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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagatatcacgattattagacaaattcgctaacacgcatatattcgcattttatatttctttctgtaagataccacatgtcaagttagggttcacctctatttgtaggcaatctaacgttgaaaacattgtggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAACGATGAGGAGGCGCTGAAAAAGGCAGTTGCAGGACAGCCAGTCAGCGTTG

Basic information

species Physcomitrella patens
transcript PP1S292_39V6.2
intron # 2
splice site 3'
intron type U2

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|162241027|gb|FC416658.1|FC416658
EST:     AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAG                         ATGAATGCCCGTGTAGTGGCCATCGATTCATACGAGGATGTGCCAGAGAAC
genomic: AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC
EST: gi|162256348|gb|FC432358.1|FC432358
EST:     AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAG                         ATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC
genomic: AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC
EST: gi|208384383|gb|DC928134.1|DC928134
EST:     GAAGGA-TACCCTTACCCAGGCTATGATGGGCCGCTGCGATGTCAACAAG                         ATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC
genomic: GAAGGATTACCCTTACCAAGGCTATGAT-GGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC
EST: gi|208399474|gb|DC908471.1|DC908471
EST:     AGAAGGATNACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCA-CAAN                         ATGAATGCCCGTG
genomic: AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTG
EST: gi|162255229|gb|FC431539.1|FC431539
EST:     AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAG                         ATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC
genomic: AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC
EST: gi|100402354|gb|BY954794.1|BY954794
EST:     AGAAGGAT-ACCCTTACAAAGGCTATGATGGCCGCTGCGATGTCAACAAG                         ATGAATGCCCGTGT
genomic: AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTGT
EST: gi|162244210|gb|FC420966.1|FC420966
EST:     AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAG                         ATGAATGCCCGTGTAGTGGCCATCGATTCATACGAGGATGTGCCAGAGAAC
genomic: AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC
EST: gi|100400530|gb|BY954523.1|BY954523
EST:     AAGGGAT-ACCCTTTAC-AAGGCTATGATGGCCGCTGCGATGTCAACCAG                         ATGAATGCCCGTGTAGTGACCATCGATTCATA
genomic: AAGG-ATTACCCTT-ACCAAGGCTATGATGGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATA
EST: gi|162176978|gb|FC353655.1|FC353655
EST:     AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAG                         ATGAATGCCCGTGTAGTGGCCATCGATTCATACGAGGATGTGCCAGAGAAC
genomic: AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC
EST: gi|100406077|gb|BY991528.1|BY991528
EST:     AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAG                         ATGAATGCCCGTGTAGTGACCATCGATTCATAC
genomic: AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATAC
EST: gi|162261074|gb|FC437455.1|FC437455
EST:     AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAG                         ATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC
genomic: AGAAGGATTACCCTTACCAAGGCTATGATGGCCGCTGCGATGTCAACAAGgtagagatat ... tggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagggttcacctctatttgtaggcaatctaacgttgaaaacattgtggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAACGATGAGGAGGCGCTGAAAAAGGCAGTTGCAGGACAGCCAGTCAGCGTTG
                         atctaac  putative branch site (score: 2)
             tatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagatatcacgattattagacaaattcgctaacacgcatatattcgcattttatatttctttctgtaagataccacatgtcaagttagggttcacctctatttgtaggcaatctaacgttgaaaacattgtggtgcgcagATGAATGCCCGTGTAGTGACCATCGATTCATACGAGGATGTGCCAGAGAACGATGAGGAGGCGCTGAAAAAGGCAGTTGCAGGACAGCCAGTCAGCGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG