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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccgagcagcaactagccatctcgatttcccctaggtcatggccgtgtgcgttctccggctgttgtttttctcattgagataacgtgttgatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAGACAGGTGCTGCCGAGGAGGTTGAGTCCGCGGAGGAGTAGATCAAATGTG

Basic information

species Physcomitrella patens
transcript PP1S79_253V6.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------taccgagcag-caactagccatctcgattt-cccctaggtcatggccgtgtgcgttctccggctg------ttgtttttctcattgagataacgtgttgatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAGACAGGTGCTGCCGAGGAGGTTGAGTCCGCGGAGGAGTAGATCAAATGTG
                                                         |  |    |  |   ||   || |  ||||       ||| ||     | ||| || |    |        |   |||   | ||    |     |    || |  ||||||| || ||||| ||||||||||||||||| |||| |||||||||| |||   ||| ||     |     |||   | |    |    |     |   
gtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctgatacatatgtttatttattttcgggtaatttaattatgctttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G04280.2 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------taccgagcagcaactagccatctcgattt-cccctaggtcatggccgtgtgcgttctccggctg------ttgtttttctcattgagataacgtgttgatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAGACAGGTGCTGCCGAGGAGGTTGAGTCCGCGGAGGAGTAGATCAAATGTG
                                                              |      |    | ||   || |  ||||       ||| ||     | ||| || |    |        |   |||   | ||    |     |    || |  ||||||| || ||||| ||||||||||||||||| |||| |||||||||| |||   ||| ||     |     |||   | |    |    |     |   
gtagtctctctctctctctctctctctctctctctctctctctcttttatgtttttgggttctcttttactctga-tacatatgtttatttattttcgggtaatttaattatgctttttttaacaaaataaataaatttatgcgtttgtgttgttggcaattggtgtagATGGATCCCAAGTTTCTGAGGAATCAGAGGTACGCGAGGAAGCACAACAAGAAGAGTGGTGAAACAGCCACCGAGGAAGAGTGAAATGGCACTTTCTAAC

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G06700.3 (Arabidopsis thaliana), 3'ss of exon 2
taccgagcagcaactagccatctcgatttcc--cctaggtcatggccg-tgtgcgttctccggctgttgtttttctcattgagataacgtgt--tgatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAGACAGGTGCTGCCGAGGAGGTTGAGTCCGCGGAG-GAGTAGATCAAATGTG--
         | || |  |    |  | |||   ||||  | ||  | | |  | ||| |   | ||  | |||  | |||| | | | |||   ||||| |||||||||||||||||||||||||||| |||||||| || | ||||||||||  | || | || | |||| | | |    | |  ||   |||   |  | | |   
---------gtaagtctcttattacagttctaacctaactgatttcagattcgggttatagtgttggaggtttgattattgcgtttatgtgaaatgatgtttcagATGGACCCTAAGTTCCTGAGGAACCAGAGGTACGCAAGGAAGCACAAC--GTCAAG-GCCGGCGAGAATGCTAGCGCTGAAGAATAAGTGTTTTGATTATCTG

upper sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv05s0077g01220.t01 (Vitis vinifera), 3'ss of exon 1
--taccgagcagcaactagccatctcgatttcccctaggtcatggccgtgtgcgttctccggctgttgtttttctcattgagataacgtgttgatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAGACAGGTGCTGCCGAGGAGGTTGAGTCCGCGGAGGAGTAGATCAAATGTG------
   |     || |    |   |      |  |||||   |  ||   |  |  ||  |      | ||  ||| |  ||   |    |   |||     ||||||||||| |||||| ||||||| |||||||| |||| |||||||||| |||   | | ||      |    |   ||| ||| || |||| |||   ||      
gtaatttctcaactttgatttactcttttccccccttttttctgaa-gaatatgtgattgatgcgatgaatttgtgttttgaaatctgaaatgaa----cagATGGACCCGAAGTTCTTGAGGAACCAGAGGTACGCGAGGAAGCACAACAAGAAGAGCGGTG------AATCCGCCACCGAGGAAGAATAGACCAACAATGATTAGG

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|19788741|gb|BQ040890.1|BQ040890
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67698803|gb|BJ959036.1|BJ959036
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|15729775|gb|BI741482.1|BI741482
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|162211739|gb|FC387403.1|FC387403
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|18355369|gb|BJ187428.1|BJ187428
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|162205341|gb|FC382050.1|FC382050
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|162268442|gb|FC444315.1|FC444315
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|19790443|gb|BQ041872.1|BQ041872
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|37830111|gb|BJ588123.1|BJ588123
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|7046835|gb|AW476729.1|AW476729
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67697573|gb|BJ957806.1|BJ957806
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|6167355|gb|AW145619.1|AW145619
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|7147953|gb|AW509875.1|AW509875
EST:     GTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: GTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67574175|gb|BJ946999.1|BJ946999
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67691467|gb|BJ951700.1|BJ951700
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|15261508|gb|BI436818.1|BI436818
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|162207702|gb|FC383787.1|FC383787
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67569906|gb|BJ942730.1|BJ942730
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|37832318|gb|BJ590330.1|BJ590330
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|7067530|gb|AW497385.1|AW497385
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCATAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67693178|gb|BJ953411.1|BJ953411
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|6167007|gb|AW145271.1|AW145271
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|6166984|gb|AW145255.1|AW145255
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|15261330|gb|BI436640.1|BI436640
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|7584238|gb|AW700135.1|AW700135
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCANAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|7047192|gb|AW477086.1|AW477086
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|18350784|gb|BJ182835.1|BJ182835
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
EST: gi|67575340|gb|BJ948164.1|BJ948164
EST:     AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGG                         ATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG
genomic: AGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAGGAAGGGGgtaagcgttt ... gatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgcgttctccggctgttgtttttctcattgagataacgtgttgatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAGACAGGTGCTGCCGAGGAGGTTGAGTCCGCGGAGGAGTAGATCAAATGTG
                  ttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccgagcagcaactagccatctcgatttcccctaggtcatggccgtgtgcgttctccggctgttgtttttctcattgagataacgtgttgatgattcagATGGACCCTAAGTTCCTGAGGAATCAGAGGTATGCGAAGAAGCACAACCAGACAGGTGCTGCCGAGGAGGTTGAGTCCGCGGAGGAGTAGATCAAATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA