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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtccagatatttttcataattgtaaagcgaccattcctacaattattttatcagatcacactgagtgtatgataaaattctgaggtgggaactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATCATGATCATGGATTGTCACAATGTCTTGTACGAGTGGGTTGGCCAGCATG

Basic information

species Physcomitrella patens
transcript PP1S100_30V6.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_30V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: EFJ08608 (Selaginella moellendorffii), 3'ss of exon 15
cgtccagatatttttcataattgtaaagcgaccattcctacaattattttatcagatcacactgagtgtatgataaaattctgaggtgggaactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATCATGATCATGGATTGTCACAATGTCTTGTACGAGTGGGTTGGCCAGCATG
                                         |   ||| | | |  |       ||| | ||    || | || |          ||||| |    |||      |||||||||||||| ||||| |||||||| || ||||||||| | |||   |    ||   ||   |  ||| |||| ||  | |
---------------------------------------gtacgcattct-tgaacttggggctagtatgtg---taactttgtg-------tcatacagTTTGAAGAAACTTTTAATTTCACTCAAGACGATCTCCTGAGTGACGACATCATGATCCTTGATACCCGGTGTGAACTGAGTGTTTGGATTGGTCAAAACG

upper sequence: PP1S100_30V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: EFJ19773 (Selaginella moellendorffii), 3'ss of exon 15
cgtccagatatttttcataattgtaaagcgaccattcctacaattattttatcagatcacactgagtgtatgataaaattctgaggtgggaactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATCATGATCATGGATTGTCACAATGTCTTGTACGAGTGGGTTGGCCAGCATG
                                         |   ||| | | |  |   |   ||  | |   | || | || |          ||||| |    |||      |||||||||||||| ||||| |||||||| || ||||||||| | |||   |    ||   ||   |  ||| |||| ||  | |
---------------------------------------gtacgcattct-tgaacttggagctagcatgt---ataactttgtg-------tcatacagTTTGAAGAAACTTTTAATTTCACTCAAGACGATCTCCTGAGTGACGACATCATGATCCTTGATACCCGGTGTGAACTGAGTGTTTGGATTGGTCAAAACG
















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|162250497|gb|FC428400.1|FC428400
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
EST: gi|162161220|gb|FC337283.1|FC337283
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTTTCACTCA
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTT-CACTCA
EST: gi|162256364|gb|FC432374.1|FC432374
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
EST: gi|100388954|gb|BY988830.1|BY988830
EST:     GAAATTTGAAG                         GTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: GAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
EST: gi|162184987|gb|FC362433.1|FC362433
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
EST: gi|100393142|gb|BY989764.1|BY989764
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
EST: gi|162185667|gb|FC362054.1|FC362054
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
EST: gi|100406380|gb|BY955598.1|BY955598
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
EST: gi|162180210|gb|FC355527.1|FC355527
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
EST: gi|162228276|gb|FC404056.1|FC404056
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
EST: gi|162222679|gb|FC397491.1|FC397491
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC
EST: gi|162199756|gb|FC375829.1|FC375829
EST:     CAGTTTATCACAAGGAAATTTGAAG                         GTGACTGAAGTGCACAATTCCACTCAAGATGATCTTCTGAGTGATGATATC
genomic: CAGTTTATCACAAGGAAATTTGAAGgtaatgattt ... aactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatcagatcacactgagtgtatgataaaattctgaggtgggaactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATCATGATCATGGATTGTCACAATGTCTTGTACGAGTGGGTTGGCCAGCATG
                     tgtatgataaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtccagatatttttcataattgtaaagcgaccattcctacaattattttatcagatcacactgagtgtatgataaaattctgaggtgggaactgtacagGTGACTGAAGTGCACAATTTCACTCAAGATGATCTTCTGAGTGATGATATCATGATCATGGATTGTCACAATGTCTTGTACGAGTGGGTTGGCCAGCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA