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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccgttttgaggcgactttgtgcatgtgctgccaccttttctcgagttggtgaatcgcgtccgtgttaacttgtgtttcatcaaattctcggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG

Basic information

species Physcomitrella patens
transcript PP1S490_20V6.1
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|208365088|gb|DC947324.1|DC947324
EST:     CTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|162211664|gb|FC387952.1|FC387952
EST:     GCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: GCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|18348930|gb|BJ180979.1|BJ180979
EST:     TTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: TTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|162248628|gb|FC424481.1|FC424481
EST:     CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|67573475|gb|BJ946299.1|BJ946299
EST:     CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|100447101|gb|CJ971400.1|CJ971400
EST:     CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|37821329|gb|BJ579395.1|BJ579395
EST:     CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|208388041|gb|DC941694.1|DC941694
EST:     CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|18353181|gb|BJ185236.1|BJ185236
EST:     CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|100446255|gb|CJ970554.1|CJ970554
EST:     GCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: GCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|100440583|gb|BY962270.1|BY962270
EST:     CTCGCGCTCTCGCATTACTTGCACAGATTGCGGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|208388103|gb|DC933181.1|DC933181
EST:     CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|18355140|gb|BJ187199.1|BJ187199
EST:     TTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: TTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|18372883|gb|BJ204485.1|BJ204485
EST:     CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
EST: gi|67575457|gb|BJ948281.1|BJ948281
EST:     CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAG                         GAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA
genomic: CTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGA

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: 17 (upstream exon), 35 (downstream exon)
Score: 9

ATGAGTTGAATCTCGGTTTTTCTACCACTCGCGCTCTCGCATTACTTGCACAGATTGCAGCTTCTCTCCATCGCCAGgtgcctgcac ... cggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttggtgaatcgcgtccgtgttaacttgtgtttcatcaaattctcggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG
                   tgttaac  putative branch site (score: 9)
                                         ttctc  putative PPT
                                   atcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccgttttgaggcgactttgtgcatgtgctgccaccttttctcgagttggtgaatcgcgtccgtgttaacttgtgtttcatcaaattctcggtcagcagGAATCGGACGTCCTGTGCGCGACTTGTTATTCTTGTGCTAAAGGCTGCAGAAGGGGCTAACTGAGATGATTTCAGGAGGCTCTGTAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - -tgctgcc