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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTTGCAATGAAGAGAGGAATTCCCATCCCTTTTTCACCATCATTTTCGAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttgaaagttttattgttttttgccttagtttactttacatgtttgtgctgattgttcctttacaaaaccttcgaatattatatggtacgtggct...

Basic information

species Physcomitrella patens
transcript PP1S79_105V6.1
intron # 10
splice site 5'
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|67573788|gb|BJ946612.1|BJ946612
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|37842479|gb|BJ600487.1|BJ600487
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|208367986|gb|DC955393.1|DC955393
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|67700799|gb|BJ961032.1|BJ961032
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|208352691|gb|DC921425.1|DC921425
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|162256291|gb|FC432197.1|FC432197
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|208377554|gb|DC922657.1|DC922657
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|162259818|gb|FC435953.1|FC435953
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|208367694|gb|DC955025.1|DC955025
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|162220174|gb|FC396569.1|FC396569
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|67700542|gb|BJ960775.1|BJ960775
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|67697174|gb|BJ957407.1|BJ957407
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|37846724|gb|BJ604732.1|BJ604732
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|67578914|gb|BJ951081.1|BJ951081
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|162276086|gb|FC452362.1|FC452362
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
EST: gi|67577666|gb|BJ949833.1|BJ949833
EST:     GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATG                         CAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA
genomic: GAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTA

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: 20 (upstream exon), 35 (downstream exon)
Score: 5

GAGCTTGCAATGAAGAGAGGAATTCCCATCCCTTTTTCACCATCATTTTCGAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttga ... ctggtaatagCAATGGGTTTGGCAGACCTTGGCATCACATCTCACAAAATCGGGGGTCTTACCATCGAGCATTTGAACGCTTATCGGACTGGTGGCCCGTCAGTAGGCAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTTGCAATGAAGAGAGGAATTCCCATCCCTTTTTCACCATCATTTTCGAAGGATTACCTGGACCAATTGGCGTGCGACCTCATTGTCTCTCAAGATGgtatgtttgaaagttttattgttttttgccttagtttactttacatgtttgtgctgattgttcctttacaaaaccttcgaatattatatggtacgtggct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG