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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACCCGGAGAATTTGAATGAGAATGTGAAGAAGACGGTGTATGCGGTGCGGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatttttgggtggttggttatttttgcggagttgggtttcatgttttgatttttttgatttttgatttttgttttttttttgtgaactttggtttgaatcggacattttttgttcgttctggggggtgggtgacag

Basic information

species Physcomitrella patens
transcript PP1S341_73V6.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S341_73V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA01G03260.3 (Glycine max), 5'ss of exon 2
GGACCCGGAGAATTTGAATGAGAATGTGAAGAAGACGGTGTATGCGGTGCGGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatttttgggtggttggttatttttgcggagttgggtttcatgttttgatttttttgatttttgatttttgttttttttttgtgaactttggtttgaatcggacattttttgttcgttctggggggtgggtgacag
 |||   | |    | ||||| || ||||||||||     ||||| ||  | || ||  | |||||||| || |||||||| |||||||||||||| ||||||           |||  |  ||||||||   ||   |       || || | |||| ||||| ||    |||      ||   ||| ||    |   ||||  | ||   |                             
AGACTATGGGTCAATAAATGAAAACGTGAAGAAGAGTCAATATGCTGTCAGAGGTGAATTATACCTTCGAGCTTCTGAGCTTCAGAAAGAGGGCAAAAAGgta-----------ggttttaagttattttccaggtcatttacaaaatattat-atttgtttgacttgcactttgcacccttaggttg-gaggaataaattgatcctgatcat-----------------------------
















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|100386514|gb|BY951310.1|BY951310
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|18328732|gb|BJ160737.1|BJ160737
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|18326883|gb|BJ158883.1|BJ158883
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|100406162|gb|BY991570.1|BY991570
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|162185274|gb|FC361784.1|FC361784
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|162173953|gb|FC349753.1|FC349753
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|162187116|gb|FC362898.1|FC362898
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|162158810|gb|FC335333.1|FC335333
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|18364842|gb|BJ196915.1|BJ196915
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|100435045|gb|BY979058.1|BY979058
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|100446505|gb|CJ970804.1|CJ970804
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|162165683|gb|FC342250.1|FC342250
EST:     GAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|162193527|gb|FC370430.1|FC370430
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|100389902|gb|BY971254.1|BY971254
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|162171492|gb|FC346767.1|FC346767
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|18329867|gb|BJ161873.1|BJ161873
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|18326623|gb|BJ158622.1|BJ158622
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|67576545|gb|BJ949369.1|BJ949369
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|162151892|gb|FC328138.1|FC328138
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|18363059|gb|BJ195131.1|BJ195131
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|67572677|gb|BJ945501.1|BJ945501
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|67568954|gb|BJ941778.1|BJ941778
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
EST: gi|162157215|gb|FC332849.1|FC332849
EST:     GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAG                         ATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC
genomic: GGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatt ... tgggtgacagATCATTTTCACCAATGTTGGTAACCCGCATGCTCTTGGTCAGAAGCCTCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACCCGGAGAATTTGAATGAGAATGTGAAGAAGACGGTGTATGCGGTGCGGGGAGAGCTTTACCTTCGCGCCTCTGAGCTGCAGAAAGAGGGCAAGAAGgtactggatttttgggtggttggttatttttgcggagttgggtttcatgttttgatttttttgatttttgatttttgttttttttttgtgaactttggtttgaatcggacattttttgttcgttctggggggtgggtgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG