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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttctggtgcccttgctgttcatattcctgatcactattcctcgaagtttgcaaccgactcctggatcctgacaaacgtaaacgtgagtattctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCATGGAGACGTCGGCGGTTGAATTGCAAATGTCTACAGACGCAGTCCATCAGAGAGAAACTGGAGAAA

Basic information

species Physcomitrella patens
transcript PP1S6_102V6.2
intron # 1
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|18351983|gb|BJ184035.1|BJ184035
EST:     TGTGTGCGACGTTTGGTTGACTGCATTTTGCACCCGCGTCGCAGTTTACG                         TGTGTTCACCGTATATCTGGTCAATTCTTGATCATGGAGACGTCGG
genomic: TGTGTGCGACGTTTGGTTGACTGCATTTTGCACCCGCGTCGCAGTTTACGgtaaacgatt ... attctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCATGGAGACGTCGG
EST: gi|18363015|gb|BJ195087.1|BJ195087
EST:     GTGTGCGACGTTTGGTTGACTGCATTTTGCACCCNG-GTCGCAGTTTACG                         TGTGTTCACCGTATATCTGGTCAATTCTTGATCAT
genomic: GTGTGCGACGTTTGGTTGACTGCATTTTGCACCC-GCGTCGCAGTTTACGgtaaacgatt ... attctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCAT
EST: gi|18352059|gb|BJ184112.1|BJ184112
EST:     GTGTGCGACGTTTGGTTGACTGCATTTTGCACCCCGCGTCGCAGTTTACG                         TGTGTTCACCGTATATCTGGTCAATTCTTGATCATGGAGACGTCGGCGGTT
genomic: GTGTGCGACGTTTGGTTGACTGCATTTTGCACCC-GCGTCGCAGTTTACGgtaaacgatt ... attctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCATGGAGACGTCGGCGGTT
EST: gi|18360607|gb|BJ192670.1|BJ192670
EST:     TGTGTGCGACGTTTGGTTGACTGCATTTTGCACCCGCGTCGCAGTTTACG                         TGTGTTCACCGTATATCTGGTCAATTCTTGATCATG
genomic: TGTGTGCGACGTTTGGTTGACTGCATTTTGCACCCGCGTCGCAGTTTACGgtaaacgatt ... attctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCATG
EST: gi|18359222|gb|BJ191282.1|BJ191282
EST:     GTGTGCGACGTTTGGTTGACTGCATTTTGCACCCNG-GTCGCAGTTTACG                         TGTGTTCACCGTATATCTGGTCAATTCTTGAT
genomic: GTGTGCGACGTTTGGTTGACTGCATTTTGCACCC-GCGTCGCAGTTTACGgtaaacgatt ... attctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGAT
EST: gi|18328311|gb|BJ160315.1|BJ160315
EST:     TGTGTGCGACGTTTGGTTGACTGCATTTTGCACCCGCGTCGCAGTTTACG                         TGTGTTCACCGTATATCTGGTCAATTCTTGATCATGGAGACGTCGGCGGTT
genomic: TGTGTGCGACGTTTGGTTGACTGCATTTTGCACCCGCGTCGCAGTTTACGgtaaacgatt ... attctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCATGGAGACGTCGGCGGTT
EST: gi|18344217|gb|BJ176256.1|BJ176256
EST:     TGTGTGCGACGTTTGGTTGACTGCATTTTGCACCCGCGTCGCAGTTTACG                         TGTGTTCACCGTATATCTGGTCAATTCTTGATCATG
genomic: TGTGTGCGACGTTTGGTTGACTGCATTTTGCACCCGCGTCGCAGTTTACGgtaaacgatt ... attctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCATG
EST: gi|18345734|gb|BJ177777.1|BJ177777
EST:     GTGTGCGACGTTTGGTTGACTGCATTTTGCACCCCGCGTCGCAGTTTACG                         TGTGTTCACCGTATATCTGGTCAATTCTTGATCATG
genomic: GTGTGCGACGTTTGGTTGACTGCATTTTGCACCC-GCGTCGCAGTTTACGgtaaacgatt ... attctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCATG

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), 10 (downstream exon)
Score: 3

CTCGGAACGGTGCTGTGATCTTGACTGGGTGGCACTGCCAGCAGCAGTTGTGTGTGCGACGTTTGGTTGACTGCATTTTGCACCCGCGTCGCAGTTTACGgtaaacgatt ... attctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCATGGAGACGTCGGCGGTTGAATTGCAAATGTCTACAGACGCAGTCCATCAGAGAGAAACTGGAGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttgcaaccgactcctggatcctgacaaacgtaaacgtgagtattctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCATGGAGACGTCGGCGGTTGAATTGCAAATGTCTACAGACGCAGTCCATCAGAGAGAAACTGGAGAAA
                      tcctgac  putative branch site (score: 3)
                                            tattctc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttctggtgcccttgctgttcatattcctgatcactattcctcgaagtttgcaaccgactcctggatcctgacaaacgtaaacgtgagtattctcgcagTGTGTTCACCGTATATCTGGTCAATTCTTGATCATGGAGACGTCGGCGGTTGAATTGCAAATGTCTACAGACGCAGTCCATCAGAGAGAAACTGGAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA