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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG

Basic information

species Physcomitrella patens
transcript PP1S79_45V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
      |||| |||    |  || |    ||||    |  |   |   ||   ||  |   |||        |||  ||  |  ||||    |  |  |||||||| || |||||||| || ||||| || || ||||| |||||||| || || ||||||||||| || ||||| ||||| |||||| | || ||||  
---gtaagttttgatctgaaattattatcttactacctgtagttggttaa--catcctcacctt--------aaaaagatta--tgaactctt--tttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA

upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM5G871520_T01 (Zea mays), 3'ss of exon 2
accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttg-tcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
    ||  |         | | | |  ||  || | ||| |  | |      |  |||||  |||    ||    | |      |    | ||     ||| ||||| || || |||||||| ||||||||||| |||||||| |||||||| || ||||| |||||||| ||| | || |||||| | || || |||| |
-ttcgtgctatcacaataattgttttcctacactttgtacacagcagtgtcttgctttttatttgactcgattttatttttttttctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGCCATCTTCTTGTTAAGAGCGATGTCTACAGTTATGGGGTTGTCTTGCTGGAACTTATATCAGGAAGGAAG

upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G102163_T01 (Zea mays), 3'ss of exon 7
accagtagttatgagtccactttgtagctttacatagtaaaacggacca-agatattttttgcttgtcggaccaaagtgacaaattga----atcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
     |    |  |  || ||    |     | | | |  |  |  |   ||   |  |||  ||    |||   | |   |  || |     | ||     ||| ||||| || || |||||||| |||||||| || |||||||| ||||||||||| ||||| || ||||| ||| | || |||||||| || || |||| |
----tttcgaactaaaccgctaca-aataaaaaagaatggagtgagcagtaggcttgctttttttacttgactcgattttaatttttatctctttgactgcacagTTATGTTGCTCCAGAATATGCAATGACGGGTCATCTTCTTGTGAAGAGCGACGTCTACAGTTACGGGGTTGTCTTGCTGGAACTTCTATCAGGAAGGAAG

upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
accagta-gttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
    ||| | |     |  || |  || ||||||||  | | |         | ||      ||| |  |  | || |   |   | |||   |  |  ||||| || |||||||||||||| ||||| ||||| ||||| |||||||| || || |||||||| || || || || ||||| || ||| | |||| ||  
----gtacgctgaatctgaacctactatctttacatttttatagatgattcaacatcaccaacttat--gttccaaattttatggtcaatttttctt--agGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA

upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
accagta-gttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
    ||| | ||    |  | ||  || |||||| |  | | |         |||   |   ||  |   || ||| |  |   |  | |   |     |||||| | || ||||||||||| ||||| ||||| ||||| |||||||| || || |||||||| || || || || ||||| |||||| | |||||||  
----gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaatt--ctggtcaatt---tctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA

upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G171620_T02 (Zea mays), 3'ss of exon 1
----------------------------------acca-gtagttat-gagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcg---ataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
                                  | ||   | || | |  | |||||| |     |    | | |||| |   | | | |  | |   |   ||| ||   |||   |||    |        |||||||| || || || || ||||||||||| || || || ||||| ||||||||||| |||||||| || ||||| || || || || || || ||  | |  
gtaagacctcagctagtgttaatcaacaagtgccatcatacaattcttgcatgcacttt-tgatgatggtgatttaaacagttaatgttgtgctatatattatggatcatc-tgattcattttcccacatgctctgcagGTACGTTGCCCCAGAGTATGCGATGACAGGGCATCTGCTTGTCAAGAGCGACGTCTACAGCTACGGAGTGGTGCTCCTGGAGCTGCTGTCAGGCCGAAAA

upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
----------------------------------------------------------------------------------------------------accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaa-attgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
                                                                                                     |  ||  |||| || |   | ||  | | |||||       |    |     ||||  |     |   ||  |  |    | ||||      |  ||||| || ||||| ||||||||||| ||||| ||||| |||||||| || || || || ||||||||||| || || || ||||| || ||  | || || | |
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattac----catttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG

upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA09G07140.1 (Glycine max), 3'ss of exon 9
----accagtagttatgagtccact-ttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggac-caaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
    || | |  || |      ||| |||||  | |   | ||   ||         |||||  | | ||    |   |   |  || |||  |   |  || ||| ||||| || || || ||||| |||||||| || |||||||| ||||| || || ||||||||||| || ||||| ||||| ||| |  | || || |  
ctgaactattttttgtttcaaaactattgtaattctttgttgttttactat------tatttactccctgatatatatattctttcatatttgaaaaactattcagTTATGTGGCTCCGGAGTATGCAATGACGGGACATCTTCTTGTGAAGAGTGATGTTTACAGCTATGGTGTTGTCCTCCTTGAGCTTTTGACCGGAAGAAAA

upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
------accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
      |   ||| ||  |       ||||| ||  |  ||   || |  | |  |    |||    ||| ||        |    ||||||  |  ||  ||||||||||| || ||||||||||| |||||||| || || ||||| || || || |||||||| |||||||| ||  | ||||| ||||| || || || |  
catttaatgcgtattttaggtgtttgtttgt-gccatgtatctcaagaatggc--aagcttttaacacttttctttgtggggatttaaattg--tttatt-tgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA

upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ34792 (Selaginella moellendorffii), 3'ss of exon 2
accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
                                    |||        | |  | ||||||  |       |  | |||     ||   ||       ||| ||||| ||||| || || || ||||| || ||||||||||| ||||||||||| |||||||| || ||||| || || ||  | || ||||| || |  
------------------------------------gtacgttttctccatctttttttttatatcttatctcatgtgttcttttctctc-------cagTTATGTGGCACCCGAGTACGCCATGACCGGTCACCTTCTTGTTAAGAGCGACGTTTACAGCTACGGCGTGGTACTCCTCGAGTTGCTCTCGGGTAGAAAA

upper sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ23539 (Selaginella moellendorffii), 3'ss of exon 4
accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
                                         |||           |||||  |||||  | |    | |    ||   |      | ||| ||||| ||||| || || || ||||| || ||||||||||| ||||||||||| |||||||| || ||||| || || ||  | || ||||| || |  
---------------------------------------gtacgttttctccatctttttttttgtcttatc----tcatgtgttc--ttttctctccagTTATGTGGCACCCGAGTACGCCATGACCGGTCACCTTCTTGTTAAGAGCGACGTTTACAGCTACGGCGTGGTACTCCTCGAGTTGCTCTCGGGTAGAAAA

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: 34 (upstream exon), 22 (downstream exon)
Score: 3

TGGACTACACTCCTAAAGTGTCTGATTTTGGTCTTGCTAAGGCAGCTGCTGAAGGAGGAAACAGTCAGCACATATCTACTCGTGTGATGGGCACTTTTGGgtgagttcaa ... gataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
      atatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaaattgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG