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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtctttttttaatcccctgattagtttttgtgttactctttgagctttcaggatctttcaggacgtgcaggtaagagtcacattcaagcaggttta...

Basic information

species Physcomitrella patens
transcript PP1S78_56V6.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S78_56V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: LOC_Os07g22720.1 (Oryza sativa), 5'ss of exon 17
GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaa-gtctttttttaatcccctgattagtttttgtgttactctttgagctttcaggatctttcaggacgtgcaggtaagagt-cacattcaagcaggttta
|| ||||| || || || || |||||||| |||||||| ||||| ||||||||||| ||||| |||||||||||  | || ||  | ||  ||||  || ||||    |  | ||   |   |  || ||||     | | || |||    ||      || |    |  |    |||  | |  | ||| |      ||  
GGCACATTCACCATATCAAACTTGGGAGGTCCTTTTGGAATTAAGCAATTTTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTTCTGgtaataagtcatgttgcacttttactttgtttccac-taattcgttgccacttagcttactctgtaaaaataattgtagcattatatatttatctgcatta-

upper sequence: PP1S78_56V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: GLYMA16G00590.1 (Glycine max), 5'ss of exon 17
GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtctttttttaatcccctgattagtttttgtgttactctttgagctttcaggatctttcaggacgtgcaggtaagagtcac-attcaagcaggttta
|| ||||||||| |  | ||  ||||||| || |||||  | |||||||| ||||| ||||||||||||||||| |||| ||||||||| |||||  || || ||     |||   ||   |  ||   |||| | |   |  || |          | ||     |  | |  | |    | || |    |||||     
GGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGATCTGgtgagaacagttt-ggtcattt--ttcccttttatttcgtttattaattgcagtcacttttctcttatcttcgtgcattgctgactacatgagcag-----

upper sequence: PP1S78_56V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: GLYMA07G03930.1 (Glycine max), 5'ss of exon 17
GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtctttttttaatcccctgattagtttttgtgttactctttgagctttcaggatctttcaggacgtgcaggtaagagtcacattcaagcaggttta
|| ||||||||| | || ||  ||||||| || |||||  | | |||||| ||||| ||||||||||||||||| || | ||||||||| |||||  || || ||     |||        |      | ||| | | | |  |||   || |       ||      |||||  |       ||||   |||||     
GGTACATTTACAGTGTCTAACCTGGGAGGGCCATTTGGTGTCAGACAATTCTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGATCTTgtgagaacagtttggtcattttttcctttatttctttcattaattgcagttacttttctcttatctttgtgcat-tgctgactacat--gagcag-----

upper sequence: PP1S78_56V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: AT3G13930.1 (Arabidopsis thaliana), 5'ss of exon 18
GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtctttttttaatcccctgattagtttttgtgttactctttgagctttcaggatctttcaggacgtgcaggtaagagtcacattcaagcaggttta
|||||||| ||| |||||||  |||| ||||||||||| || ||||| || |||||  |||||||||| ||||||||||||||||| ||  | ||  || ||||||| ||     |  |    | |   |    ||    |  ||  || |     |  | | |    ||    ||  || || ||   || |||     
GGAACATTCACAGTCTCCAACCTGGGGGGACCTTTTGGCATCAAACAGTTCTGTGCCGTCATCAATCCACCTCAAGCAGCCATTCTAGCAATCGGATCTGgtaagtccttagcatactcatccactttatccgttgaagtttcttccgcgt----aacttattatagtgttggtgtctgaatctca---aaacag-----

upper sequence: PP1S78_56V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 5'ss of exon 17
GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtctttttttaatcccctgattagtttttgtgttactct-ttgagctttcaggatctttcaggacgtgcaggtaagagtcacattcaagcaggttta
|||||||||||  |||| || ||||||||||||||||| || || ||||| |||||  || | ||||| |||||||| |||||||| || |||||  |  ||| |   | | | ||| |       ||||||| |  |||| |    |   | ||  | |      |   ||    | |   | | |   ||  |      
GGAACATTTACTGTCTCTAACTTGGGAGGACCTTTTGGCATCAAGCAATTCTGTGCAGTCGTTAATCCACCTCAAGCCGCCATTCTAGCAGTTGGATCCGgtatgctctctctcaatgcagaagagagtttttttactactttaccaaagatccaataaccgattcgtgttgtgtctgattcttaaaaaaaaaaaaaacag

upper sequence: PP1S78_56V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 18
GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtctttttttaatcccctgat-tagtttttgtgttactctttgagctttcaggatctttcaggacgtgcaggtaagagtcacattcaagcaggttta
|| ||||||||  | || ||| |||||||||| ||||| || || ||||| ||||| |||||||||||||||||  ||| |||||| ||  ||||| || |||||      |  |  | | | || |   |    | ||   | || | | |        |  |    |     | | |         |   ||||     
GGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGTCTGgtaaga-----taaagacgcttaatattaatgcccttttgtacattcatcatcatcatcatccccatcctcattgatgaactctgttcttttgcag-----

upper sequence: PP1S78_56V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 5'ss of exon 17
GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtctttttttaatcccctgattagtttttgtgttactctttgagctttcaggatctttcaggacgtgcaggtaagagtcacattcaagcaggttta----------------------------------
|| || |||||  | || || ||||||||||| |||||  | |||||||||||||| || ||||||||||| ||| | | ||| || || |||||| || ||| | ||     | |||      ||  | ||  | ||  ||||    | ||     |    | |    |        || |  ||||      | ||||                                  
GGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGTCTGgtatg-ctgcagctgatcattgccttcatcttcttcttcttcttcttccattttctgttggcctgttgcttttacctggactatcattagttttgttttacttttactaagcactgtacaattttcttgaccag

upper sequence: PP1S78_56V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: EFJ28117 (Selaginella moellendorffii), 5'ss of exon 12
GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtctttttttaatcccctgattagtttttgtgttactctttgagctttcaggatctttcaggacgtgcaggtaagagtcacattcaagcaggttta
|| || || ||  |||| || ||||| ||||| ||||| || |||||||||||||||||||||||||| || ||  |   ||||||||| || || || |||||||    ||| ||   |          |||     |   ||      |    |||| ||  |   ||                              
GGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCACGAgtaagt----tttcaacgtctcaggcgccatttcc--caactttgatatatcttcgatcgttttgtttgtag----------------------------

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|208389144|gb|DC945720.1|DC945720
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|208372298|gb|DC948487.1|DC948487
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|208363391|gb|DC946989.1|DC946989
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|67696740|gb|BJ956973.1|BJ956973
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|208374118|gb|DC952549.1|DC952549
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|162172597|gb|FC349370.1|FC349370
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|67695414|gb|BJ955647.1|BJ955647
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|208370468|gb|DC952171.1|DC952171
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|208385745|gb|DC952906.1|DC952906
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|15327043|gb|BI487519.1|BI487519
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|67693244|gb|BJ953477.1|BJ953477
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
EST: gi|67698433|gb|BJ958666.1|BJ958666
EST:     TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTA                         CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA
genomic: TTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCA

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), 29 (downstream exon)
Score: 4

GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtcttt ... tcatccacagCTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCACTTTTATGACTGTTACAATGAGCTGTGATCATCGTGTTATTGATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGACTAgtaagtctttttttaatcccctgattagtttttgtgttactctttgagctttcaggatctttcaggacgtgcaggtaagagtcacattcaagcaggttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT