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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatcgcaacatcttactattgctttaattgcatggatgttagtcgcttttatctatttgatgtcaaaaacttttgtataggtctggtatgtttggatcgaggacatatcacgatgatgtttaatgtaatttatttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG

Basic information

species Physcomitrella patens
transcript PP1S99_42V6.3
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|100440899|gb|BY962387.1|BY962387
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|100379974|gb|BY968783.1|BY968783
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|162195534|gb|FC371835.1|FC371835
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|208386797|gb|DC937189.1|DC937189
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|162257183|gb|FC433059.1|FC433059
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|100437064|gb|BY961333.1|BY961333
EST:     GGCTAGCTACCGTTTACTGGGAAAACAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|100427559|gb|BY977558.1|BY977558
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|100386075|gb|BY970014.1|BY970014
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTTGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|162159901|gb|FC336154.1|FC336154
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|162227790|gb|FC402705.1|FC402705
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|67508225|gb|BJ941096.1|BJ941096
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
EST: gi|100440507|gb|BY962234.1|BY962234
EST:     GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCT                         GGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT
genomic: GGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCT

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), 32 (downstream exon)
Score: 15

ATACAGCTTACCAACTTGGGCAGACTTTGAGATGGGGCTAGCTACCGTTTACTGGGAAACCAGCAATGGCCTACCACCAACTTCTgtaagcatcg ... tttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttggatcgaggacatatcacgatgatgtttaatgtaatttatttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG
                              gtttaat  putative branch site (score: 15)
                                         tttattt  putative PPT
                         atgatgtttaatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatcgcaacatcttactattgctttaattgcatggatgttagtcgcttttatctatttgatgtcaaaaacttttgtataggtctggtatgtttggatcgaggacatatcacgatgatgtttaatgtaatttatttgtggcagGGACAACTGCTGACTATCTACTTTAATCCGTCTGCTAGCGAGCTGACACCTAACACTGAATATGGAATCGGGTTCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA