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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA

Basic information

species Physcomitrella patens
transcript PP1S51_322V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagc--atggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAAT-CAAGCCAA
                | |||| ||  |   ||       |  ||  | || |||  |||   |    |    |||  |  | |    |   | || ||||||||||||||||||||| ||||||||| | || || || || ||| | || || |||||||| || |||||||| |||||||||    | ||| ||||    
-------------gtatgtttgcaatgagttattgttttactcatactgctagat--gatttgaatgttactcgttaaccatatttctattgtatcttgcagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG-

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA
             ||||  |   ||  ||  || |      | | | ||| ||  |||    | | | || ||||   ||           || |   |||||| || ||||||||||||||||| ||||| || ||||| ||| | || || ||||| ||||| |||||  ||||||| ||| | || ||  ||||   
-----------gtaagtcctctgaagcaaccatgatatgatacgattcttcat--gatatttctattaactgtttgaatttca--------tttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 5
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgca-accacttacagttttctttgtgctgaaactttcgt--gcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAAT-CAAGCCAA
    |  |||  | |   | |  |   |   || ||     |      ||   || ||    |  | || ||          ||||||   | |  |    ||||||||| |||||||||||||||||  |||| || || || ||| | || || |||||||| || ||||| || |||||||||    | ||| | ||    
---gtatgtgtgacacactgttgatttactcattagatgaaacaaagattacctgtatttttagaatttgcatcgccaagcatgctgattttgtatttattagTGTACAAGAAGCACTACCCACCTGCGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCCAGTGG-

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA15G07330.2 (Glycine max), 3'ss of exon 5
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttct--ttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA
                                  | | | |||   |||| ||||  |     |  |     || | |  |  | || | ||||   |||||| ||||| |||||||||||||||||||||||||| ||||| ||| |  |||| |||||||| || |||||| | || |||||  | || ||| ||||   
--------------------------------gtaagta-cataa-acttcattgtttatgttctatccttcttctgtaatgatacttatacttgattgcagTATACAAGAAGCACTACCCACCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGTTCCTTTCACAAAAGGCTAAATAAAGCAGG

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA07G10440.1 (Glycine max), 3'ss of exon 2
--------ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCG-TCTTAATCAAGCCAA
        ||   | ||   || |  |||  |   |  | | |      ||  ||  |   |  ||   |   ||| |  |||| ||| |      || ||  || |||||||||||| |||||||| ||     |  | ||||| ||||||||||| || ||||| || |||||||| |||||||||| |   |  | ||||      
ctaacatttttgccagttgtaaggaattt--atttatcattgatattatatactaaatatctacattttatttcttcctattttttttttat----acatt--tgaagTGTACAAAAAACACTACCCTCCAATGCTTCACGACGAAGTGTGGCGCTTAGAGAAGATAGGTAAAGATGGAGCTTTCCACAGGAAATTGTCATCAGAGGG-

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA05G34760.1 (Glycine max), 3'ss of exon 3
ttgttcggtgccaaagtttt--tgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacag-----ttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA
      |   || ||  |||  || | |  | | |     |   | ||| ||  || | ||    |   || ||     || | | | || |   |      || ||||||||| || || |||||||||    | |||||||| ||||||||| | || |||||||| ||||| || |||||||||||     |     |||    
-----tgacacctaaaatttggtggatatgaaagtttattattgttgtaatt--tttgttgttgtcgtatatagaaaatttatatatttgttttcatacatttgaagTGTACAAGAAACATTACCCACCTAAGCTCAATGACGAAGTGTGGCGCCTAGAGAAGATTGGTAAAGACGGAGCTTTCCACAAAAAATTGTCCAAAGAGGG

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA
            |  || ||  ||        |       ||  ||||     |||     ||  |||  |||||  |      |     ||  ||||||||||||| ||||| || ||||||||  ||||||| || |||||| | ||||||||||| || || ||||| || ||||| ||    |||| |   |    
----------gtatggtcttaaaagctccccttttcttctcactgtacc-atctggtgtttacttcttttagtttgatgcacatttct-tttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA
    |  || |     ||  |   | |     | || ||     |||  ||| |   ||       ||    ||| | |  || |     |||| | |||||||||| || || ||||||||||| ||| |||| ||||| ||| | ||||| |||||||| || || || |||||||| |||   || ||| ||||   
---gtaagttcttgctttcctttgata-----ttagtcattgatgtatctgaatctttgt------ttttcttttgcctaatgttttt-ttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
--------ttgttcggtgccaaagtttttgaaaaaaagaatcaggca-gcatgg-tacttg-attggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA
         ||||| ||| |||| | ||    |       | |   | ||||   |   || ||  | ||  |  | |    ||     |        |  |||    |||| ||||| ||||||||||| ||||| |||||||| || || ||||| ||||| |||||||| ||||||||  | ||||||||| |  | ||| ||||   
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatga-tggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv17s0000g07780.t01 (Vitis vinifera), 3'ss of exon 4
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgt--gcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA
  |    ||| |    |||||           |        ||  ||  |||||  |||      | ||        |  |  ||   | ||  ||  ||||||||||| |||||| |||| ||  |  |||  ||||| |||||||| || || |||||||| |||||||| ||||||||||||||| | | |   |  | 
-ggccttgtgacccttttttttttctttttttttttattttata-tatatgattaaatgttttttcataagaaaaattacgacctctgatttctgtttgcagTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAGAGAAGATTGGAAAAGATGGAGCTTTCCACAAGCGTTTGAGTAGGGAAAG

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA
             |||||   ||   ||    |    |    |  |  ||| ||        |  ||||| | | | |  ||||     || | ||||||||||||| ||||| || |||||||| || |  ||||||||||||||  |||| ||||| || || || || |||||||||||||| || ||||||  |  
-----------gtaagttggcgactgaactgttt---cttttttttgtttggttttgacatgctgcttaccgatgt-tacgtgc----gctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG

upper sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ11323 (Selaginella moellendorffii), 3'ss of exon 4
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA
             |||||    |   ||    |    |    |  |  ||| ||        |  ||||| | | | |  ||||     || | ||||||||||||| ||||| || |||||||| || |  ||||||||||||||  |||| ||||| || || || || |||||||||||||| || ||||||  |  
-----------gtaagttggccacttaactgttt---cttttttttgtttggttttgacatgctgcttaccgatgt-tacgtgc----gctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG

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|162254899|gb|FC431084.1|FC431084
EST:     TCGAGAAGCCAAGACTGAAGCCTTCACCGTCAAAGATCATCGTGGAGAAC                         TGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGG
genomic: TCGAGAAGCCAAGACTGAAGCCTTCACCGTCAAAGATCATCGTGGAGAACgtacgttctt ... tttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGG
EST: gi|100365865|gb|BY967185.1|BY967185
EST:     TCGAGAAGCCAAGACTGAAGCCTTCACCGTCAAAGATCATCGTGGAGAAC                         TGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGG
genomic: TCGAGAAGCCAAGACTGAAGCCTTCACCGTCAAAGATCATCGTGGAGAACgtacgttctt ... tttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGG

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: 29 (upstream exon), 34 (downstream exon)
Score: 11

TTCCGGTTAGGTGTGAGACTTGCGTCTGGTCAATGTGAAGGCATGAGAATTCGAGAAGCCAAGACTGAAGCCTTCACCGTCAAAGATCATCGTGGAGAACgtacgttctt ... tttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA
                  cacttac  putative branch site (score: 11)
                                            ctttcgt  putative PPT
                           ttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG