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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctcttgccttgtcgcctcatgttctgtactcttttcttttggtttgagaacttattttgaaaattcctgaatcacttgcctgggaattggaaaa...

Basic information

species Physcomitrella patens
transcript PP1S219_94V6.4
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S219_94V6.4 (Physcomitrella patens), 5'ss of exon 9
lower sequence: LOC_Os06g49110.1 (Oryza sativa), 5'ss of exon 9
TTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgta-atgctcttgc--cttgtcgcctcatgttctgtactcttttcttttggtttgagaacttattttgaa--aattcctgaatcacttgcctgggaattggaaaa
||||||||||||||||||||||||| |||||||| || || ||    ||| | |||   |  |||   || ||||| || || ||| | ||||| || ||||| || |   ||   ||  |  | |||| || | | ||  | ||   | |      | ||| || | |   || |  || ||   |   ||  |  |  | |  
TTAGCCCTAGTGACATGATGGATGGCCGTGTTGGAGCAATACGTGCTGCTTTGGATGCTGAGGGTTTCCATGATGTCTCCATTATGTCCTATACTGCAAAgtacatacctatgtcactgattccatcatattattt-ctagtatcccatagcactgaaccttcttgtaagttaaataatgcatatgtcaactatgcttatgcag-
















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|208397534|gb|DC916404.1|DC916404
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162270288|gb|FC447300.1|FC447300
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162149641|gb|FC325834.1|FC325834
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162179399|gb|FC355399.1|FC355399
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162270289|gb|FC447301.1|FC447301
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162166751|gb|FC342720.1|FC342720
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162152577|gb|FC328855.1|FC328855
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162179008|gb|FC354316.1|FC354316
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|37840646|gb|BJ598654.1|BJ598654
EST:     TGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: TGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162192024|gb|FC367237.1|FC367237
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162166619|gb|FC343511.1|FC343511
EST:     CATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|208382503|gb|DC923173.1|DC923173
EST:     TGATCTAGCTGGTCATCAAGATGNTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: TGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162150766|gb|FC327038.1|FC327038
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162156545|gb|FC332153.1|FC332153
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162179121|gb|FC355586.1|FC355586
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162179122|gb|FC355587.1|FC355587
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|208373778|gb|DC956294.1|DC956294
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|208396900|gb|DC915948.1|DC915948
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162150767|gb|FC327039.1|FC327039
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|208349261|gb|DC918011.1|DC918011
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|18338206|gb|BJ170230.1|BJ170230
EST:     AGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: AGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162270867|gb|FC446896.1|FC446896
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTNTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162190654|gb|FC367540.1|FC367540
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162149669|gb|FC326720.1|FC326720
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
EST: gi|162156546|gb|FC332154.1|FC332154
EST:     CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAA                         ATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC
genomic: CTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctct ... ggctgtgcagATACGCTAGTGCCTTTTACGGCCCTTTCAGAGAAGCACTAGACTCCAACCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAGCCCTAGTGACATGATGGATGGGCGTGTTGGTGCCATCCGAAAAGCTCTTGATCTAGCTGGTCATCAAGATGTTTCTATCATGGCTTATACAGCCAAgtaatgctcttgccttgtcgcctcatgttctgtactcttttcttttggtttgagaacttattttgaaaattcctgaatcacttgcctgggaattggaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG