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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctcgaactgtctacctttgataactgttctattcttgatacgctgaacttcttgtttgtgtccgagtccacttgaaggtctcattctgtcatt...

Basic information

species Physcomitrella patens
transcript PP1S215_28V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S215_28V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT1G23310.1 (Arabidopsis thaliana), 5'ss of exon 6
CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctcgaactgtctacctttgataactgttctat-tcttgatacgctgaacttcttgtttgtgtccgagtccacttgaaggtctcattctgtcatt
 || || ||    ||||| ||||||||||||||||||||||||||    ||| | ||||||    | || |||| | |    ||||||||||| |   |            ||     || |  | |  |||   ||  |  | || |   || | |     |||  |||   |               
TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGGgtaatgctctgtctcaagaggtcttttctgctatgatttaccttctgacatttcatttataagttttattt---tccgtttggcag---------------
















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|162184664|gb|FC361902.1|FC361902
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAA
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAA
EST: gi|162207832|gb|FC384125.1|FC384125
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|208400418|gb|DC908645.1|DC908645
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|100371525|gb|BY968022.1|BY968022
EST:     AAGGTGTAGCACAAGTTTTGGATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCA
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCA
EST: gi|100395972|gb|BY972219.1|BY972219
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATAT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATAT
EST: gi|100448661|gb|CJ972960.1|CJ972960
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|100393479|gb|BY953418.1|BY953418
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162214587|gb|FC390618.1|FC390618
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|100417952|gb|BY993265.1|BY993265
EST:     NAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162155910|gb|FC332459.1|FC332459
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162151638|gb|FC327767.1|FC327767
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162153918|gb|FC329425.1|FC329425
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|100392222|gb|BY953255.1|BY953255
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|100384799|gb|BY969534.1|BY969534
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCA
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCA
EST: gi|162186627|gb|FC363599.1|FC363599
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162152068|gb|FC328463.1|FC328463
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|100437194|gb|BY961398.1|BY961398
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162155922|gb|FC332471.1|FC332471
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162176654|gb|FC352499.1|FC352499
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|100448584|gb|CJ972883.1|CJ972883
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTAT-CCACAATATCCTTNGTACTCA
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCA
EST: gi|100448006|gb|CJ972305.1|CJ972305
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162177756|gb|FC354590.1|FC354590
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162178101|gb|FC354403.1|FC354403
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162186048|gb|FC361876.1|FC361876
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162161643|gb|FC339058.1|FC339058
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|100390035|gb|BY989115.1|BY989115
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGACGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162269857|gb|FC445387.1|FC445387
EST:     CGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: CGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162151906|gb|FC328152.1|FC328152
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|162181637|gb|FC357939.1|FC357939
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|100418930|gb|BY975809.1|BY975809
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTG
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTG
EST: gi|100398360|gb|BY972565.1|BY972565
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCCCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT
EST: gi|100437396|gb|BY961497.1|BY961497
EST:     AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG                         GTACTGGTTCCTATTCCACA-TATCCTTTGTACTCAGCAACGATTCAGCTT
genomic: AAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTT

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), 35 (downstream exon)
Score: 43

CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctc ... tatgtcgcagGTACTGGTTCCTATTCCACAATATCCTTTGTACTCAGCAACGATTCAGCTTCTAGGAGGCACACTGGTGCCGTATTATTTGGCTGAGGAGGATAACTGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGGgtaatccctcgaactgtctacctttgataactgttctattcttgatacgctgaacttcttgtttgtgtccgagtccacttgaaggtctcattctgtcatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG