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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactaagatcccttcattcctcctttggaagcacacccttcctttgacattcagatccacaatggcattcagatgctgtggagatgttgataaaattggacgttggtgcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGAAGAAGGAACGAGGAAGCCTTTGCACTCCTATATATTCCATTAAAATAAA

Basic information

species Physcomitrella patens
transcript PP1S29_267V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S29_267V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 4
gtatactaagatcccttcattcctcctttggaagcacacccttcctttgacattcagatccacaatggcattcagatgctgtggagat--gttgataaaattggacgttggtgcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGAAGAAGGAACGAGGAAGCCTTTGCACTCCTATATATTCCATTAAAATAAA
              ||  | | ||   || ||         ||  | || ||| |  || |     |    |||  |  | |    |   | |  |||||||   | |   | |||||||||| |||||||| |||||||||||||| |||||  |    |||   |  ||  | ||||| |    |    | || |||||||||||| | |||  
--------------ctatacttctttcttagattgtggtggttaatatgtcatacttattcgtttcgctggtcatctttttttccaactggctagtaaaattt--catccattcagGAGGTTTTAATCAGCCAATTATGTGTGGTGGTGAGCCAAGGGCTATGCTTAGAAAATATCGAGGCAAAGCTGATGCCCCAATATATTCCATTCAGATATG

upper sequence: PP1S29_267V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ11008 (Selaginella moellendorffii), 3'ss of exon 2
gtatactaagatcccttcattcctcctttggaagcacacccttcctttgacattcagatccacaatggcattcagatgctgtggagatgttgataaaattggacgttggt--gcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGAAGAAGGAACGAGGAAGCCTTTGCACTCCTATATATTCCATTAAAATAAA
                                                                   || |       || |  |  | |    |||    | |||| ||  |||||||| ||||| ||||| ||||||||||| || ||||| || |||||| | |||||||| || || | |  |||  ||||| | ||   ||| || || ||
---------------------------------------------------------------gtaagcgtctgcggtctatc-atttttcctcaaatcctggcgtttgtttgcagGAGGATTCAACCAGCCAATTATGTGTGGAGGCGAGCCACGAATCATGACAAAGAAGGATCGCGGCAACTCTTGTGCTCCTTTGTACAGCATCAAGATCAA

upper sequence: PP1S29_267V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ04906 (Selaginella moellendorffii), 3'ss of exon 2
gtatactaagatcccttcattcctcctttggaagcacacccttcctttgacattcagatccacaatggcattcagatgctgtggag-atgttgataaaattg-gacgttggt--gcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGAAGAAGGAACGAGGAAGCCTTTGCACTCCTATATATTCCATTAAAATAAA
                                                                   | |  |   ||| ||  |  || ||  | ||||   | |||| ||  |||||||| ||||| ||||| ||||||||||| || ||||| || |||||| | |||||||| || || | |  |||  ||||| | ||   ||| || || ||
-------------------------------------------------------------------gtaagcgtctgcggtctatcattttcctcaaatcctggcgtttgtttgcagGAGGATTCAACCAGCCAATTATGTGTGGAGGCGAGCCACGAATCATGACAAAGAAGGATCGCGGCAACTCTTGTGCTCCTTTGTACAGCATCAAGATCAA

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|162188549|gb|FC363731.1|FC363731
EST:     GTCTGCAAGTAGTCTGACACCTAATTCCGAATATGGGATTGGATTCAACG                         GAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGA
genomic: GTCTGCAAGTAGTCTGACACCTAATTCCGAATATGGGATTGGATTCAACGgtatactaag ... gttggtgcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGA
EST: gi|67572626|gb|BJ945450.1|BJ945450
EST:     GTCTGCAAGTAGTCTGACACCTAATTCCGAATATGGGATTGGATTCAACG                         GAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGA
genomic: GTCTGCAAGTAGTCTGACACCTAATTCCGAATATGGGATTGGATTCAACGgtatactaag ... gttggtgcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGA
EST: gi|67569618|gb|BJ942442.1|BJ942442
EST:     GTCTGCAAGTAGTCTGACACCTAATTCCGAATATGGGATTGGATTCAACG                         GAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGA
genomic: GTCTGCAAGTAGTCTGACACCTAATTCCGAATATGGGATTGGATTCAACGgtatactaag ... gttggtgcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGA
EST: gi|162256502|gb|FC432533.1|FC432533
EST:     GTCTGCAAGTAGTCTGACACCTAATTCCGAATATGGGATTGGATTCAACG                         GAGGTTTCAATCAGCNTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGA
genomic: GTCTGCAAGTAGTCTGACACCTAATTCCGAATATGGGATTGGATTCAACGgtatactaag ... gttggtgcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacaatggcattcagatgctgtggagatgttgataaaattggacgttggtgcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGAAGAAGGAACGAGGAAGCCTTTGCACTCCTATATATTCCATTAAAATAAA
                            tgttgat  putative branch site (score: 4)
                           atgttgataaaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatactaagatcccttcattcctcctttggaagcacacccttcctttgacattcagatccacaatggcattcagatgctgtggagatgttgataaaattggacgttggtgcagGAGGTTTCAATCAGCCTATTATGTGTGGTGGAGAGCCGCGTATCATGGCGAAGAAGGAACGAGGAAGCCTTTGCACTCCTATATATTCCATTAAAATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA