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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattctcatggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC

Basic information

species Physcomitrella patens
transcript PP1S152_13V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
----gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttga--tgattctcatggtgc--aacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
    |||| |  || |      |      |  | | || |  | | ||  | | ||  ||     |||    |||| | |  ||       |||||   |  |   ||||||| || || ||||| || |||||||| || ||||||||||| |||||||||||||||||||| || || |||||  | |||||||||||||||||||
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G110185_T03 (Zea mays), 3'ss of exon 7
gtgctaatttattgtttatttgtttagatgaacatt-agttttcatgtgacgtattttgatgattctcatggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
            |||  ||  ||  | | |  |||  ||||||  |    |  |  | | | ||  |  ||   |||  | | | | ||        | ||||||| || ||||||||||| ||||||||||| |||||||| || ||||| ||||| |||||||| ||||| |||||  | || ||||| |||||||| |
---------ggctgtgaatccgta-aaaggttcatccagtttttttcctgcacacat-gttaatatttctgaaacaaaatattc-tatt--------gtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 7
gtgctaattta---ttgtttatttgtttagatgaacatt-agttttcatgtgacgtattttgatgattctcatggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
  |   || ||    |||  ||  ||  | | |  |||  ||||||  |    |  |  | | | ||  |  ||   |||  | | | | ||        | ||||||| || ||||||||||| ||||||||||| |||||||| || ||||| ||||| |||||||| ||||| |||||  | || ||||| |||||||| |
--gtatatctagggctgtgaatccgta-aaaggttcatccagtttttttcctgcacacat-gttaatatttctgaaacaaaatattc-tatt--------gtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
gtgc-taatttattgtttatttgtttagatgaacattagttttcatgtg-acgtattttgatgattctcatggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
||   ||  |   |||  || |||  | || | |   ||| ||    || |||| | || |  ||  |  ||     |  | | |        | || | ||||||| || |||||||| || ||||||||||| || ||||| || ||||||||||| |||||||| ||||| |||||  |||| || || |||||||| |
gtatatatatggctgtgaatctgtaaatattatc-ccagtcttttcatgtacgtgtgttcaacatatttctgaaatgaattcttc--------tatg-gtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattctcatggtgcaacctgtccatgttact----------tgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
                       | | ||| |||  | |  || | |  | | |||| || ||| |     || ||      ||| | |||            |    |||||||||||||||||||||| |||||||| ||||||||||| || ||||| ||||||||||| || ||||| |||||  | || ||||| ||||||||||
----------------------gtaaaatgcacaagactcgtcctctagcttttttttatcattgtttccatgaaaataaatcatttgactaaaattttctcatttttagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattctca-tggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
             ||  ||   |  ||| |  | ||     |  ||     | |||  ||||   ||| |  |   ||      || |||  | |  | |||||||||||||||||||||| |||||||| ||||||||||| || ||||| ||||||||||| || ||||| |||||  | || ||||| ||||||||||
-------------gtaaatacata-agacgtgccttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaa--attttatctctt-gtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
gtgctaat--ttattgtttatttgtttagatgaacattagttttcatgtgacgtattttg-atgattctcatggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
|||  |||   ||   |  | || |||   |  | |||  |||||  || |  |   |   |||||| |||| |  | |    |  ||||    |      ||||||| |||||||||||||| |||||||| ||||| ||||| || ||||| ||||| ||||| |||||||| |||||  | || ||||||||||||||||
gtgagaatggctaagatgcactttttt---tttaaattttttttcccgttatttccatgacatgatt-tcatcgaactaaaattttatgtcctct------agATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattct----catggtgcaacctgtccatg--ttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC------------------
               | | | | | ||||| || ||  | || || | |  | ||| | || |||     |||| |   | ||| | |    ||  |       ||||||| || || |||||||| |||||||| ||||||||||| || ||||| ||||| ||||| |||||||| |||||  | || ||||||||||||||||                  
--------------gtgaatggctaagatgcaccttc-tatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattct----catggtgcaacctgtccatg--ttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
               | | | | | ||||| || ||  | || || | |  | ||| | || |||     |||| |   | ||| | |    ||  |       ||||||| || || |||||||| |||||||| ||||||||||| || ||||| ||||| ||||| |||||||| |||||  | || ||||||||||||||||
--------------gtgaatggctaagatgcaccttc-tatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv11s0016g00230.t01 (Vitis vinifera), 3'ss of exon 7
gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattctcatggtgcaacctgtccatg-----ttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
                        || | ||| ||   ||| |||||  |    ||| || |   | |   |  |||| |    ||     ||| ||    | ||||||| || ||||||| ||| |||||||| ||||||||||| || ||||| || || ||||| || ||||| |||||   ||| || || |  || ||||
-----------------------gtaaaggaatatatatttccatgtttcactatttaattaaa-taacaatttaaccagcatttgtggcattaatttgctgtagATGGCACGCTCAAAGAGGGCTTGCATTGTCTTTTTTGATGAAGTTGATGCCATAGGTGGTGCACGTTTTGATGATGGTAAGGGTGGAGACAGAGAAGTTC

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|208364215|gb|DC947291.1|DC947291
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
EST: gi|208368723|gb|DC947956.1|DC947956
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
EST: gi|162256307|gb|FC432317.1|FC432317
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
EST: gi|208350436|gb|DC926183.1|DC926183
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
EST: gi|37847976|gb|BJ605984.1|BJ605984
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
EST: gi|208399150|gb|DC912407.1|DC912407
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
EST: gi|67720349|gb|BJ970608.1|BJ970608
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
EST: gi|162267487|gb|FC444238.1|FC444238
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
EST: gi|208366359|gb|DC947569.1|DC947569
EST:     CAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGC-TTTTCAG                         ATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: CAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
EST: gi|162257097|gb|FC432557.1|FC432557
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGGCTCNGTTCA
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTC-GTTCA
EST: gi|67720715|gb|BJ970974.1|BJ970974
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGNCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
EST: gi|162257096|gb|FC432556.1|FC432556
EST:     TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAG                         ATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT
genomic: TTCAGAAATATGTAGGAGAGGGAGCTCGCATGGTTCGTGAGCTTTTTCAGgtaagataca ... ttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgacgtattttgatgattctcatggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC
        ttttgat  putative branch site (score: 4)
      tattttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattctcatggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA