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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgcaaaagtaatcttttgatcaatccaattttggtgatgaactgaccgatgaaaggttcttcgaagggttagtgacatgaaagggtgatgaatt...

Basic information

species Physcomitrella patens
transcript PP1S79_54V6.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 13
TCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgta-agttgcaaaagtaatcttttgatcaatccaattttggtgatgaactgaccgatgaaaggttcttcgaagggttagtgacatgaaagggtgatgaatt
|| ||||| |||   ||| ||||    | ||||||||| || || ||||||||||||||||||||||| |||||  | || ||||| |||||  | ||||||| ||   |     |  |  | | | || |   || |      | |  |    |||       ||||       | ||                      
TCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTGGCATCAGGATGGgtacaggctctttgttgcttctgttaccatttttatgtcttcagtcagttacatgattt----ctcttgtggaattcag----------------------

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA18G27710.1 (Glycine max), 5'ss of exon 14
TCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgcaaaagtaatcttttgatcaatccaattttggtgatg-aactgaccgatgaaaggttcttcgaagggttagtgacatgaaagggtgatgaatt
|| ||||| |||   ||| ||||    | ||||||||| || || ||||||||||||||||||||||| |||||  | || ||||| |||||  | |||||||     |||      | ||      | |  ||||||  || |  || | ||  |    |  |   | |  |  ||                        
TCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTGGCATCAGGATGGgta-----caagctctttgttgcttctattataatttttatgttttaattcacttacatgatttctcttgtggaattcag---------------------

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA02G38160.2 (Glycine max), 5'ss of exon 13
TCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgcaaaagtaatcttttgatcaatccaattttggtgatgaactgaccgatgaaaggttcttcgaagggttagtgacatgaaagggtgatgaatt
||||| || |||   ||  ||||    | |||||| || || || ||||| |||||||| || ||||| |||||| | || |||||||||||||| |||||||   |       | |||||||      |  |   ||| |  || |   |   || | | |||  | ||||  | | |        ||           
TCTAGGGTTGAGAAGGTACTGGAAGCAGTTCATATAGCTGCCAATAAAAATACTGTTCCAGGGGATGTGTCTGCTATGGTTCCTGGAGGCATTCGAATGGgtacagtctgttgctcatctttt------tttatgcttgttagtggatctat-aattacatgttaat-gaagattaacttgtgattcag-----------

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 5'ss of exon 13
TCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgcaaaagtaatcttttgatcaatccaattttggtgatgaactgaccgatgaaaggttcttcgaagggttagtgacatgaaagggtgatgaatt
|||||||| |||  |||| ||||   || ||| |||||  | |||||||||||||||||||||||||| |||||  | || ||||| || ||  | ||||||||    || |  ||| | |||  ||  |    | || |  ||| | |      ||| |   ||| | |  | ||| |  ||                 
TCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCATCCAACAAAAACACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatcacatttaaccatttt-tctttttggtattcg-aatggagttcttcttgatatcctctgccattg-ttattttcag----------------

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 5'ss of exon 13
TCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaag--ttgcaaaagtaatcttttgatcaatccaattttggtgatgaactgaccgatgaaaggttcttcgaagggttagtgacatgaaagggtgatgaatt
|| ||||| ||    ||| | ||   || ||||||||  || |||||||||||||||||||||||||| || ||  | || ||| | |||||  | |||||||    ||       | |  |  || |   |   |||||  |  | |  |     ||   |    ||     |  | ||                      
TCCAGAGTTGAAAAGGTGTTAGAATCTGTTCATATTGTAGCTAACAAAAACACTGTTCCTGGAGATGTGTCGGCCATGGTTCCTAGTGGCATCAGGATGGgtagagtttttgttgatcacatggtgcttg-tgtgatttttattttaagtt---ttatttgatccgctctcttgcttcag----------------------

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 13
TCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgcaaaagtaatcttttgatcaatccaattttggtgatgaactgaccgatgaaaggttcttcgaagggttagtgacatgaaagggtgatgaatt
|||||||| ||    ||  | ||    | ||| ||||| || || ||||||||||||||||| ||||| |||||  | || ||||| |||||||| |||||||   | |     |  || |||| |         | |  ||||     ||    |       | |    | |     |  | |     ||      |  
TCTAGAGTTGAAAAGGTTCTTGAATCAGTTCACATTGCAGCCAATAAAAACACTGTTCCTGGGGATGTGTCTGCCATGGTTCCTGGTGGCATTCGAATGGgtagtgtac-----tcctcctttgtttctcttgcctctactgattgctagataattacttcactttgatgaagtcatctctcttctgttggcacctcag-

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|37851231|gb|BJ609239.1|BJ609239
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|162182304|gb|FC357175.1|FC357175
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|37852647|gb|BJ610655.1|BJ610655
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|162155360|gb|FC331766.1|FC331766
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|37845693|gb|BJ603701.1|BJ603701
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|37850584|gb|BJ608592.1|BJ608592
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|37847210|gb|BJ605218.1|BJ605218
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|37850496|gb|BJ608504.1|BJ608504
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|67698707|gb|BJ958940.1|BJ958940
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|208388379|gb|DC949323.1|DC949323
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|37840030|gb|BJ598038.1|BJ598038
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|162222596|gb|FC398747.1|FC398747
EST:     GGCATTCGCATGG                         GAACCCCTGGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAA
genomic: GGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCT-GCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAA
EST: gi|37838492|gb|BJ596500.1|BJ596500
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|37833067|gb|BJ591079.1|BJ591079
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|67575248|gb|BJ948072.1|BJ948072
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|37838309|gb|BJ596317.1|BJ596317
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
EST: gi|162179834|gb|FC355905.1|FC355905
EST:     CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGG                         GAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG
genomic: CACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgca ... cttggaaaagGAACCCCTGCTTTGACAAGCAGAGGCTTCATAGAGGAAGATTTCGAGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAGGCATTCGCATGGgtaagttgcaaaagtaatcttttgatcaatccaattttggtgatgaactgaccgatgaaaggttcttcgaagggttagtgacatgaaagggtgatgaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagtaa