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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgatgtgacagaatgccacatactacacgacgaagtggaaaaccaaataatgaacaagtgggacgtttaagttcattggttcttctgtttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTATTACATTTTTGCCAGCGTTTGGGGTCACAAAATTTATACCATCTACAGCA

Basic information

species Physcomitrella patens
transcript PP1S373_13V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S373_13V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ24166 (Selaginella moellendorffii), 3'ss of exon 7
tctgatgtgacagaatgccacatactacacgacgaagtggaaaaccaaataatgaacaagtgggacgtttaagttcattggttcttctgtttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTATTACATTTTTGCCAGCGTTTGGGGTCACAAAATTTATACCATCTACAGCA
                                           |   ||   |    |  |||  |   | ||||  |     |    | || |  ||||||||||||||| |||||||| || ||||| || ||||| |||||||| || || ||||| ||||| || ||||| ||||| || ||||| || |||||||
----------------------------------------gtgattgaaacttctctacttggttccagttagttgctcacaacgcacgctttgccgcagATGTGCATGGCCGGTTTCCTTCCTTTCAGCGCCATCTATATCGAGCTGTACTATATTTTCGCCAGTGTCTGGGGGCACAAGATCTATACAATTTACAGCA

upper sequence: PP1S373_13V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ35228 (Selaginella moellendorffii), 3'ss of exon 7
tctgatgtgacagaatgccacatactacacgacgaagtggaaaaccaaataatgaacaagtgggacgtttaagttcattggttcttctgtttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTATTACATTTTTGCCAGCGTTTGGGGTCACAAAATTTATACCATCTACAGCA
                                           |   ||   |    |  |||  |   | ||||  |     |    | || |  ||||||||||||||| |||||||| || ||||| || ||||| |||||| | || || || || ||||| || ||||| ||||| || ||||| || |||||||
----------------------------------------gtgattgaaacttctctacttggttccagttagttgctcacaacgcacgctttgccgcagATGTGCATGGCCGGTTTCCTTCCTTTCAGCGCCATCTATATCGAGTTGTACTATATCTTCGCCAGTGTCTGGGGGCACAAGATCTATACAATTTACAGCA

upper sequence: PP1S373_13V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ30210 (Selaginella moellendorffii), 3'ss of exon 7
tctgatgtgacagaatgccacatactacacgacgaagtggaaaaccaaataatga-acaagtgggacgtttaagttcattggttcttctgtttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTATTACATTTTTGCCAGCGTTTGGGGTCACAAAATTTATACCATCTACAGCA
                                              |||||     ||  |   |||  |   | | |||  | |   || |    ||||||||||||||||||| || || ||||| |||||||||||||||||||| || ||||| ||||| || || ||||| |||||||| || || || |||||||
--------------------------------------------gtaaataccatcacttggaagactctcggggttatttatccg--tgatcccttgcagATGTGCATGGCAGGATTTCTCCCGTTTAGTGCAATCTACATCGAGCTTTACTACATATTTGCGAGTGTGTGGGGACACAAAATCTACACGATTTACAGCA

upper sequence: PP1S373_13V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ24924 (Selaginella moellendorffii), 3'ss of exon 7
tctgatgtgacagaatgccacatactacacgacgaagtggaaaaccaaataatga-acaagtgggacgtttaagttcattggttcttctgtttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTATTACATTTTTGCCAGCGTTTGGGGTCACAAAATTTATACCATCTACAGCA
                                              |||||     ||  |   |||  |   | | |||  | |   || |    ||||||||||||||||||| || || ||||| |||||||||||||||||||| || || || ||||| || || ||||| |||||||| || || || |||||||
--------------------------------------------gtaaataccattacttggaagactctcggggttatttatccg--tgatcccttgcagATGTGCATGGCAGGATTTCTCCCGTTTAGTGCAATCTACATCGAGCTTTACTATATATTTGCGAGTGTGTGGGGACACAAAATCTACACGATTTACAGCA

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|162274855|gb|FC451090.1|FC451090
EST:     ATCCTCGTGAGATTCCTGCTCTGCCGTGGTACCGCAGAACTGTTCCACAG                         ATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTAT
genomic: ATCCTCGTGAGATTCCTGCTCTGCCGTGGTACCGCAGAACTGTTCCACAGgtatgcgacg ... ttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTAT
EST: gi|162274854|gb|FC451089.1|FC451089
EST:     GTACCGCAGAACTGTTCCACAG                         ATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTAT
genomic: GTACCGCAGAACTGTTCCACAGgtatgcgacg ... ttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTAT
EST: gi|37839558|gb|BJ597566.1|BJ597566
EST:     TGGTACCGCAGAACTGTTCCACAG                         AAGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTAT
genomic: TGGTACCGCAGAACTGTTCCACAGgtatgcgacg ... ttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTAT
EST: gi|162197721|gb|FC374971.1|FC374971
EST:     ATCCTCGTGAGATTCCTGCTCTGCCGTGGTACCGCAGAACTGTTCCACAG                         ATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTAT
genomic: ATCCTCGTGAGATTCCTGCTCTGCCGTGGTACCGCAGAACTGTTCCACAGgtatgcgacg ... ttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTAT
EST: gi|162217240|gb|FC391980.1|FC391980
EST:     CTGCCGTGGTACCGCAGAACTGTTCCACAG                         ATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTAT
genomic: CTGCCGTGGTACCGCAGAACTGTTCCACAGgtatgcgacg ... ttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaataatgaacaagtgggacgtttaagttcattggttcttctgtttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTATTACATTTTTGCCAGCGTTTGGGGTCACAAAATTTATACCATCTACAGCA
                                    ttcttctgttt  CT-rich tract
                      tttaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgatgtgacagaatgccacatactacacgacgaagtggaaaaccaaataatgaacaagtgggacgtttaagttcattggttcttctgtttgggtgcagATGTGCATGGCAGGTTTCCTGCCGTTCAGTGCAATCTACATCGAGCTCTATTACATTTTTGCCAGCGTTTGGGGTCACAAAATTTATACCATCTACAGCA

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