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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGGCCCACCCGGTACTGGCAAGACCCTCATGGCTCGTGCGTGTGCAGCTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcctgctctctccttagtgttttcttctggactggattttgtattttcagctttttgagaaacatgtacagaatctcactgtagaacttgttttaagaagttgggtcattcacttggctaagctcaaggcccttgttctcctcctgatcgttgcag

Basic information

species Physcomitrella patens
transcript PP1S218_133V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 5'ss of exon 5
ATATGGCCCACCCGGTACTGGCAAGACCCTCATGGCTCGTGCGTGTGCAGCTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcctgctctctccttagtgttttcttctggactggattttgtattttcagctttttgagaaacatgtacagaatctcactgtagaacttgttttaagaagttgggtcattcacttggctaagctcaaggcccttgttctcctcctgatcgttgcag
 || || ||||| || ||||| |||||||| ||||||||||| ||||| || ||||| || || || ||  |||| |||||||| || |||||||| |||||     | | || |||  | |      | ||     ||   |  | |   | |  | |  | |   | || ||   || ||||   |    || |  |    |||                                                        
GTACGGACCACCTGGCACTGGAAAGACCCTAATGGCTCGTGCATGTGCTGCCCAAACTAACGCCACATTTCTGAAACTTGCTGGTCCACAGCTTGTCCAGgt---agcttactttctg-tgataaggctgttgaaagctatgtgatatccctgct-cctgctaattcaaatatatgaaagctcaa-atgatgctagggtccttaag--------------------------------------------------------

upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G032505_T02 (Zea mays), 5'ss of exon 5
ATATGGCCCACCCGGTACTGGCAAGACCCTCATGGCTCGTGCGTGTGCAGCTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgtt-ttgtcctgctctctccttagtgttttcttctggactggattttgtattttcagctttttgagaaacatgtacagaatctcactgtagaacttgttttaagaagttgggtcattcacttggctaagctcaaggcccttgttctcctcctgatcgttgcag
 || || ||||| || ||||||||||| |||||||||||||| ||||| || || || ||||| || ||  | ||  | ||||| || || ||||| |||||  |     | ||       |  ||||||||| |  | ||  |||  ||| |  ||||||   ||   | | ||    ||   |   || |  || |  |  |                                                           
GTACGGACCACCAGGAACTGGCAAGACACTCATGGCTCGTGCATGTGCTGCACAGACGAATGCAACGTTTCTTAAATTAGCTGGTCCACAACTTGTGCAGgtaatcagtttacttgagaagtgttgttttctttttta-tgtgtttgttatat--agctttgc-aggtgcgtctatttgatgataaaatatattttttcctctg-----------------------------------------------------------

upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ37626 (Selaginella moellendorffii), 5'ss of exon 5
ATATGGCCCACCCGGTACTGGCAAGACCCTCATGGCTCGTGCGTGTGCAGCTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcctg---ctctctccttagtgttttcttctggactggattttgtattttcagctttttgagaaacatgtacagaatctcactgtagaacttgttttaagaagttgggtcattcacttggctaagctcaaggcccttgttctcctcctgatcgttgcag
 ||||| || || || || || ||||| ||||||||  | ||||||||||||||||| ||||| || | | | ||||||||||| |||||||| || |||||| |||   |   |||| | | |   |  |||||     |  | || ||  |  ||                                                                                                            
CTATGGTCCTCCGGGCACGGGAAAGACTCTCATGGCCAGGGCGTGTGCAGCTCAAACTAATGCAACGTACCTCAAGCTTGCTGGTCCTCAGCTCGTGCAGgttctgtgtaggaactctttacctgtcgggttcttaaactcaagcttctggttcgtcgcag--------------------------------------------------------------------------------------------------------

upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ15061 (Selaginella moellendorffii), 5'ss of exon 5
ATATGGCCCACCCGGTACTGGCAAGACCCTCATGGCTCGTGCGTGTGCAGCTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcctg---ctctctccttagtgttttcttctggactggattttgtattttcagctttttgagaaacatgtacagaatctcactgtagaacttgttttaagaagttgggtcattcacttggctaagctcaaggcccttgttctcctcctgatcgttgcag
 ||||| || || || || || ||||| ||||||||  | ||||||||||||||||| ||||| || | | | ||||||||||| |||||||| || |||||| |||   |   |||| | | |   |  || ||           ||  | ||    ||                                                                                                         
CTATGGTCCTCCGGGCACAGGAAAGACTCTCATGGCCAGGGCGTGTGCAGCTCAAACTAATGCAACGTACCTCAAGCTTGCTGGTCCTCAGCTCGTGCAGgttctgtgtaggaactctttacctgtcgggttgtta-aactcaagcttcttgttcgttgcag-------------------------------------------------------------------------------------------------------

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|162279774|gb|FC455682.1|FC455682
EST:     GGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: GGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|162195316|gb|FC370837.1|FC370837
EST:     CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|162155456|gb|FC330952.1|FC330952
EST:     CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|162162467|gb|FC339198.1|FC339198
EST:     TTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATNGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: TTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|208379283|gb|DC927280.1|DC927280
EST:     CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|162279775|gb|FC455683.1|FC455683
EST:     CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|162260448|gb|FC435061.1|FC435061
EST:     CTCANACAAATGCTACTTTCTTGAAGCTTGCTGGACTTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGNCAAA-CTTGTGAGGGACGCGTTTCAGTTGGC
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTG-CAAAACTTGTGAGGGACGCGTTTCAGTTGGC
EST: gi|162173414|gb|FC349793.1|FC349793
EST:     GAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATNGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: GAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|162168239|gb|FC344969.1|FC344969
EST:     GCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: GCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|208346751|gb|DC917534.1|DC917534
EST:     TGAAGCNTGCTGGACCTCAGCNTGTTCAG                         ATGNTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: TGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|162176625|gb|FC352470.1|FC352470
EST:     TTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATNGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: TTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|208353165|gb|DC921867.1|DC921867
EST:     CTCAAAC-AATGCTACTTTTTTGAAGCTTGCTNGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|208348181|gb|DC920972.1|DC920972
EST:     AAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTNTCAGTTGGCG
genomic: AAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|208360654|gb|DC946420.1|DC946420
EST:     AAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: AAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|208395421|gb|DC924475.1|DC924475
EST:     AAGCNTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGC-AAACCTGTGAGGGACGCGTTTCAGTTGGCG
genomic: AAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|208373658|gb|DC952483.1|DC952483
EST:     CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|162155457|gb|FC330953.1|FC330953
EST:     CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|208395675|gb|DC924197.1|DC924197
EST:     CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|15590637|gb|BI675253.1|BI675253
EST:     CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|162167872|gb|FC344810.1|FC344810
EST:     CTCANACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
EST: gi|162195315|gb|FC370836.1|FC370836
EST:     CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAG                         ATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG
genomic: CTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCG

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: 35 (upstream exon), 29 (downstream exon)
Score: 13

ATATGGCCCACCCGGTACTGGCAAGACCCTCATGGCTCGTGCGTGTGCAGCTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcct ... atcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCGAAAGAAAAGGCTCCTTGTATCATTTTCATTGATGAGGTGGATGCTATTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGGCCCACCCGGTACTGGCAAGACCCTCATGGCTCGTGCGTGTGCAGCTCAAACAAATGCTACTTTCTTGAAGCTTGCTGGACCTCAGCTTGTTCAGgttttgtcctgctctctccttagtgttttcttctggactggattttgtattttcagctttttgagaaacatgtacagaatctcactgtagaacttgttttaagaagttgggtcattcacttggctaagctcaaggcccttgttctcctcctgatcgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT