genomic: TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
EST: gi|162186404|gb|FC362960.1|FC362960
EST:     GACCTTGAGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAA-TGNCGGGAAG
genomic: GACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTG-CGGGAAG
EST: gi|162232388|gb|FC408822.1|FC408822
EST:     TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
genomic: TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
EST: gi|162186405|gb|FC362961.1|FC362961
EST:     TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
genomic: TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
EST: gi|22492339|gb|BU052262.1|BU052262
EST:     TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
genomic: TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
EST: gi|162243414|gb|FC425110.1|FC425110
EST:     TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
genomic: TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
EST: gi|67726581|gb|BJ976840.1|BJ976840
EST:     TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
genomic: TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
EST: gi|162269244|gb|FC445801.1|FC445801
EST:     AGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
genomic: AGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
EST: gi|22133223|gb|BQ827614.1|BQ827614
EST:     TGTTTCGTCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
genomic: TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
EST: gi|162252752|gb|FC428789.1|FC428789
EST:     TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
genomic: TGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
EST: gi|162243413|gb|FC425109.1|FC425109
EST:     GTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAG                         TTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA
genomic: GTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGA

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), 27 (downstream exon)
Score: 17

ATGTGTGGCAATGGAATTCGCTGTTTCGCCAAGTATCTTGCTGACCTTGAGCAGGCATCAGCACCCAGGAGgtatttcccg ... gagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGACGGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacatttaagcatgttgttgagctcattaaattcacgtgcgttttgagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGACGGACAG
 ctttgac  putative branch site (score: 17)
                       tcattaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcccgtttcagctttcacactggggatttatctcttgcattccatcctctactttgacatttaagcatgttgttgagctcattaaattcacgtgcgttttgagttcgcagTTACAAAGTCCTCACTCTCGCAGGCCACATGATTCTTGAATTGCGGGAAGACGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA