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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttagtttgctctccatatgtaatggaacttgattatcagtcaactgcaacagattggtattaggtaggttttcggatcttgtgtaattagctaattctctgtgattgcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT

Basic information

species Physcomitrella patens
transcript PP1S214_34V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 11
gtaccttagtttgctctccatatgtaatggaacttgattatcagtcaactgcaacagattggtattaggtaggttttcggatct-tgtgtaattagctaattctctgtgat-tgcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT
                                        ||  ||   |   |   | |   |||   |   ||||     |  |   ||| ||    |  | || |    | |  |  ||| |||||||||||||| |||||||| ||||||||| |||||||  | |||||||| || ||     | 
---------------------------------------gtctctctcttaacatgaaatctcattgactcaatttttttcccaatagctaactaaaagaaccactctctcctcctctttcagagTTCCAAACATCAAATTTAACGTGGCCAAAATGATGCAATCTCTCATTCCGATAGTCGACCAAGCG

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G13320.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaccttagtttgctctccatatgtaatggaacttgattatcagtcaac-tgcaacagattggtattaggtaggttttcggatcttgtgtaattagctaattctctgtgattgcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT
                                |  |  | ||  | ||| || ||     | |  | |  |   ||  |      |   |||       | |||||     | |  |  ||| |||||||||||||| |||||||| ||||||||| |||||||  | |||||||| || ||     | 
-------------------------------gcaagtctctctcttaacatgaaatctcattgactcaatttttttcccaatagctaactaaaagaaccactctctcc---tcctctttcagAGTTCCAAACATCAAATTTAACGTGGCCAAAATGATGCAATCTCTCATTCCGATAGTCGACCAAGCG

upper sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaccttagtttgctctccatatgtaatggaacttgattatcagtca--actgcaacagattggtattaggtaggttttcggatcttgtgtaattagctaattctctgtgattgcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT
                      |  ||| ||  | |||||   |  |  | |    || | | || ||| | |   ||     | ||   |   | | |  | | |     ||       ||| ||||||||||||||||| ||||| |||||| | ||||||||| | || || || || ||     | 
---------------------gtacaataga--tagattagaggatatgaataagccaaactagt-ttaagaacacttcttagtttttaatgtgttgttgttgcacacctcttatctctgcagAGTTCCAAACATCAAGTTCAACGTTGCCAAACTTCTGCAATCCCTCATCCCCATAGTCGACCAATCA

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|37829837|gb|BJ587849.1|BJ587849
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCGAAAGACAG                         GGTTCCAAACATCAAGTTTNACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|18338950|gb|BJ170976.1|BJ170976
EST:     GCCAGACAATGTTGCCTGTGGTCATCANATGCAGCAAAAGACAGG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATNNTGCAATCCATGATTC
genomic: GCCAGACAATGTTGCCTGTGGTCATCA-ATGCAGCAAAAGACA-Ggtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTC
EST: gi|37821365|gb|BJ579431.1|BJ579431
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|208392785|gb|DC953682.1|DC953682
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|18335295|gb|BJ167313.1|BJ167313
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|37821299|gb|BJ579365.1|BJ579365
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|37821624|gb|BJ579690.1|BJ579690
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCGAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|37828113|gb|BJ586125.1|BJ586125
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|162153519|gb|FC330120.1|FC330120
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|37843689|gb|BJ601697.1|BJ601697
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|162170520|gb|FC347666.1|FC347666
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|162179207|gb|FC355672.1|FC355672
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|37829768|gb|BJ587780.1|BJ587780
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|37830897|gb|BJ588909.1|BJ588909
EST:     CCACTTGCCAGACAAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: CCACTTGCCAGAC-AATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|37845416|gb|BJ603424.1|BJ603424
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|162254923|gb|FC431108.1|FC431108
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|37841224|gb|BJ599232.1|BJ599232
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAAATGCTGCAATCCATGATTC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCC-AAAATGCTGCAATCCATGATTC
EST: gi|162258176|gb|FC433958.1|FC433958
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
EST: gi|37844214|gb|BJ602222.1|BJ602222
EST:     GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAG                         GGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC
genomic: GCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCC

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: 34 (upstream exon), 32 (downstream exon)
Score: 16

TGACGGTACTTGTTGCGATTTCTCTTCTTGCTCCAGTAGTTGGTTCCGAAGCCACTTGCCAGACAATGTTGCCTGTGGTCATCAATGCAGCAAAAGACAGgtaccttagt ... gcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtaggttttcggatcttgtgtaattagctaattctctgtgattgcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT
                           agctaat  putative branch site (score: 16)
                    tgtaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccttagtttgctctccatatgtaatggaacttgattatcagtcaactgcaacagattggtattaggtaggttttcggatcttgtgtaattagctaattctctgtgattgcgatgacagGGTTCCAAACATCAAGTTTAACGTCGCCAAAATGCTGCAATCCATGATTCCGATTGTTGATTCCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC