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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttccacatataatatagatatagtggcgattttacttctcatttttatttttgcaacatacacctaatattcgttcggattcgttcacggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT

Basic information

species Physcomitrella patens
transcript PP1S84_125V6.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: LOC_Os10g36210.1 (Oryza sativa), 3'ss of exon 14
ttttccacatataatatagatatagtggcgattttacttctcatttttatttttgcaacatacacctaat-attcgttcggattcgttcacggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT
  |    | |||  | |     |   |   |  | | |  | | |   |   ||| |   || |   |   ||||  |   | |  |    ||| | |  |||||||||||||||| || ||||||||||||||  ||||||||||||||||||||||| | || || |||||||||||  |||| ||||| |    ||  
-gtatatcctattttcttttctttaggaaaacataattggtaaatcgcaacattggatagtagaataacccattcacttctactgttctgtggtaaca--gATGGCTTGAAAACATACGTGATTGGTGTATTTCAAGACAGCTTTGGTGGGGACACCGTATACCAGCTTGGTATGTAACGCTAGAAGATGATGAGGAGAAA

upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: LOC_Os03g21740.1 (Oryza sativa), 3'ss of exon 16
--------------ttttccacatataatatagatatagtggcgatttta------cttctcattttt---atttttgcaacatacacctaatattcgttcggat--tcgttcacggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT
              |||| || |  |  |||| || |        |||||      | | |||||| |   ||   || || | |||   || |   | | | |   | | |   |    |  |||||||||||||| || || ||||||||| ||||  | || | |||||||||||||||||| |||||||||||||| ||  |||| ||||||     ||  
gtacatttatccacttttacatacttgttatatatttgtcacatcttttaaaaaatcatgtcatttgtcaaatcaatgaaataaacagaaaacaaatgatagaacaattgcttgtgtcattgcagATGGCTTGAAAATATACGTGATTGGTGTGTTTCAAGGCAACATTGGTGGGGACACCGTGTACCTGCATGGTATGTGACACTAGAAGATGACCAGGAGAAA

upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: LOC_Os03g48850.1 (Oryza sativa), 3'ss of exon 14
-------ttttccacatataatatag-atatagtggcgattttacttctcatttttatttttgcaacatacacctaat---attcgttcgga-----ttcgttcacggtga------tatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT
        | ||  | | | || |   |  |       || | || | | |||   | |      | ||| |   |||   ||| |   | |     | | | ||  || |      || |||||||||| ||| || || ||||||||||||||| | ||||||||||||||||| || || ||||| |||||||| |   |||| |||||      ||  
gtaatgtctatcaccttctcatttgtcagttgagaattatctcacctattattgcaaatggcatcatatataggcaatggaattagaaggaaaataatccatccattgtcatgcccttacagATGGCTTGCAAATATACGTGATTGGTGTATTTCGAGGCAGCTTTGGTGGGGACATCGCGTTCCTGCTTGGTATGTTATACTAGAAGATGATCAAGAGAAA

upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: LOC_Os03g02100.2 (Oryza sativa), 3'ss of exon 13
-----ttttccacatataatatagatatagtggcgattttacttctcatttttatttttgcaacatacacctaat--attcgttcg-----gattcgttcacggtgatat------agATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGA-CGCCAGGACT
     | |  ||| | |    |   | |  ||   ||| | |     |||   | |      |  |  |  ||||  | ||    |     ||| | ||||  || || |      |||||||||| ||| || || ||||||||| ||||  | ||||||||||||||||| ||||||||||| ||||||||     |||| ||||| |   || || 
gtatgtctatcacct-tctcgtttgtctcttgagaattatgccatctattgcaaatgacatcatgtcaaagtaatgaaatcagaagaaaatgatccattcattgttatgtccttacagATGGCTTGCAAATATACGTGATTGGTGTGTTTCAAGGCAGCTTTGGTGGGGACATCGTGTGCCTGCTTGGTATGTTGTACTAGAAGATGATCAAGAGAAC-

upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GRMZM2G117870_T02 (Zea mays), 3'ss of exon 15
ttttccacatataatatagatatag-tggcgattttacttctcatttttatttttgcaacatacacctaatattcgttcggattcgttcacggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT
  |   ||||  ||  |   | |   | || ||| |     |||  |  ||      ||  |  |   |||   |  || |  |   | | |    | ||||||||||||||| || || ||||||||| | ||  | || |||||||||||||| ||||| |||||||||||||| ||  |||||||||||      |  
-gtattacattcaacgtgtttgtctcttgcaattat-taggtcaaatgaatgcgataaatctgaaataaatgacctatccg--ttactgatgtctttgtagATGGCTTGAAAATATACGTGATTGGTGTGTCTCAAGGCAACTTTGGTGGGGACATCGTGTACCTGCATGGTATGTGACACTAGAGGATGACCTGGATAAA

upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GRMZM2G106974_T01 (Zea mays), 3'ss of exon 6
ttttccacatataatata-gatatagtggcgattttacttctcatttttatttttgcaacatacacctaatattcgttcggattcgttcacggtga---tatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT
         ||| | |||  || |  || |  || || ||  ||| |  | |     |    || |  ||||   |  |  || | ||   | |     |  |||||||||||||| || || ||||||||| | ||  | || ||||||||||| || ||| | |||||||||||||| ||  |||| ||||||      |  
--------gtattacatacaatgtgttgtcacttgtaattaccatgtcaaatgaatgagataactctgaataaatgacct-atccattactgctatctttgcagATGGCTTGAAAATATACGTGATTGGTGTGTCTCAAGGCAACTTTGGTGGGGTCATCGTATACCTGCATGGTATGTGACACTAGAAGATGACCTGGATAAA

upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA10G38450.1 (Glycine max), 3'ss of exon 13
-------------------------------------------------------------------------------------ttttccacatataatatagatatagtggcgattttacttctcatttttatttttgcaacatacacctaatat--tcgt-tcggattc--gttcacggtgat-atagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT
                                                                                       |        |  | |  || || |     | | |  |  | ||||| || ||   | |  ||  | ||||   | | ||  | |   | | |   || | | |||||||| |||||||| || |||||||| ||||| |||||||| |||||||| ||||   | |||||||||||||| ||| | |||||||| |        
gtacttgtatctttgtttgctttttgcaaattcttgtaatgaacattaaattacatttatggcaccatgttgtggtcggaacttggctctttggcgtgctctgtatctaattttcttctcatgtgcctttttttttcttcttataatcatatgatataaccatgtcatactgaaggtaattttgtttacagATGGCTGGAAAACATACGTGATTGGTGCATTTCACGACAGCTATGGTGGGGTCACCAAATACCTGCATGGTATGTCACTTTGGAGGATGATGTTCTTCGG

upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: AT1G14610.1 (Arabidopsis thaliana), 3'ss of exon 14
-------------------------------ttttccacatataatatagatatagtggcgattttacttctcatttttattt-----ttgcaacatacacctaatat-tcgttcgg--attcgttcacggt------gatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT--
                                ||||   || ||    |  |||||  ||  | ||||  | ||  | |||        ||| |        ||| || || ||     ||   || ||  |        || |||||||| || ||||| || || |||||||||||  |||||||||||||||||||| |  | || ||||||||||  ||| ||||||| ||   |||  |   
gtttctttcatttatcttttactctataatggtttcttaatctaccccatctatagaagc--tcttacagcacagctgtatggataagctgcgatggcggtttaagatgtcattacaccatctattaacaatctttaccttacagATGGCTAGAGAACATACGTGACTGGTGTATTTCAAGACAGCTTTGGTGGGGACACAGAATACCAGCATGGTATGCCACTCTAGAGGAGGAT--CAGCTCAAG

upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: Vv16s0100g00370.t01 (Vitis vinifera), 3'ss of exon 17
ttttccacatataatatagatatagtggcgattttacttctcatttttatttttgcaacatacacctaatattcgttcgg--attcgttcacggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT
   | ||    |  | ||  |  ||| |    ||||  |  ||  |||    |     |  | | || ||  ||  |     ||   ||     ||  | ||||||||||| ||||| |||||||||||  | ||  | || ||||||||||| |||||  | |||||||||||||| ||  | |||||||||   | ||  
-ccttcatgcctt-tctattttcagttgactatttatctgccacattttaactgctgtccaaaagctgattatcactaaattatggatttcaaatgtcacagATGGCTTGAGAACATTCGAGATTGGTGCGTCTCAAGGCAACTTTGGTGGGGCCACCGCATTCCTGCATGGTATGTGACATTGGAGGATGACAAAATGAAG

upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: EFJ35310 (Selaginella moellendorffii), 3'ss of exon 11
ttttccacatataatatagatatagtggcgattttacttctcatttttatttttgcaacat-acacctaatat-tcgttcggattcgttcacggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACG--CCAGGACT
                                                      | ||  | | |  || | | ||  |  |  |  ||  |     |  || ||||| |||||||| ||||| |||||| |||||||||||||||||||||| || |   | || || ||||||   ||  | || | |||||  | |  |  
------------------------------------------------------gtaagttgagatttattctctcactttggcttatttgctcatttgcagGTGGCTCGAAAACATTCGAGACTGGTGTGTTTCGCGACAGCTTTGGTGGGGGCATCAGATCCCAGCCTGGTATTGTACGTTTGAAGGTGACGAGCTAAAA--

upper sequence: PP1S84_125V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: EFJ27321 (Selaginella moellendorffii), 3'ss of exon 11
ttttccacatataatatagatatagtggcgattttacttctcatttttatttttgcaacat-acacctaatat-tcgttcggattcgttcacggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACG--CCAGGACT
                                                      | ||  | | |  || | | || ||     |   |  |     |  || ||||| |||||||| ||||| |||||| |||||||||||||||||||||| || |   | || || ||||||   ||  | || | |||||  | |  |  
------------------------------------------------------gtaagttgagatttattctctcattttagcttacttgctcatttgcagGTGGCTCGAAAACATTCGAGACTGGTGTGTTTCGCGACAGCTTTGGTGGGGGCATCAGATCCCAGCCTGGTATTGTACGTTTGAAGGTGACGAGCTAAAA--

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|162161017|gb|FC337522.1|FC337522
EST:     GATGGTCGGTTAGAGATCATCCCAAATCAGTTCGAAGATACGTGGTTCAG                         ATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGG
genomic: GATGGTCGGTTAGAGATCATCCCAAATCAGTTCGAAGATACGTGGTTCAGgtctttgagc ... ggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGG




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 34 (downstream exon)
Score: 14

GTATGTGAACTGCAAGGATATGGCAAAGGAGGCTTGCGATGTTGTACGCGATGGTCGGTTAGAGATCATCCCAAATCAGTTCGAAGATACGTGGTTCAGgtctttgagc ... ggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttttgcaacatacacctaatattcgttcggattcgttcacggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT
                  acctaat  putative branch site (score: 14)
                     taatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttccacatataatatagatatagtggcgattttacttctcatttttatttttgcaacatacacctaatattcgttcggattcgttcacggtgatatagATGGCTTGAAAACATCCGAGATTGGTGTATTTCGCGACAGCTTTGGTGGGGACACCGTGTGCCTGCATGGTATGTAACTGTAGAGGATGACGCCAGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG