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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCAAAGCACCGTTGGATGTGGATGGAAAGACGTGGCTGATGACGTGTGTTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttttactcgtagcttcagtatgttatagtatcgtcatcatcatcattattattactccgcataaaaataatgatttgagctgagtgttaaattaacttgacttctagtggtgtgtacttatgttatatgctgtgtataatag

Basic information

species Physcomitrella patens
transcript PP1S51_241V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S51_241V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 5
TGTCAAAGCACCGTTGGATGTGGATGGAAAGACGTGGCTGATGACGTGTGTTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttttactcgtagcttcagtatgttatagtatcgtcatcatcatcattattattactccgcataaaaataatgatttgagctgagtgttaaattaacttgacttctagtggtgtgtacttatgttatatgctgtgtataatag
|||  | |||  | | | ||| ||||||   |  |||    ||||||||||||| |||||||||||||||  |||||| || ||  |  | || |||  |||  | ||||   |  |||  |    ||  |||  | | |||  || | | | | || |||       |||   |  || |||| |   |                                                           
TGTTGAGGCAGAGCTAGTTGTTGATGGAGTAAGCTGGAATGTGACGTGTGTTAGTATGGGCAATCCTCACTGTATCACATTTGGTAAAAAGGGTGGACCGgtgcgtgtttcgttactagacttctaatcatattat-ttgtctaca-cgtgaat-ttcttatcatttgtaa---ttttggtttgtgtcaaccag-------------------------------------------------------
















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|162269245|gb|FC445802.1|FC445802
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|37834821|gb|BJ592833.1|BJ592833
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|37835319|gb|BJ593331.1|BJ593331
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|162186404|gb|FC362960.1|FC362960
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|162252751|gb|FC428788.1|FC428788
EST:     AAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: AAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|162232388|gb|FC408822.1|FC408822
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|162186405|gb|FC362961.1|FC362961
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|22492339|gb|BU052262.1|BU052262
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|22491789|gb|BU051712.1|BU051712
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|37834965|gb|BJ592977.1|BJ592977
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|162243414|gb|FC425110.1|FC425110
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|67726581|gb|BJ976840.1|BJ976840
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|162269244|gb|FC445801.1|FC445801
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|37849296|gb|BJ607304.1|BJ607304
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|37841391|gb|BJ599399.1|BJ599399
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|22133223|gb|BQ827614.1|BQ827614
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|162252752|gb|FC428789.1|FC428789
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|37827317|gb|BJ585329.1|BJ585329
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|162233272|gb|FC409614.1|FC409614
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
EST: gi|162243413|gb|FC425109.1|FC425109
EST:     TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAG                         GGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG
genomic: TTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAG

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: 22

TGTCAAAGCACCGTTGGATGTGGATGGAAAGACGTGGCTGATGACGTGTGTTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttt ... tgtataatagGGGTTGAATGTTGATGCACTTCCTTTGGAGCAAATTGGACCTCTATTTGAGCACCACGAAGTGTTTCCTGCGAGAACAAACACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCAAAGCACCGTTGGATGTGGATGGAAAGACGTGGCTGATGACGTGTGTTAGCATGGGCAATCCTCACGCTATCACCTTCGGACAGGAAGGAGGAGAGgtaagggttttactcgtagcttcagtatgttatagtatcgtcatcatcatcattattattactccgcataaaaataatgatttgagctgagtgttaaattaacttgacttctagtggtgtgtacttatgttatatgctgtgtataatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA