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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcatcaagctggaatgctcagtgagtgatatatccatcctattctcgctgattatatgtgctgggcacctgctgtgtgcatgagttatgttatcgagaatcccctctaagatttgagctttcctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTCTGTGGTATTGGGTCCATGGAAGGAATGAGCTTCATGTATATTGGTCACC

Basic information

species Physcomitrella patens
transcript PP1S234_46V6.1
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|100439014|gb|BY961917.1|BY961917
EST:     ATCCTAACCGGCCAATTTTCTTGGAC-ACGTCATGAATATGACCGACAAG                         TGGGTGGGACTTCATGGCGATCGAGCTGGATCCGATGACCCTGC
genomic: ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGC
EST: gi|67570256|gb|BJ943080.1|BJ943080
EST:     ATCCTAACCGGNCAACTTTCTTGGACCACGTCATGAATATGACCGACNAG                         TGGGTGGAACTTCCTGGNGATCGAGCTGGATTC
genomic: ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTC
EST: gi|208391184|gb|DC938158.1|DC938158
EST:     ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAG                         TGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
genomic: ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
EST: gi|208397563|gb|DC912181.1|DC912181
EST:     ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAG                         TGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
genomic: ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
EST: gi|100399143|gb|BY954221.1|BY954221
EST:     ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAG                         TGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
genomic: ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
EST: gi|67718764|gb|BJ969023.1|BJ969023
EST:     ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAG                         TGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
genomic: ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
EST: gi|208363866|gb|DC943323.1|DC943323
EST:     ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAG                         TGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
genomic: ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
EST: gi|208363993|gb|DC939586.1|DC939586
EST:     ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAG                         TGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
genomic: ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
EST: gi|208389733|gb|DC938309.1|DC938309
EST:     ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAG                         TGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
genomic: ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
EST: gi|100356295|gb|BY946293.1|BY946293
EST:     ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAG                         TGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC
genomic: ATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTC

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: 29 (upstream exon), 26 (downstream exon)
Score: 4

AGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTGGCCCGTCATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGACCGACAAGgtaattcatc ... cctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTCTGTGGTATTGGGTCCATGGAAGGAATGAGCTTCATGTATATTGGTCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgagttatgttatcgagaatcccctctaagatttgagctttcctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTCTGTGGTATTGGGTCCATGGAAGGAATGAGCTTCATGTATATTGGTCACC
                                         ctttcctatt  CT-rich tract
        ttatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcatcaagctggaatgctcagtgagtgatatatccatcctattctcgctgattatatgtgctgggcacctgctgtgtgcatgagttatgttatcgagaatcccctctaagatttgagctttcctattgcagTGGGTGGAACTTCATGGCGATCGAGCTGGATTCGATGACCCTGCTTTAGTCTGTGGTATTGGGTCCATGGAAGGAATGAGCTTCATGTATATTGGTCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT