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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttaaggttcttgtttctatcaaacagattaaaactctttcatttaagtcctgacgacttatgggtaatgttaactttggcataatctggttggacttttatttgcgattttatttaagcttgattctatctattgtgcatggtatgtagGTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTTCACAATGTTGTTTGACTAAGCATGTCTTCAAGATGAGCAAGCAGTATTTAGCAAATGT

Basic information

species Physcomitrella patens
transcript PP1S7_194V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 12
gtatgttaaggttcttgtttctatcaaacagattaaaactctttcatttaagtcctgacgacttatgggtaatgttaactttggcataatctggttggacttttatttgcgattttatttaagcttgattctatctattgtgcatggtatgtagGTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTTCACAATGTTGTTTGACTAAGCATGTCTTCAAGATGAGCAAGCAGTATTTAGCAAATGT
                                   ||   |  ||   ||| | ||    |  |||   || | | |||| |  |||| | |          | |  |   | ||||| ||   || |  | || ||   | |||  | |||||||||  | ||       ||||| ||||   ||||  || | ||||||||||| || || |||||||| || ||||| ||||||||||| || ||||||||
---------------------------------gtaagtgccatctgctaattgctttgaatatataattact-tcaactcttacatatttta---------tcagatataactttatatatatttaaagcgatataactt-cata-tgtgtagGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT

upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 4
gtatgttaaggttcttgtttctatcaaacagattaaaactctttcatttaagtcctgacgacttatgggtaatgttaactttggcataatctggttggacttttatttgcgattttatttaagcttgattctatcta-ttgtgcatggtatgtagGTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTTCACAATGTTGTTTGACTAAGCATGTCTTCAAGATGAGCAAGCAGTATTTAGCAAATGT
               ||   |  ||||  | | ||||| |   | || ||     ||  || |  |   |  |   |   | || | |     | |    | | | ||   ||| ||  ||  | | |||  || || || |   | || |  ||||||||| |||      ||||| || | ||| ||  |  |||| |||||||||||||||||||||||||| ||||| |  ||||||||||| || |||||
------------gtatgcccccttcaattataataaaagtacatgatatataaattggtgattgttattttcttcaattgtcgggacatataagctatgttctgagtttaaattctaaatattcataatttcatataattatattttgttttcagGTGATCTCAAGCGTATTTGTGAAACGGACCTTGGTTTAATTTCTCAATGTTGTTTGACTAAGCATGTCTTTAAGATCACTAAGCAGTATTTGGCTAATGT

upper sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 12
gtatgttaaggttcttgtttctatcaaacagattaaaactctttcatttaagtcctgacgacttatgggtaatgttaact-ttggcataatctggttggacttttatttgcgattttatttaagcttgattctatcta-ttgtgcatggtatgtagGTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTTCACAATGTTGTTTGACTAAGCATGTCTTCAAGATGAGCAAGCAGTATTTAGCAAATGT
                                                       | |  | |  |   | ||  ||| | |||| | |     |      |   | ||   ||| ||  ||    | |||  || ||  | |   | || |  ||||||||| |||      ||||| || | ||| ||  |  |||| |||||||||||||| ||||||||||| ||||| |  ||||||||||| || |||||
-------------------------------------------------------taataaat-gtacatgattataattgttgggacatataagcaatgttccgagtttaaattctaaatatttataatttcatataactatattttgttttcagGTGATCTCAAGCGTATTTGTGAAACCGACCTTGGTTTAATTTCTCAATGTTGTTTGACAAAGCATGTCTTTAAGATCACAAAGCAGTATTTGGCTAATGT

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|162168543|gb|FC344467.1|FC344467
EST:     CTTGGATCTCCTCATAGCTATTCTACCAGACAACAACGGGCCTTTATATG                         GTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTTCACAATGTT
genomic: CTTGGATCTCCTCATAGCTATTCTACCAGACAACAACGGGCCTTTATATGgtatgttaag ... tggtatgtagGTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTTCACAATGTT
EST: gi|162272458|gb|FC449071.1|FC449071
EST:     CTTGGATCTCCTCATAGCTATTCTACCAGACAACAACGGGCCTTTATATG                         GTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTT
genomic: CTTGGATCTCCTCATAGCTATTCTACCAGACAACAACGGGCCTTTATATGgtatgttaag ... tggtatgtagGTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttatttgcgattttatttaagcttgattctatctattgtgcatggtatgtagGTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTTCACAATGTTGTTTGACTAAGCATGTCTTCAAGATGAGCAAGCAGTATTTAGCAAATGT
                       gcttgat  putative branch site (score: 5)
            attttatttaagctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttaaggttcttgtttctatcaaacagattaaaactctttcatttaagtcctgacgacttatgggtaatgttaactttggcataatctggttggacttttatttgcgattttatttaagcttgattctatctattgtgcatggtatgtagGTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTTCACAATGTTGTTTGACTAAGCATGTCTTCAAGATGAGCAAGCAGTATTTAGCAAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG