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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaggagaacgactgtaaccctagcatatgcaattaatttcttcatgcagcggagacttcggtttctcatgccttctgtgtggtatcatgtattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGGCTAATGGTGGTGGGTTACAGCATCCGAAATATTGAAGTTCGATATGACA

Basic information

species Physcomitrella patens
transcript PP1S207_10V6.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S207_10V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA06G02100.1 (Glycine max), 3'ss of exon 6
agaggagaacgactgtaaccctagcatatgcaattaatttcttcatgcagcggagacttcggtttctcatgccttctgtgtg----gtatcatgt---attgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGGCTAATGGTGGTGGGTTACAGCATCCGAAATATTGAAGTTCGATATGACA
      |   || | |  |  | |   |   ||     ||||   |||    |  | | ||||   | ||  | | ||  |     |  |||  |   |||  |||||     |  ||  | |||| |||||||||| | || | | | ||||| ||| | |||||||| || |||||||| || |||||||||||||| |||||||
-----cgtgtgattattgcgatggaggagtgaacagccttctctttgc--ttgttattacggtaaataatatcatttgaataagttgcttcaattctgattttacagACTAGCGTGACCGAGACTAGTGCAGCTGAACTTGCGAAGCTGCTTTATTGGTTGATGGTGGTTGGGTACAGCATTCGCAATATTGAAGTTCGTTATGACA

upper sequence: PP1S207_10V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA04G02000.1 (Glycine max), 3'ss of exon 6
agaggagaacgactgtaaccctagca-tatgcaattaatttcttcatgcagcggagacttcggtttctcatgccttctgtgtggtatcatgtattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGGCTAATGGTGGTGGGTTACAGCATCCGAAATATTGAAGTTCGATATGACA
 ||  |    ||  |       | ||   | |  ||   || ||  | | |   | || |  |   ||  ||  |    ||    |      |||  |||||     |  ||  | |||| |||||||||| | || | | | ||||| ||| | |||||||| || |||||||| || |||||||||||||| |||||||
-gattattgtgagggaggagtgaacagccttctctttgcttgtttttactgtaaatacatttgagacttttgaataagttgcttcaattctgattttacagACTAGCGTGACCGAGACTAGTGCAGCTGAACTTGCGAAGCTGCTTTATTGGTTGATGGTGGTTGGGTACAGCATACGCAATATTGAAGTTCGTTATGACA

upper sequence: PP1S207_10V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ23149 (Selaginella moellendorffii), 3'ss of exon 6
agaggagaacgactgtaaccctagcatatgcaattaatttcttcatgcagcgg-agacttcggtttctc-atgccttctgtgtggtatcatgtattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGGCTAATGGTGGTGGGTTACAGCATCCGAAATATTGAAGTTCGATATGACA
                                              |||||   |  |||   | |||  |   || ||||| | |   ||   |   ||||||  | || ||  | || |  ||    ||| |||| ||  |  | |||||||| ||||||||||| ||||||||||| || || |||||||| || ||||
-------------------------------------------gtagcagccatatgcttttctctctttagatctcctgtgcgatgcgatcactc--acagAGAACTGCGACCGAGACGAGCGCGAAAGAACTGGCGAGATTGTTATACTGGCTCATGGTGGTGGGATACAGCATCCGGAACATCGAAGTTCGCTACGACA

upper sequence: PP1S207_10V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ05416 (Selaginella moellendorffii), 3'ss of exon 6
agaggagaacgactgtaaccctagcatatgcaattaatttcttcatgcagcggagacttcggtttctcatgccttctgtgtggtatcatgtattga--acagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGGCTAATGGTGGTGGGTTACAGCATCCGAAATATTGAAGTTCGATATGACA
                                              | ||| |  |  |   ||||||        | |   ||   ||| ||     ||||||  | || ||  | || |  ||    ||| |||| ||  |  | |||||||| ||||||||||| ||||||||||| || || |||||||| || ||||
----------------------------------------------gtagcagccatatgcttttctctctttagatctcctgtgcgatggatcactcacagAGAACTGCGACCGAGACGAGCGCGAAAGAACTGGCGAGATTGTTATACTGGCTCATGGTGGTGGGATACAGCATCCGGAACATCGAAGTTCGCTACGACA

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|162262190|gb|FC437101.1|FC437101
EST:     ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAG                         AGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
genomic: ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAGgttccgcaat ... tattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
EST: gi|208363990|gb|DC950366.1|DC950366
EST:     ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAG                         AGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
genomic: ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAGgttccgcaat ... tattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
EST: gi|162262189|gb|FC437100.1|FC437100
EST:     ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAG                         AGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
genomic: ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAGgttccgcaat ... tattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
EST: gi|208355316|gb|DC949824.1|DC949824
EST:     ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAG                         AGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
genomic: ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAGgttccgcaat ... tattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
EST: gi|208361261|gb|DC957730.1|DC957730
EST:     ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAG                         AGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
genomic: ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAGgttccgcaat ... tattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
EST: gi|37845373|gb|BJ603381.1|BJ603381
EST:     ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAG                         AGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
genomic: ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAGgttccgcaat ... tattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
EST: gi|162265319|gb|FC440437.1|FC440437
EST:     ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAG                         AGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
genomic: ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAGgttccgcaat ... tattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
EST: gi|162178752|gb|FC354502.1|FC354502
EST:     ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAG                         AGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG
genomic: ATACTTTTGTAGCACGTTTGATTGGAGTTGCTGAACCAGACAAGCTCAAGgttccgcaat ... tattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagcggagacttcggtttctcatgccttctgtgtggtatcatgtattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGGCTAATGGTGGTGGGTTACAGCATCCGAAATATTGAAGTTCGATATGACA
                                          atgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaggagaacgactgtaaccctagcatatgcaattaatttcttcatgcagcggagacttcggtttctcatgccttctgtgtggtatcatgtattgaacagAGGGCAGCTACACAAACTACTGCAGCTGAATTGGCAAGGATACTTTACTGGCTAATGGTGGTGGGTTACAGCATCCGAAATATTGAAGTTCGATATGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG