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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACGACTTGGAGGTCTCGAAGCAGGTGCAGCAGTTGGTGCAGTTTATCCGCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccatcacgtcccagccttttttttttttttttttttttttttttcgtttttttgtttcctgcagtttctcttgtgatgaggcactcgtcaatca...

Basic information

species Physcomitrella patens
transcript PP1S269_14V6.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S269_14V6.3 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os01g46980.1 (Oryza sativa), 5'ss of exon 1
GAACGACTTGGAGGTCTCGAAGCAGGTGCAGCAGTTGGTGCAGTTTATCCGCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccatcacgt-cccagccttttttttttttttttttttttttttttcgtttttttgtttcctgcagtttctcttgtgatgaggcactcgtcaatca----
|||||||   || ||| | |||||| | |||||| |||||| ||| ||||||||||| || ||||||||||| |  ||||| || || || || ||||||||     ||  || | |||  ||  |    |    | |          |      ||   |   |||   | | | |   |    ||    ||  |   |     
GAACGACGCCGATGTCGCCAAGCAGATCCAGCAGATGGTGCGGTTCATCCGCCAGGAGGCCGAGGAGAAGGCCAGCGAGATCTCCGTCTCCGCCGAGGAGgt-----cagtacttacccctcccctcgcctcgcctctcccccgcgcgtcgaagcttcgggaagcctctcgatccgcgcctccgaagcttttcacccgcccgatc

upper sequence: PP1S269_14V6.3 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA05G37150.1 (Glycine max), 5'ss of exon 1
GAACGACTTGGAGGTCTCGAAGCAGGTGCAGCAGTTGGTGCAGTTTATCCGCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccatcacgtcccagccttttttttttttttttttttttttttttcgtttttttgtttcctgcagtttctcttgtgatgaggcactcgtcaatca
|||||||   || ||||| |||||  | |||||| |||||||||| |||||||||||||| ||||| ||||| || ||||| || || || || || |||||   | |||       || | |||| |   ||||  |||    ||  | |  |     |  ||   |  || ||  ||                     
GAACGACGCAGATGTCTCAAAGCAAATCCAGCAGATGGTGCAGTTCATCCGCCAGGAAGCTGAGGAAAAGGCCAACGAGATCTCTGTCTCCGCCGAAGAGgtttcttcatt-----tcaccattttctcccttttcgtttccaattcatgctctaaacggagtcgcacttttccttctgcag------------------

upper sequence: PP1S269_14V6.3 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA05G37160.1 (Glycine max), 5'ss of exon 1
GAACGACTTGGAGGTCTCGAAGCAGGTGCAGCAGTTGGTGCAGTTTATCCGCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccatcacgtcccagccttttttttttttttttttttttttttttcgtttttttgtttcctgcagtttctcttgtgatgaggcactcgtcaatca
|||||||   || |||||||||||  | |||||| |||||| ||| |||||||||||||| ||||| ||||| || ||||| || || || || || |||||   | |||  || |    |||  | |||  |||    ||  |  | ||         |  || | |  || ||  ||                     
GAACGACGCAGATGTCTCGAAGCAAATCCAGCAGATGGTGCGGTTCATCCGCCAGGAAGCTGAGGAAAAGGCCAACGAGATCTCTGTCTCCGCCGAAGAGgtttcttcatttcgccatttcctcctctttcgtttcaaattcatgctcttaaacg----gaatcgtacttttccttctgcag------------------

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|100355126|gb|BY965017.1|BY965017
EST:     GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAG                         GAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGNNNNNNNGAAGATC
genomic: GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATC
EST: gi|100432720|gb|BY978714.1|BY978714
EST:     GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAG                         GAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGNNNNNNNGAAGATC
genomic: GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATC
EST: gi|67569806|gb|BJ942630.1|BJ942630
EST:     GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAG                         GAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGNNNNNNNGAAGATC
genomic: GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATC
EST: gi|208374436|gb|DC940709.1|DC940709
EST:     GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAG                         GAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGNNNNNNNGAAGATC
genomic: GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATC
EST: gi|208359991|gb|DC934908.1|DC934908
EST:     GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAG                         GAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGNNNNNNNGAAGATC
genomic: GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATC
EST: gi|18345670|gb|BJ177713.1|BJ177713
EST:     GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAG                         GAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGNNNNNNNGAAGATC
genomic: GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATC
EST: gi|18343505|gb|BJ175543.1|BJ175543
EST:     GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAG                         GAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGNNNNNNNGAAGATC
genomic: GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATC
EST: gi|100390559|gb|BY952967.1|BY952967
EST:     GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAG                         GAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGNNNNNNNGAAGATC
genomic: GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATC
EST: gi|100352781|gb|BY945445.1|BY945445
EST:     GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGATGAG                         GAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGNNNNNNNGAAGATC
genomic: GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATC
EST: gi|18328236|gb|BJ160240.1|BJ160240
EST:     GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAG                         GAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGNNNNNNNGAAGATC
genomic: GCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATC

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: 21 (upstream exon), 31 (downstream exon)
Score: 6

GAACGACTTGGAGGTCTCGAAGCAGGTGCAGCAGTTGGTGCAGTTTATCCGCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccat ... cttatttcagGAATTCAACATTGAGAAGCTACAGATTGTGGAAGCTGAAAAAAAGAAGATCCGACAGGAGTTCGAGCGCAAGGAGAAGCAAGTGGAAGTTCGTCGTAAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACGACTTGGAGGTCTCGAAGCAGGTGCAGCAGTTGGTGCAGTTTATCCGCCAGGAAGCGGAGGAGAAGGCTAATGAGATTTCAGTTTCGGCTGAGGAGgtacttccatcacgtcccagccttttttttttttttttttttttttttttcgtttttttgtttcctgcagtttctcttgtgatgaggcactcgtcaatca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG