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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG

Basic information

species Physcomitrella patens
transcript PP1S88_180V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os10g27050.1 (Oryza sativa), 3'ss of exon 2
taaattatatattatattcacgctatggttcagcacgc---tcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
 | ||| ||    || |  ||    | | |  ||       | |  | |  ||    |    ||  | ||   ||   |  | ||  | |    | ||| |||||||| ||| |||| |||||||||||||||||||| ||||| |||||||||||||| |  || ||||| || || || || | |
aatattttacccaatgtcaacatattaggtatgcctttatgttataaggtctaggaaaatataagatatgactataaccatttgt--ttactttacata-cagCCAGTTAAGAGCCCAGTCACAATTTGTGGTGATATCCATGGGCAATTCCATGATCTAGTAGAGCTCTTTCGGATTGGTGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g59060.1 (Oryza sativa), 3'ss of exon 2
taaattatatattatattcacgctatggttcagcacgctcaggatgcgta--tctgacccaaaactctggaaattttctgtggtggt-gatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
  || | || | |   | |  |  ||||||  |  |   |   ||    |  | |||          ||  |||||    |  |  | |    |      ||||| |||||| | ||||| ||||| ||||||||||||||||| || || ||||| ||||| ||||| ||||||||||| |||| |
--aact-tacagtgattccttgagatggttatgtgcctcccatataataaattatgaattcttttgttgataatttaacattttctttgccatgcttctgcagCCTGTAAAGAGTCCTGTTACAATATGTGGTGATATTCATGGGCAGTTTCATGACCTTGCAGAACTGTTCCGAATCGGTGGAAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g07150.1 (Oryza sativa), 3'ss of exon 2
taaattat-atattatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
 |  || | | | ||| | || | | || | ||      |  ||    |||  |||        | |     ||| |  |  |  |  | ||      ||||| || ||  |||| || || ||||||||||||||||| || ||||||||||||||||  ||||| || || ||||| || | |
-acgttctcaaaatatttgcatgttctgttccatggtaatttggtaaggtagatgagtactggttttaaggttttgccttttttttttttgggttatgcagCCTGTCAAAAGCCCAGTAACGATTTGTGGTGATATTCACGGACAATTCCATGATCTTGTAGAACTTTTTCGGATCGGTGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G108355_T01 (Zea mays), 3'ss of exon 2
----taaattatatattatattcacgctatggttcagcacgctcaggatg-cgtatctgacccaaaactctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
    |  || || |    | || |      || |   ||    | |   | ||| |         |  | ||   ||||  | || |     ||     |  ||||| |||||| | ||||| || || || |||||||||||||| ||||| ||||||||||||||||||||||||||||| |||| |
tctttggataatctgcgctgtttatatggcggattcacagatgcggttggtcgtgttatttgttgacttttgccgatttgttttgttatcattg-----ttgcagCCTGTAAAGAGTCCTGTTACTATATGCGGTGATATTCATGGACAATTTCATGATCTTGCTGAACTCTTCCGAATCGGTGGAAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G062394_T01 (Zea mays), 3'ss of exon 2
taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaact---ctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
   |  || |||    || |     ||| |   ||    |||      | |  | |     | |   ||  | |   | |||  || | ||    | |  ||||| |||||| | ||||| || || || |||||||||||||| ||||| |||||||||||||||||||||||||| || |||| |
-ggacaatttatgccgtttagatgctggattcacagatgcagctcttattttggtcatgttatttgacttaagacgatttgttttg-tcatcattgttg-cagCCTGTAAAGAGTCCTGTTACTATATGCGGTGATATTCATGGACAATTTCATGATCTTGCTGAACTCTTCCGAATTGGTGGAAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G382077_T01 (Zea mays), 3'ss of exon 2
--taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctgga--aattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
   ||  | ||| | | ||| |   |       |  | |||  | ||   | |   | |  || || ||    || ||    |  |  || |        | ||||||| ||  ||||||| || ||||||||||||||||||||||||||||||||||||   ||||| ||||| || || || | |
tgcaagctttatgt-acatttaacatgcatgcaactatgct--gtat-tatgttccagcagaagctatgttttaacttggcctttttatgctacatatgtatagCCAGTTAAAAGCCCTGTGACGATTTGTGGTGATATTCATGGCCAATTCCATGATCTTTTAGAACTTTTCCGGATTGGTGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G112793_T01 (Zea mays), 3'ss of exon 2
taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatggga----gataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
|   ||||| | |   | || || ||      ||| | |  |    ||||  ||    |  | | | |  ||||  | |   | |  ||  |    | |  ||||| || ||| | || || ||||| ||||||||||| ||||| ||||||||||||||||  || || |||||||| || || | |
tggcttataaactgagtgcatgc-atataatggcatgat--gttcacgtagttgtggtagcaatttaggtatttcttctaa-gcttctgtaactttgcttgcagCCTGTCAAGAGTCCAGTTACAATATGTGGTGATATACATGGACAATTCCATGATCTTGTAGAGCTTTTCCGAATTGGTGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA19G39170.1 (Glycine max), 3'ss of exon 2
-taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtg---atgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
 | |||   |  |||| ||   ||    ||| |      ||  | | | | ||| |   | |       || ||||   ||| |||     |     |  |||||| || ||  ||||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||| || ||||| || || | |
attaatgccactttattttagtgcatctgttaatt----tctagtttcttgtcttatagagagaaaactaattttttcttgggggtttctctcctgtaccacagCCTGTTAAAAGCCCTGTGACAATTTGTGGCGATATTCATGGGCAATTTCATGATCTTGCTGAACTGTTTCGAATTGGAGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA05G28790.2 (Glycine max), 3'ss of exon 2
--taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatc--tgacccaaaactctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
  ||  || | || ||| |  |   | | |  |   |  |||| ||||  | |   ||||  ||||  ||  | |  || | |  |  |        ||  ||||| || ||  | ||||| ||||||||||||||||||||||| ||||||||||||||||| || || || || || || || | |
tatactttgtttaatatgtctat-ttgtagggcttta-actcatgatgattttgaatgactgaaaaaactaaagagattatttcat--ttgccaataattgcagCCTGTGAAAAGTCCTGTTACAATTTGTGGTGATATTCATGGGCAATTCCATGATCTTGCAGAGCTTTTTCGCATTGGAGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA08G11940.1 (Glycine max), 3'ss of exon 2
--taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatc--tgacccaaaactctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
  ||  || | || ||| || |   | | |  |   |  |||| ||||  | |   ||||  | ||  ||  | |  || | |  |  |        ||  ||||| || ||  | ||||| ||||||||||||||||||||||| ||||||||||||||||| || || || || || || || | |
tttactttgtttaatatgtttat-ttgtagggcttta-actcatgatgattttgaatgactgagaaaactaaagacattatttcat--ttgccaataattgcagCCTGTGAAAAGTCCTGTTACAATTTGTGGTGATATTCATGGGCAATTCCATGATCTTGCAGAGCTTTTTCGCATTGGAGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA03G36510.1 (Glycine max), 3'ss of exon 2
taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctgg---aaattttctgtggtggtg---atgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
     |   | |  ||| ||    |||     ||    | ||  ||  | |      | |   ||| |   || ||||   ||| |||     |     |  |||||| || ||  ||||||| ||||||||||| ||||||||||| || || ||||||||||||||||| || ||||| || || | |
-----tgcttttgctatacatctaatgccattgctt-ttaagtgtgtctgttaattactagtttcttgtctaattttttcttgggggtttctctcctgtaccacagCCTGTTAAAAGCCCTGTGACAATTTGTGGCGATATTCATGGGCAGTTTCATGATCTTGCTGAACTGTTTCGAATTGGAGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G15900.1 (Glycine max), 3'ss of exon 2
taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctgg----aaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
    || |  | || ||   | ||||      |||   |     |||   | |         ||  |     ||   ||   |  |     |     || |||||| || ||  ||||||| ||||||||||||||||||||||| || || ||||| ||||||||||| || ||||| || || | |
---cttctgcaatacatct-cactatttcaatgcaacttttaattgcccgttttttttttctcttggagagaaagcattaatttttatctctcctgtatcacagCCTGTGAAAAGCCCTGTGACAATTTGTGGTGATATTCATGGGCAGTTTCATGACCTTGCTGAACTATTTCGAATTGGAGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G15900.2 (Glycine max), 3'ss of exon 2
taaattatatattatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctgg----aaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG----------------
    || |  | || ||   | ||||      |||   |     |||   | |         ||  |     ||   ||   |  |     |     || |||||| || ||  ||||||| ||||||||||||||||||||||| || || ||||| ||||||||||| || ||||| || || | |                
---cttctgcaatacatct-cactatttcaatgcaacttttaattgcccgttttttttttctcttggagagaaagcattaatttttatctctcctgtatcacagCCTGTGAAAAGCCCTGTGACAATTTGTGGTGATATTCATGGGCAGTTTCATGACCTTGCTGAACTATTTCGAATTGGAGGGAAGGTATCAGTTCTGACTA

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G26650.1 (Glycine max), 3'ss of exon 2
------taaattatat-attatattcacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
       ||   || | | ||| |  | || |   || |   |    | | |   | | |  |  | |      | | |  | | |     |  ||    || |||||| || ||  |||| || ||||||||||||||||| ||||| || || ||||||||||||||||| || ||||| || || | |
ggatgccaacacatctcactatttcaatgcaacttttaattgc----aagttttttttttctcttagagagaaagcattaatttatatctcttctgt---atcacagCCTGTGAAAAGCCCCGTGACAATTTGTGGTGATATCCATGGGCAGTTTCATGATCTTGCTGAACTATTTCGAATTGGAGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G42500.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------taaattatatattatatt-cacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatgggagata-acagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
                               | |   || | ||  |   |||    || |||   |   ||||  ||      ||  | |  |  |  ||| || |  ||  |    ||       |  ||||| || ||  ||||||| ||||| || |||||||||||||| || |||||||||||||| || || ||||| || |||||||||
gttagttcctggtcttgcatatctctttggttgagcaatttctttcaccacacttggtgattc--tattttcagtgtggtagattgtgctactagccatgaatttattagttctttctatttcctgcatgcagCCTGTGAAAAGCCCTGTGACAATCTGCGGTGATATTCATGGACAGTTCCATGATCTTGCAGAGCTTTTCCGTATAGGGGGAATG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G58500.1 (Arabidopsis thaliana), 3'ss of exon 2
--------taaattatatattatattcacgctatggt-tcagcacgctcaggatgcgtatctgacccaaaactc----tggaaattttctgtggtggtgatggga--gataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
        |  ||  |  ||    | |    |||     |     | | ||  || ||| || | | |  | |     |  | |   |   |  |  |  |   |  |    ||||| || ||  ||||||| ||||| || |||||||||||||| || |||||||||||||| || || ||||| || ||||||| |
gtcagttcttgatcttgcatctcgtgccaattataaaacccatgtggt-agattgtgtaactaaacaatcatttggtttaaagagccttaatttttatattcttactgtatgcagCCTGTTAAAAGCCCTGTGACAATCTGCGGTGATATTCATGGACAGTTCCATGATCTTGCAGAGCTTTTCCGTATTGGGGGAAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G42500.3 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------taaattatatattatatt-cacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatgggagata-acagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
                               | |   || | ||  |   |||    || |||   |   ||||  ||      ||  | |  |  |  ||| || |  ||  |    ||       |  ||||| || ||  ||||||| ||||| || |||||||||||||| || |||||||||||||| || || ||||              
gttagttcctggtcttgcatatctctttggttgagcaatttctttcaccacacttggtgattc--tattttcagtgtggtagattgtgctactagccatgaatttattagttctttctatttcctgcatgcagCCTGTGAAAAGCCCTGTGACAATCTGCGGTGATATTCATGGACAGTTCCATGATCTTGCAGAGCTTTTCC--------------

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv13s0156g00060.t01 (Vitis vinifera), 3'ss of exon 2
-taaattatatattatattcac-gctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatgggagata-acagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
 ||  || | | || | ||| |    |||  ||    | ||     |     | | |        ||      |||| | |    |   || |   |  ||||||||||||  ||||||| || || ||||| ||||||||||| ||||| ||||||||||| ||||| || ||||| || || | |
atatgttttttgttctcttctccatcatgactccagcctcttg---tctaagtttaatttttttttcctttttttttttttttctgatttgtgtattgtacagCCAGTAAAAAGCCCTGTGACCATATGTGGAGATATTCATGGGCAATTTCATGATCTTGCAGAACTTTTTCGAATTGGAGGGAAG

upper sequence: PP1S88_180V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 2
-----taaattatatattatatt-cacgctatggttcagcacgctcaggatgcgtatctgacccaaaactctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
     |  ||  |||| |  ||| | ||  ||  || ||       |  |||  |||||     |||  | |    ||    | |  |  |  ||  |     ||||| || ||  ||||||| ||||| ||||||||||| |||||||| || |||||||| || || || |||||||| || |||| |
ctgtattgatcttataatgcattactcgtcatt-ttgagttaatgaataatgt-tatctaggg-aaatttttaatgatccctttttttttttttgtaatg---cagCCTGTGAAAAGCCCTGTGACAATCTGTGGTGATATCCATGGCCAGTTTCATGATCTAGCGGAGCTTTTCCGAATTGGAGGAAAG

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: 31 (upstream exon), 35 (downstream exon)
Score: 9

GTTAGAGGATTATGCGAGAAGGCAAAGGAAATTTTGATGCGGGAAAACAATGTTCAGgtacttgtct ... gagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtatctgacccaaaactctggaaattttctgtggtggtgatgggagataacagCCAGTAAAGTGCCCTGTCACAATTTGTGGTGATATTCATGGCCAATTCCATGATCTTGCTGAACTCTTCCGAATCGGGGGAATG
    atctgac  putative branch site (score: 9)
                       aaattttct  TA-rich tract