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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaattttcagcaggatagaaccatttttttgactcgttttgtagcaatcagaacttcctttcttaaggcatctaaaatgatcgttttattaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG

Basic information

species Physcomitrella patens
transcript PP1S22_40V6.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 18
lower sequence: AT3G55610.1 (Arabidopsis thaliana), 3'ss of exon 18
-tagaattttcagcaggatag-aaccatttttttgactcgttttgtagcaatc-agaacttcctttcttaaggcatctaaaatgatcgttttattaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG
 |||       ||   | ||  ||  || |     |          |  |||  |||| |  |  |    |     | ||  ||||  | || |||  |  ||||||||||||||||| ||||||||||||| ||||| || || ||||| |||||  |  | || || |||||
gtagggaagagagagagttaccaataatatcacatatataaaccaaacaaatggagaagtgtcaatgaataaatggccaatgtgatt-tgttcttatgtatagGTGGGAATAAGCACAAGCAGGATTCATGCCCGTGGTCCAGTTGGAGTTGAAGGATTATTGACAACAAGATG
















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|162197988|gb|FC373691.1|FC373691
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|37835735|gb|BJ593747.1|BJ593747
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|37829388|gb|BJ587400.1|BJ587400
EST:     TGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGNCTTGGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGA
genomic: TGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTT-GGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGA
EST: gi|162154554|gb|FC330764.1|FC330764
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|208396875|gb|DC920443.1|DC920443
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162167111|gb|FC343587.1|FC343587
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162154553|gb|FC330763.1|FC330763
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|37839335|gb|BJ597343.1|BJ597343
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162167110|gb|FC343586.1|FC343586
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162276247|gb|FC452601.1|FC452601
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|37821498|gb|BJ579564.1|BJ579564
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162197987|gb|FC373690.1|FC373690
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162191466|gb|FC367170.1|FC367170
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162153152|gb|FC329558.1|FC329558
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162235435|gb|FC411570.1|FC411570
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162210538|gb|FC386834.1|FC386834
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162167790|gb|FC344520.1|FC344520
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|18338412|gb|BJ170436.1|BJ170436
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
EST: gi|162164179|gb|FC339602.1|FC339602
EST:     ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG                         GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA
genomic: ATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAA

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: 31 (upstream exon), 35 (downstream exon)
Score: 23

TGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAGgtgcgtatac ... ttaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatcagaacttcctttcttaaggcatctaaaatgatcgttttattaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG
                          atctaaa  putative branch site (score: 23)
                                        ttttatt  putative PPT
                             taaaatgatcgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaattttcagcaggatagaaccatttttttgactcgttttgtagcaatcagaacttcctttcttaaggcatctaaaatgatcgttttattaaatgcagGTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG