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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgacgatttggcagtgatttttccgctttgcattctttcgaactgatactaatctcttcttcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC

Basic information

species Physcomitrella patens
transcript PP1S165_107V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------------------------------tatgacgatttggcagtgatttttccgctttgcattctttcgaactgatactaatctcttcttcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
                                                               | |   | |      ||  | |||||   || ||  ||  |    ||  | |    |     |   ||||| |  |  |  | | |||     |    |||| |||||||| || || |||||||||||| | ||||||||||| ||||||||||| ||| |||| ||||| ||||| ||||| || || || || ||  
gtagttcatgattcatgaatcctgttgtccatcctttttttccttttcccctgaacatgctcttttactggtaacatggtactgtttccatcttacac-ctagctttgtgtcaatggcattagtgtttattattttaaccat--agttttcttttgtatgcagATCAAAAGAGAGATAAAAATACTTCAGAATCTTTGTGGAGGTCCAAATATCGTGAAACTGCTTGATATTGTTAGAGATCAGCACTCAAAAACACCAAGCT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 3'ss of exon 2
tatgacgatttggcagtgatttttccgctttgcattctttcgaactgatactaatctcttcttcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
        | |   | |||| ||   |  |    || |||  || || || |  |    |     ||||  ||  || ||   ||||   ||      |||| ||||| || || || |||||||||||| | ||||||||||| || || ||| ||||  |||| ||||||||||| || || ||||||||||| ||  
-------gtatttaattgatcttattgact---gttttttttaattgctagtgttgaagtt----cttaacctacctttcatatgtttgaac------agATCAAAAGGGAGATTAAAATACTTCAGAATCTTTGTGGAGGTCCAAACATTGTGTAGCTTCTTGATATTGTCAGAGATCAACATTCTAAGACTCCTAGCT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G047855_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------tatgacgatttggcagt-gatttttccgctttgcattctttcgaactgatactaatctcttcttcacttattctggctgtctactgttcaca--ccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
                                                                   | |   | ||||    | ||  ||   ||     | |   |   |   |   || ||   |      |   |||       |||  |||| |   ||||  |||| ||||| || ||||| |||||||||||| | ||||||||||| || || |||||| || |||| ||||||||||| ||||| || |||||||||||| 
gtacttgaaggaatatgctgccttttctttgcaacattttcccttgcacattctgttttcaagtgaatttacagttttgatgatagaagttggtgccaaagagttactgtcatgaacg-tagtcatcttcatggtgggtcttttaacatacccttcatatgtcttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATTGTGAAGTTGCTTGATATTGTCAGAGATCAGCATTCAAAGACTCCCAGTT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G141903_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------tatgacgatttggcagtgatttttccgctttgcattctttcgaact--gatactaatctcttcttcacttattctggctgtctactgttcaca--ccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
                                                                         | ||||    |     ||  |  ||| |   || |    |  || | || ||  ||      |   |||       |||| |||| |    |||  |||| ||||| || ||||| |||||||||||| | ||||||||||| || || |||||  || |||| |||||||| || ||||| || |||||||||||| 
gtacttaaaggaatatgctggcagttctttgctacatttttctttccacatttatttttctagtgaactcactgttttgatgataggagttgagtgttgaagagttactgcttatgaaaatagtcattttcatggtgggtctcttaacatactcttcatatgttttggcagATCAAAAGGGAGATCAAAATACTTCAGAATCTCTGTGGAGGTCCAAACATTGTGAAATTGCTTGATATTGTCAGGGATCAGCATTCAAAGACTCCCAGTT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G143602_T03 (Zea mays), 3'ss of exon 2
------------------------------------tatgacgatttggcagtgatttttccgctttg------cattctttcgaactgatactaatctcttcttcacttattctggctgtctactgttcacaccttgt-------tagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
                                    | | |     ||    |  | |||   |  ||       | | |||  |    | ||   | |    |||| | |||     ||  |       |  ||| ||       ||||| ||||||||||| || || ||||||||| | |||||||| || || || ||||||||| | || ||||| ||||| ||||| || || || |||||  
gtagactatgaactatatcacctgccctttgtaacttgttatcccctgaacctactattttaccaatgacaggctactgttttcattccacacatgtttaaatttca-taatttcaattgattttaacctatgcctcgtgctggtgtagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTGTGGAGGCCCTAACATTGTGAAGCTGCTCGATATTGTTAGAGATCAGCATTCGAAAACGCCCAGCT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------tatgacgatttggcagtgatttttccgctttgcattctttcgaac----tgatactaat--ctcttcttcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
                                                          | |  || |       |  | ||| |  ||  ||    ||  ||     | ||   | |  |  || |   || | | |     | | ||  |    |      |||| ||||||||||| || || ||||||||| | | |||||| || || || ||||||||| |||| ||||| ||||| ||||| || || || || ||  
gtagaccatgaatcctattgtatgcagtttgcaacttgttatcccctgaacctactattttagcggtgacaggctactgttttcttttcacacctgtttaaatttcataatttcagtgacaattttcatctcagttttaacatatgcttcttgtgctggtgcagATCAAAAGAGAAATTAAAATTCTTCAGAATCTTTATGGAGGCCCTAACATTGTGAAGCTGCTTGATATTGTTAGAGATCAGCATTCAAAAACACCAAGCT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 2
tatgacgatttggcagtgatttttccgctttgcattctttcgaactgatactaatctcttcttcacttattctggc--tgtctactgttca-caccttgtt--agATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
  ||   ||||   |    || ||  | || |||| || |    |   | | |||   |     | || | ||  |  | |  ||| ||||  |   | ||  ||||||||||||| || || |||||||||||| | |||||||| || ||||| || |||||  |||| ||||||||||| || || || || ||||||||| 
--tgttaattttttaaactttattttgtttagcatactat---gccatttcaaattcttctgatatttttccttactttatgcactcttcaatattattttacagATTAAAAGAGAGATAAAAATACTTCAGAATATTTGTGGAGGCCCAAATATTGTCAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 2
---tatgacgatttggcagtgatttttccgctttgcattctttcgaactgatactaatctcttcttcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
   |      ||||    ||  ||| |     |  | |    |   | |  |  | |  | ||  |||    |||||    ||| |      ||  |||  ||||||||||||| || || |||||||||||  | ||||| || || ||||| || |||||  |||| ||||||||||| ||||| ||||| ||||| ||  
atttgaatttattttttggttgtttgttgtactaacttcagctttcaattcttgtgagatttttgtcataacttctgag-atcttcaacat-cattttgc-agATTAAAAGAGAGATAAAAATACTTCAGAACCTTTGTGGGGGGCCAAATATTGTCAAGCTTCTTGATATTGTCAGAGATCAGCACTCTAAAACTCCTAGCT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA05G22250.1 (Glycine max), 3'ss of exon 2
tatgacgatttggcagtgatttttccgctttgcattctttcgaactgat--actaatctcttcttcacttat--tctggctgtct---actgttcacaccttgtt--agATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
         |||    || ||||     | ||   | | | | |||  |  | | |  |||| |    || |  |||  |  |||   |   |  ||| | | ||  ||||||||||||| || || |||||||||||  | ||||| || || ||||| || |||||  |||| ||||||||||| ||||| ||||| ||||| ||  
---------ttgattttgtttttggttatatggtgtttcttgtactactgcattcagttcttgtgagatttttgtcttaccttctgagatcttcaacatcattttgcagATTAAAAGAGAGATAAAAATACTTCAGAACCTTTGTGGTGGCCCAAATATTGTCAAGCTTCTTGATATTGTCAGAGATCAGCACTCTAAAACTCCTAGCT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 2
tatgacgatttggcagtgatttttccgctttgcattct-ttcgaactgatactaatct--cttcttcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
  ||    |||   |    || ||  | ||  | | || | | |  | | | |  |||    | ||   ||| | |    |        |  ||  |||  ||||||||||||| || || |||||||||||| | || ||||| || ||||| || |||||  |||| ||||||||||| || || || || ||||||||| 
--tgttatttttttaaaacttattttgtttcacgtactatgccatttcaaattcttctgatattttttattactttatgagctcttcaatatcattttgc-agATTAAAAGAGAGATAAAAATACTTCAGAATATTTGCGGAGGCCCAAATATTGTTAAGCTTCTTGATATTGTCAGAGATCAACATTCGAAAACTCCCAGTT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 2
-tatgacgatttggcagtgatttttccgctttgcattctttcgaactgatactaatctcttcttcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
 |  |   | ||  |   | ||| |  |       || || |   |  || | | |  ||| ||||  |||    ||    || |     |   ||   |||| || || || || || |||||||||||  | |||||||| || ||||| ||||||||| |||| ||||||||||| ||||| || || ||||| ||  
ttgcggtaaattttcccaggtttctatgggaattcttattactggcatattccattgactt-ttcagatatcagtgcaacatatttacttctgttttgcagATAAAGAGGGAGATAAAAATACTTCAGAACCTTTGTGGAGGCCCAAATATTGTGAAGCTGCTTGATATTGTCAGAGATCAGCATTCCAAAACTCCTAGCT

upper sequence: PP1S165_107V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 2
---tatgacgatttggcagtgatttttccgctttgcattctttcgaactgatactaatctcttct-tcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
   | ||| | |||   ||   ||||      | |   | |    || | ||  |||| |  | | |||   ||      | |||     | |    |    |||| || || || || || |||||||||||  | ||||| || || ||| |||| |||||| |||| ||||||||||||||||| || || ||||| ||  
tagtctgatgtttta-tagcatttttgagaaatcgttgtgtagtaaattcat--taatatagtttatcagacatatccatt-tctttaaatgattgttgtgcagATAAAGAGGGAGATAAAAATACTTCAGAACCTTTGTGGGGGCCCAAATGTCGTCAAGCTGCTTGATATTGTCAGAGACCAGCATTCAAAAACTCCTAGCT

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|22133106|gb|BQ827548.1|BQ827548
EST:     ACAATGAGCGTTGCGTTATCAAAATTTTGAAGCCAGTGAAGAAGAAAAAG                         ATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATC
genomic: ACAATGAGCGTTGCGTTATCAAAATTTTGAAGCCAGTGAAGAAGAAAAAGgtacaggtca ... accttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatactaatctcttcttcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC
   tactaat  putative branch site (score: 1)
                                              ccttgtt  putative PPT
                   acttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgacgatttggcagtgatttttccgctttgcattctttcgaactgatactaatctcttcttcacttattctggctgtctactgttcacaccttgttagATTAAAAGAGAAATCAAGATACTTCAGAATTTGTGTGGAGGTCCCAATATCGTGAAGCTGTTTGACATTGTCAGAGACCAGCAGTCTAAGACTCCCAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT