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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaattatgtcgcctcaatttatggtttaagatgccctcgctgttggagtaacagccaattggttcagtatctcatcatggtaagcattttgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGTTCGCTTTAGCTGTGGCGTTGAGGACTATGAAGACATTCTCAATGATGTT

Basic information

species Physcomitrella patens
transcript PP1S49_246V6.1
intron # 10
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|162153102|gb|FC329508.1|FC329508
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|162159188|gb|FC334359.1|FC334359
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|162198912|gb|FC372939.1|FC372939
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|162198913|gb|FC372940.1|FC372940
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|162164565|gb|FC341860.1|FC341860
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|162165089|gb|FC341630.1|FC341630
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|37830730|gb|BJ588742.1|BJ588742
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|162156222|gb|FC332597.1|FC332597
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|162156221|gb|FC332596.1|FC332596
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|37832348|gb|BJ590360.1|BJ590360
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|37848198|gb|BJ606206.1|BJ606206
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|37851303|gb|BJ609311.1|BJ609311
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
EST: gi|67701447|gb|BJ961680.1|BJ961680
EST:     CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTG                         GGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT
genomic: CTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGT

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: 33 (upstream exon), 33 (downstream exon)
Score: 6

CAACATCAAAATTTATTGATGGCCTCAGAATCCCTTACATTGCGCCTTCCCTTGGTGGAGTAGAAAGTCTGGTTGAACAACCAACCATCATATCTTACTGgtactgtttt ... tgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGTTCGCTTTAGCTGTGGCGTTGAGGACTATGAAGACATTCTCAATGATGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagtaacagccaattggttcagtatctcatcatggtaagcattttgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGTTCGCTTTAGCTGTGGCGTTGAGGACTATGAAGACATTCTCAATGATGTT
 gagtaac  putative branch site (score: 6)
                                         atttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaattatgtcgcctcaatttatggtttaagatgccctcgctgttggagtaacagccaattggttcagtatctcatcatggtaagcattttgcatcacagGGACCAAAGCCCAGCTGAGAGAGCACGTATTGGAATCAAGGACAATTTGGTTCGCTTTAGCTGTGGCGTTGAGGACTATGAAGACATTCTCAATGATGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA