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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT

Basic information

species Physcomitrella patens
transcript PP1S147_62V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os02g09840.1 (Oryza sativa), 3'ss of exon 6
--------------tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgt-----aggctcatccacgtaatcgct-----tcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
               ||| |  | | |   ||    |    |    | |  |  | |   | |   | |||  || ||   || |     | |  |  |     | |  ||     | ||  ||||| ||||||||||| ||||||||||| ||||||||||| ||||||||||||||  |||| || || || || || || |||||  | ||| ||   |||
gtgagacattaaagcatttggtttcacattatctttgttgcttctctcctctcttatagttgttattctctttttttggggctctacaacaagtgcggcactaaagtttctcatttttgtatagGTATTTCTCATATGAGCATTTTTATGTGATATATTGCAAGTTCTGGGAGCTGGACACAGACCATGATTTCTTCATTGATAAAGAAAATCTTATTAAGTAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
tattggcatgccctcaatagaag--acagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaat--cgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
     | ||  | |  ||  |||  | | |||  ||  |     | ||   || ||| |     | | | |  |      |  |  |  |   || |  ||||| ||||||||||| || || |||||||| ||||| |||||||| |||||| ||||  ||||||| || |||||||| || |||||  ||||| |  |||||
---acgaattacttggattcaagttatattatt-tatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctgatgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G104254_T02 (Zea mays), 3'ss of exon 3
-tattggcatgccctca-atagaagacagtatggtacattgat-gtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
    |  |||    |||    |    |  |||      || |  ||    || |  |  |  |||   |  ||          | ||| |||   |  ||||| |||||||||||||| || |||||||| || |||||||||||||||||||||||| |||| ||||| |||||||| || || ||  ||||  |   ||||
cggattacatttgttcacgctgttttctttatatagtcttaacagtattctttgtataatgtttgccaaattgataatcttggctcgtgatc---tgatgcagATACTTCTCATATGAGCACTTTTATGTGATCTATTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAGAACCTCATCAAATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 7
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtat-----ctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
        ||   |   | ||  ||| |   || || || | |   | ||   |  ||  |||||||      |   |  | |   |  |     | | |||||| || |||||||||||||| |||||||| || || ||||||||||||||||||||| |||| ||||| |||||||| || || ||  | ||  |   ||||
---ccatttgttttgtgtggattacattt--gttcactgttttctttatatagtcttaactgtgtataacgtttactgagttaataatcttggatcatggtgcagATATTTCTCATATGAACACTTTTATGTGATCTACTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G040094_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctact-tgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
                                         ||||  ||     ||  |  |   |||| |  | | ||   |  |   ||   ||  | | ||     |  |   || ||     |  |     | || || |||||||||||||| ||||| ||||| ||||||||||| |||||||| |||||  |||| |||||||| || || ||||||||  | ||| ||   |||
gtgacaccttcaaatcaagtcctaacaattcccttcctttgtatttacaaaatttc--tcaagtgcagttt--ttctttaggggaaccctaaactttcattatgcaacacattgaacttattgt--ttgttttcccctgtagATACTTCTCATATGAGCATTTCTATGTGATATATTGCAAGTTCTGGGAACTGGACACAGACCACGACTTCTTTATTGACAAAGAAAATCTTATTAAGTAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G080083_T02 (Zea mays), 3'ss of exon 6
-------------------------------tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
                               |  |    ||   |   |  |   |||| |  | | |  |||  |   || | ||| | || || | |     |  | ||    |  |   | | || ||||| ||||||||||| ||||| ||||| ||||||||||| ||||||||||||||  | ||||| ||||| || || ||||||||  | ||| ||   |||
gtgacaccttcaaatcatgttctaacagttctgctcctttgtattttctcaagtgcagttt--ttcttcaatggaaccctaagcttcca-ttatgcaacacactgaacttcttgtttgtgtttccctgtagGTATTTCTCATATGAGCATTTCTATGTGATATATTGCAAGTTCTGGGAGCTGGACACCGATCATGACTTCTTTATTGACAAAGAAAATCTTATTAAGTAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
-------tattggcat-gccctcaatagaagacagt-atggtacattgatgtgaatttaggtttctacttgtgtatct---gtaggctca-tccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
       || |  |||   | | ||    | ||| | |   |   ||   |  ||  ||  ||  |||  |  |   |   ||    | | |  || ||||   |   || ||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||||||| |||||||||| || || |||||||||||  | ||| |  |||||
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 7
-------tattggcatgccctcaatagaagacagt-atggtacattgatgtgaatttaggtttctacttgtgtat-ctgtaggctca-tccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
       || |    |  | | ||    | ||| | |   |   ||   |  ||  ||  ||  ||      |    |||    | | | ||| ||||   |   || ||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||||||| |||||||||| || || |||||||||||  | ||| |  |||||
gtagatatactatattatcattaaattcacacaatgactctgtttttcagccaaaatatattcataacaaaatgcattgtgtttttacttcacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTTATAGACAAAGAGAATCTTATCAGATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
--------------------tattggcat-gccctcaatagaagacagtatggta--cattgatgtgaatt---taggtttctacttgtgtatctgtaggctcatccacgt-----aatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
                     |||   ||   | |||  | | |||  |   ||    ||| |  |||| |   ||  ||| || |    |  || ||  ||  |  || |      |  | |   |||||||||||||| ||||| ||||||||||| ||||| ||||| || |||||||||||| ||||||| || || ||||||||||||||  | ||  |  |||||
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgcct-taatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 7
--------------------tattggcat-gccctcaatagaagac---agtatggtacattgatgtgaatt---taggtttctacttgtgtatctgtaggctcatccacgt-----aatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
                     |||   ||   | |||  | | |||    || |  |  ||| |   ||| |   ||  ||| || |    |  || ||  ||  |  || |     ||    |   |||||||||||||| || || ||||||||||| ||||| ||||| || |||||||||||| ||||||| || || ||||||||||||||  | ||  |  |||||
gtagatataattgaaaatttcatttcaattaacttcagaaaatgaccttggtttcat-tattcaaacgaactaaatatatttgtattatgatgcct-taatcttttttacctttcctaaatattatctgcagGTACTTCTCTTACGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA20G35090.1 (Glycine max), 3'ss of exon 7
----tattggcatgccctcaatag-aagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
    |  ||     |  ||| |   ||   |||    |   | ||  |||| ||   ||  |   | | ||| ||     | |   |  | |  |  |  | |||||||||||||||||| |||||||||||||| || |||||||| |||||||| ||  ||||||| |||||||| || || | |||  ||||| ||  ||||
aaattcatgattgactttcattttcaatttagttctctctgtagaattgaaatt---ttcttgtctttttatttgcttcattaattatcttacggaat--ttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
----tattggcatgccctcaatag-aagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
       ||     |  ||| |   ||   |||    |   | ||  |||| ||   ||  |   | ||||| ||     | |   |  | |     |  | |||||||||||||||||| |||||||||||||| || |||||||| |||||||| ||  ||||||| |||||||| || || | |||  ||||| ||  ||||
aaatccatgattgactttcattttcaatttagttctctctgtagaattgaaatt---ttcttgtctttgtatttgcttcattaattatcttacgaaat--ttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgta--ggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
         |  ||  | | ||   | | ||    |||| |||  || | |  || |   ||   || |     | ||  || || || |     |    || |||||||||||||| ||||| ||||||||||| ||||| ||||||||||||||| | |||||||| ||  |||| ||||||||  | ||| |  |||||
---------gtact-gacaaaaacaaatttgtgctattgttgtatatatggtattgtttctgctcatttaacatgacttttctacttactt-tggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
  ||||  |      | ||      | ||||  | |||| ||   ||| | |  | |  ||          || ||| || || |  |   |      ||||||||||| ||||||||||| ||||||||||| ||||| ||||||||| ||||| ||||||| || || || || ||||||||  | ||  | ||||||
-gttggtgtcttaagattaattagtaatatg--aaattggtgcttattaacggcttttatta---------agactc-tctac-tgtttatt------agGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 7
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcg---tgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
         |  || |  | || |   |  |    |||| |||  |||||   |  |  || ||    | ||   |||      || || ||| |      || |||||||| ||||| ||||| ||||||||||| ||||| ||||||||||||||| | |||||||| ||  |||| ||||||||  | ||| | ||||||
---------gtactgacaaaaatatt-tgcgtgctattgttgt--atttatagtattgtttttgctcatttaacatcacttttctattcactttggcaattagATACTTCTCGTATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGCGATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
--tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcg--tgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
   |   |   | |      | |     || |  |  |||    | | |     ||| |  |  || ||   ||||| |   || ||  || ||||   ||||||||||| || |||||||| || ||||| ||||| ||||| ||||||||||||||  ||||||| || || ||||| ||||||||  | ||  |  |||||
aacaacagagagacacatgcatatatttgttttat-tattagattaactagttatttatgatgatgaattgctaggccc---catgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv14s0036g00750.t01 (Vitis vinifera), 3'ss of exon 4
----tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
    | | || || | ||||  | |      ||   |  | || ||||   |||   || ||      |  || |    |  |  |  ||  | |||     ||||||||||| |||||||| || ||||| ||||| ||||| ||||||||||||||| | || || || |||||||| || |||||  ||||  |  |||||
tatttgtgggaatactctcataacatttt--tagcatgtactg-tgtggtattaaaattttaacaccattgcttttttttttttgat-tatgcccttaccatagGTACTTCTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGATACCGACCATGATTTTTTGATTGATAAAGAGAACCTAATCAGATAT

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|162193203|gb|FC369963.1|FC369963
EST:     ACTGCTCTTCAGCAAGTGGATGAAGAAGAAGATATCAACAAAGTGTTGCG                         GTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCT
genomic: ACTGCTCTTCAGCAAGTGGATGAAGAAGAAGATATCAACAAAGTGTTGCGgtgagtatat ... cttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT
                                          tcgcttc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattggcatgccctcaatagaagacagtatggtacattgatgtgaatttaggtttctacttgtgtatctgtaggctcatccacgtaatcgcttcgtgcagGTACTTCTCATATGAACATTTTTATGTCATATATTGCAAATTCTGGGAGCTGGATTCAGATCACGACTTTTTGATAGACAAAGATGACCTTCTTCGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG