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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTTAACAGATATATTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGgtaaaccaattctttcagtctagttagctgggcttgcatgacgtgtttccttaattcgtaaactttattgatgggaaaccatgccattcaatttaatgct...

Basic information

species Physcomitrella patens
transcript PP1S4_73V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 7
GTTGTTAACAGATATATTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGgtaa--accaattctttcagtctagtt---agctgggcttgcatgacgtgtt--tccttaattcgtaaactttattgatgggaaaccatgccattcaatttaatgct
|| || ||||||||||||||| ||||  | ||||||||||| || |||||||| ||| | |||||||||    |  ||| | || || |  ||   || |       |     | | |  |  |  | ||  ||| |  |   |||    |   ||   ||  ||        
GTGGTCAACAGATATATTGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTCTGTTCATTGATGAGgtatcttcttattttatccgtatgattgaaagtttactgctctcagtgggctaattttggagtcagaaagtacaaatatgaatgatggtgtgtttatatg-------

upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA08G21830.1 (Glycine max), 5'ss of exon 7
GTTGTTAACAGATATATTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGgtaaaccaattctttcagt--ctagttagctgg-gcttgcatgacgtgtttcct-taattcgt-aaactttattgatgggaaaccatgccattcaatttaatgct
||||||||| ||||||||||| ||||||| |||||||||||||| || ||||| ||| | |||||||| | ||   ||||| |||  ||      ||   |  ||||     | || | | |||||  | |||||||| || |     ||                     
GTTGTTAACCGATATATTGATGAAGGTGTAGCAGAGCTTGTTCCTGGAGTTCTATTCATTGATGAGgtga-ccgtatctttaagtttctcaccgactaatgtctgcaaatactattgcatctaattaatcaaactttaatgcttttttacag-------------------

upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: GLYMA07G02170.1 (Glycine max), 5'ss of exon 7
GTTGTTAACAGATATATTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGgtaaaccaattctttcag--tctagttagctgg-gcttgcatgacgtgtttc-cttaattcgtaaactttattgatgggaaaccatgccattcaatttaatgct
||||| ||| ||||||||||| ||||||| |||||||||||||| || ||||| ||| | |||||||| | |    ||||| |   |||    | ||   |  ||||     | || |   |||||  | ||     || |||                           
GTTGTCAACCGATATATTGATGAAGGTGTAGCAGAGCTTGTTCCTGGAGTTCTATTCATTGATGAGgtga-ctgtgtctttaaatttctcaccaactaatgtctgcaaatactattgcatctaatttatcaaaaaatttaatgtttttttgcag----------------

upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 5'ss of exon 7
GTTGTTAACAGATATATTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGgtaaaccaattctttcagtctagttagctgggcttgcatgacgtgtttccttaattcgtaaactttattgatgggaaaccatgccattcaatttaatgct----
||||| ||| ||||||| ||| ||||||||||||||||||||||||| ||||| ||  | |||||||||      ||     | |  ||||   |    || ||  |    |   |||  |  | |  |   |    |  |||  | |    || | | |||  |     
GTTGTGAACCGATATATAGATGAAGGTGTGGCAGAGCTTGTTCCAGGAGTTCTATTTATTGATGAGgtat-----tttcccaaataaagttttttttcattccactattgat---cttgctcaggactcaggagcagtaagaatacctttgtttaattataaaacctcag

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|37832087|gb|BJ590099.1|BJ590099
EST:     TCGTGGATGAG                         GTGCATATGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAA
genomic: TCGTGGATGAGgtaaaccaat ... cgtactgcagGTGCATATGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAA
EST: gi|67728088|gb|BJ978347.1|BJ978347
EST:     TTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAG                         GTGCATATGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAA
genomic: TTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGgtaaaccaat ... cgtactgcagGTGCATATGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAA
EST: gi|67726395|gb|BJ976654.1|BJ976654
EST:     TTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAG                         GTGCATATGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAA
genomic: TTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGgtaaaccaat ... cgtactgcagGTGCATATGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAA
EST: gi|162252177|gb|FC425855.1|FC425855
EST:     TTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAG                         GTGCATATGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAA
genomic: TTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGgtaaaccaat ... cgtactgcagGTGCATATGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAA
EST: gi|162237932|gb|FC412533.1|FC412533
EST:     TTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAG                         GTGCATATGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAA
genomic: TTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGgtaaaccaat ... cgtactgcagGTGCATATGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTTAACAGATATATTGATCAAGGTGTGGCAGAGCTTGTTCCAGGTGTTCTTTTCGTGGATGAGgtaaaccaattctttcagtctagttagctgggcttgcatgacgtgtttccttaattcgtaaactttattgatgggaaaccatgccattcaatttaatgct

- - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - -  GAGCTT