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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttattaaatgttttctggaattatcgtagtcatagcttgtttttattagacgccagctaacccgtgttagaaaatatgtaatgtaatgtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCAGCCATTATCTTTATTGATGAAATTGATGCAATTGCAACAGCTCGTTTCG

Basic information

species Physcomitrella patens
transcript PP1S243_67V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
-----actttattaaatgttttctggaattatcgtagtcatagcttgtttttat-tagacgccagctaacccgtgttagaaaatatgtaatgtaatgtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCAGCCATTATCTTTATTGATGAAATTGATGCAATTGCAACAGCTCGTTTCG
       |  |   ||  ||||      || || |  |   ||||  |   ||| |     | |       |||||||  |  | | || |    |||      |||| ||  | ||||||||||| ||||||||  |||| |||||||| |||||||| || || || ||||||||  ||||||| || || || |||||||| |
cctgtcgtggacataaaattttgcatttttttcttcttttcagctgttcaatatatcagtcctattcttgacgtgttatgatctttctacttctttgt------agGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 2
actttattaaatgttttctggaat-tatcgtagtcat---agcttgtttttattagacgccagctaacccgtgttagaaaat-atgtaatgtaatgtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCAGCCATTATCTTTATTGATGAAATTGATGCAATTGCAACAGCTCGTTTCG
   ||| |   | ||    |  || | | || | |||   |  |||   ||  |      | |||   |    ||||  | | || |  | |||     |   |||| ||  | ||||||||||||||||||||  |||| |||||||| || ||||| || || || ||||||||  ||||||| || || || ||||| || |
---ttagtggttattcgtagatatatgttgtcgacataaaaatttgcagttccttttt-tcggctgttcaacattagtcagtcatattct-taactcctttgtagGGCCCTAGAATGGTGCGTGATGTGTTCCGTTTGGCTAAGGAGAATGCTCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGCTTTG

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 2
actttattaaatgttttctggaattatcgtagtcatagcttgtttttatt--agacgccagct--aacccgtgttagaaaatatgtaatgtaatgtg-gtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCAGCCATTATCTTTATTGATGAAATTGATGCAATTGCAACAGCTCGTTTCG
    |  |||| |||| ||||   | ||  | |||| | |||| | | ||     |    | |   | |    |    |||| |    ||  || |   | ||||||||| || ||||| |||||||| || || || || || ||||| ||||| || ||||| |||||||||||  |||||||||| || || ||| | ||  
---ctcctaaa-gtttcctgggggtttcaaattcattgattgtatatgttcttatcaatggtttagagcaacatcttcaaatcttccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT-

upper sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 2
actttattaaatgttttctggaattatcgtagtcatagcttgtttttattagacgccagctaacccgtgttagaaaatatgtaatgtaatgtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCAGCCATTATCTTTATTGATGAAATTGATGCAATTGCAACAGCTCGTTTCG
                                              | |   ||     ||      | |      |    |  | |  ||||| | ||||| || || |||||||||||||| ||| | |||||||| |||||||| || || || |||||||| ||||| |||||||| ||||| || ||||| || |
---------------------------------------------gtgtggaaccttttcttttttctttctcttcacgc-ttgtcttctgtgg-cacagGGACCTCGAATGGTGCGTGATGTTTTCAGGCTGGCGAAAGAGAACGCACCGGCAATCATCTTTATCGATGAGATTGATGCCATTGCCACGGCTCGGTTTG

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|100439418|gb|BY961923.1|BY961923
EST:     CTTTCATCCGTGTTGTTGGTTCTGAGTTTGTACAAAAGTATCTCGGAGAG                         GGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
genomic: CTTTCATCCGTGTTGTTGGTTCTGAGTTTGTACAAAAGTATCTCGGAGAGgtaaggcttg ... gtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
EST: gi|162186125|gb|FC361329.1|FC361329
EST:     CTTTCATCCGTGTTGTTGGATCTGAGTTTGTACAAAAGTATCTCGTAGAG                         GGTCCCCATATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
genomic: CTTTCATCCGTGTTGTTGGTTCTGAGTTTGTACAAAAGTATCTCGGAGAGgtaaggcttg ... gtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
EST: gi|208367978|gb|DC951003.1|DC951003
EST:     TTTGTACAAAAGTATCTCGGAGAG                         GGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
genomic: TTTGTACAAAAGTATCTCGGAGAGgtaaggcttg ... gtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
EST: gi|67724576|gb|BJ974835.1|BJ974835
EST:     CTTTCATCCGTGTTGTTGGTTCTGAGTTTGTACAAAAGTATCTCGGAGAG                         GGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
genomic: CTTTCATCCGTGTTGTTGGTTCTGAGTTTGTACAAAAGTATCTCGGAGAGgtaaggcttg ... gtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
EST: gi|208398297|gb|DC916436.1|DC916436
EST:     CTTTCATCCGTGTTGTTGGTTCTGAGTTTGTACAAAAGTATCTCGGAGAG                         GATCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
genomic: CTTTCATCCGTGTTGTTGGTTCTGAGTTTGTACAAAAGTATCTCGGAGAGgtaaggcttg ... gtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
EST: gi|37851697|gb|BJ609705.1|BJ609705
EST:     CTTTCATCCGTGTTGTTGGTTCTGAGTTTGTACAAAAGTATCTCGGAGAG                         GGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
genomic: CTTTCATCCGTGTTGTTGGTTCTGAGTTTGTACAAAAGTATCTCGGAGAGgtaaggcttg ... gtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
EST: gi|208387168|gb|DC945467.1|DC945467
EST:     TGAGTTTGTACAAAAGTATCTC-GAGAG                         GGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
genomic: TGAGTTTGTACAAAAGTATCTCGGAGAGgtaaggcttg ... gtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
EST: gi|37832812|gb|BJ590824.1|BJ590824
EST:     TGTTGTTGGTTCTGAGTTNGTACAAAAAGTATCTCGGAGAG                         GGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA
genomic: TGTTGTTGGTTCTGAGTTTGTAC-AAAAGTATCTCGGAGAGgtaaggcttg ... gtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattagacgccagctaacccgtgttagaaaatatgtaatgtaatgtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCAGCCATTATCTTTATTGATGAAATTGATGCAATTGCAACAGCTCGTTTCG
            agctaac  putative branch site (score: 2)
                        ttagaaaatatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttattaaatgttttctggaattatcgtagtcatagcttgtttttattagacgccagctaacccgtgttagaaaatatgtaatgtaatgtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCAGCCATTATCTTTATTGATGAAATTGATGCAATTGCAACAGCTCGTTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC