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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA

Basic information

species Physcomitrella patens
transcript PP1S156_133V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os04g58750.2 (Oryza sativa), 3'ss of exon 5
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttat------cagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
                            ||  |   || | |||  |   |  |   |    | | ||  ||||  | |   || | ||   ||||       |||||  |  ||||  | || || |||||||| ||||||||||||||  ||||||| ||||||||||| ||||||||||| |  |||||||| |||||| | |
---------------------------gtgagtatcatatagattgtttttgtaacgtgatcatctgtgtgttttgtaacatttctatgttgtttacatggcacagGACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGATGGTAAAAGCTACAGTACCAATCTGGCGTTTACTCCTCCAGAGTACATGA

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------------------------------ttttgtggttt----ttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaa-acggttag---tttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
                                                                                |  ||||   |    | | ||   |  |    |   |  | | || |  ||  || | ||||  ||  || |  ||   | ||  | |||     |  | | |||||||| || || || || || ||  ||||||| || |||||||||||| | ||||||||||| || ||||| |||||||||||||| || |||||||   || 
gtatgtttgttgctgctagtacattccactcaaaacaccttttgtttctgctgattttgcattgcttttcacttccttcctcctgtgaactcggatgctttctgatcaaaatttactactttctgaagctttgctgatgtctgtaactaccgagagaattctaactttggcatgatttattctatcagGAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGATGGGAAAAGTTATAGCACTAATCTGGCTTACACCCCGCCTGAGTTTCTAC

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g61010.1 (Oryza sativa), 3'ss of exon 4
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
           |   |  | ||  |  || ||| |||  |   | ||| ||   |  |  |  |   | ||     | ||| ||   ||  |  |   |||||||  ||||  | || || || || || || |||||||||||||| |||||||| ||||| || |||||| |||||| ||| |||||||||||| | |
----------gtgagtcagtacctgtgctacttagtaact---tcttagcttgggcttccagta--ataaggcatgtaatgttttgatgataaatcatagGATGGTAACCCCAGACTGTCGTGCTTCGGTCTGATGAAGAACAGCAGGGATGGGAAGAGCTATAGTACCAATTTGGCTTTCACGCCTCCTGAGTACCTTA

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 4
ttttgtggtttttcctttgaactagc-tctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttattt--atggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
 | ||  |||     | |||  |  |  ||| |     ||   || ||| ||   | ||| | ||    |    | ||   ||   | |||      |||||||| || || || ||  | ||  |||||||  | |||||||||||| | ||||||||||| || ||||| || |||||||||||||| || ||||   || 
atatgaagttgccaatgtgatttttcacctgttataattgattatcttagct---gcctaaagaatacctcacctgttgtaatcaatttctattccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGGAAAAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTAC

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G177445_T01 (Zea mays), 3'ss of exon 4
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
    || | | ||  |||    ||| |  ||||   |  |   |  ||   ||   ||||       ||  ||||    |||       ||||||   |||||||  ||||| |  | || |||||||| || |||||||||||| ||||||| || |||||||| || ||| |||| | ||| |||||||| ||  | |
----gtaggtcttg-tttaccttagtt--gcttcccagatcttttatacaaaagcgctagtctttttttgttttaaccgtggac-----caattttgtagGATGGTAACCCAAGATTATCATGTTTTGGTCTGATGAAGAACAGCCGAGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAATATCTTA

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 5
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggt-tagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
                       ||    |  || | |||   |   |  | |     ||       | ||    | |||||  | |||  |   || |||||  |  ||||  | || |||||||| || ||||||||||||||| | ||||| ||||| ||||| |||||| |||| |  || ||||| || ||| | |
--------------------gtgagtatcgtgtgatttgttttttcaacatgatcagcagtgggttctgtaacacagttatg-ctgtctatatacta-cagGACTGTAACCCTAGACTTTCCTGTTTCGGTCTCATGAAGAACAGCCGGGATGGAAAAAGTTACAGTACCAATTTGGCATTTACGCCTCCAGAATACATGA

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G121826_T01 (Zea mays), 3'ss of exon 4
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
    |||| | ||   |||   | ||  |  ||| | |   ||  ||   || |    |  || |  || || | || || ||   |  ||||||   |||| ||  ||||| | || || |||||||| || |||||||||||| | ||||| || |||||||| || ||| |||| | ||| |||||||||||  | |
----gtgggtctttacttg--ttcgcgttagttgcttttctgagttttgatacaaagcattaacctttttgtgttttgattgtgggc--caattttatagGAAGGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTA

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G121826_T02 (Zea mays), 3'ss of exon 4
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTA-CTTAA---
    |||| | ||   |||   | ||  |  ||| | |   ||  ||   || |    |  || |  || || | || || ||   |  ||||||   |||| ||  ||||| | || || |||||||| || |||||||||||| | ||||| || |||||||| || ||| |||| | ||| ||||||||||| |||||   
----gtgggtctttacttg--ttcgcgttagttgcttttctgagttttgatacaaagcattaacctttttgtgttttgattgtgggc--caattttataggaagGTAACCCAAGACTATCATGTTTTGGTCTGATGAAGAACAGCCGTGATGGAAAGAGCTACAGTACTAATTTGGCCTTCACGCCTCCTGAGTATCTTAAGAC

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G169080_T01 (Zea mays), 3'ss of exon 4
ttttgtggtttttcctttgaactagctctgcttggtatg-tggatgttaactaaagtctagaaaacggttagtttattt--atggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
 | ||| |||     | ||   |   | | | || | |  | |||  |       | |||   ||    | |  | ||   |  | | |||      |||||||| || || || || || ||  |||||||  | |||||||||||| | ||||| |||||||| || || || |||||||||||||| || ||||   || 
atctgtagttgcctatgtggttt---tttacctgttgtaattgattattgtagctgcctaaggaatacatcgcctgttgtaaccgatttctattccctatcagGAAGGTGATCCCCGCCTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGAAAAAGCTATAGTACTAACCTGGCTTACACTCCACCAGAGTTTCTAC

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA03G15830.1 (Glycine max), 3'ss of exon 4
ttttgtggtttttcctttg-aactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
   | |  ||  |  ||   || |   ||    |  ||  |  || ||   |     |||        || |  |   |   ||| | | ||      |||||||   | ||  |  | || || ||||| |||||||||||||| |||||||| || || ||||| || || ||||||| ||| ||||||||||||||||
--gtataattggtggttaataaatgcttccaagttctaactaaatcttgtttctt-cctatttgtaacttggactggcttgtgttgtataca------cagGATGCTAATCCCAGGTTGTCTTGCTTTGGTCTCATGAAGAACAGTAGAGATGGCAAGAGTTACAGTACAAACCTGGCTTTCACCCCTCCTGAGTACTTAA

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA01G26690.1 (Glycine max), 3'ss of exon 6
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
    ||     |    || ||  |   || |   || | |   |   | ||    |||    |   || | ||   ||  || |         | | |||||||   | ||  |  | || || ||||| ||||||||||| ||||||||||| || || |||||||| || ||||||| ||| ||||||||        
----gtataactggtgtttaataaatgcttccaagt-tctaactaa-accttgtttcttcctatttgtaacttggatt--ggcttgtgatgtatcaacagGATGCTAATCCCAGGTTGTCTTGCTTTGGACTCATGAAGAAGAGCAGAGATGGCAAGAGTTACAGCACAAACCTGGCTTTCACCCCTCCTGA--------

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G41600.1 (Glycine max), 3'ss of exon 4
ttttgtggtttttcctttg-aactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
    ||  ||   | |||   || ||  | ||||   |||  | | |    ||   ||           | |||||   ||||| |||      |   ||||||||| ||||  | ||||| |||||||| |||||||| |||||||||||||| | |||||| || || ||| | |||| ||| || |||||||| || |
----gtacttaagcttttatgaccaggccagctt---atgccgttatgttttattatcc---------cttgtttac--atggt-atccaatggtggacagGATGGAAACCCTAGGCTCTCTTGTTTTGGACTCATGAAAAACAGCAGAGATGGCAGAAGCTATAGTACAAATTTAGCTTTCACCCCACCTGAGTATTTGA

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 4
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggtt---agtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
 |  | |     |    | ||   ||  ||      ||  |    |||    | ||||| |  | || |   | ||| ||  |  ||   |    | | ||||||||| || || ||  | ||  |||||||||| ||||| || ||  ||||||||||||||||||| || ||| | ||||| ||||| ||||| |  ||  
-tacgcgaggaatgtcataaat--gccatgaacatcattggttcattagtacatgtctaaattatggattgaaatttgttactaatttattcatttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA05G06140.1 (Glycine max), 3'ss of exon 4
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggtt---agtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
  |   |     |  |   ||   ||  ||      || |     |||    | ||||| |  | || |   | ||| ||  |  ||   |    | | ||||||||| || |||||  | ||  |||||||||| ||||| || ||  ||||||||||||||||||| || ||| | ||||| ||||| ||||| |  ||  
-ctcacgaagaatgttaataat--gccatgaacatcattttttcattagtacatgtctaaattatggattgaaatttgttactaatttattcatttctgtcagGATGGTGATCCACGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv06s0004g05810.t01 (Vitis vinifera), 3'ss of exon 4
ttttgtggtttttcctttgaactagctctgcttggta--tgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
    ||  |||  || ||      |   || ||  |     |    |||   ||   | |||       ||||| || | ||||| |      ||||  ||||||||  | ||  | |||||||| ||||| || |||||||| ||||||||||| |||||||| || || ||  |||| | ||| || || || ||||| |
----gtactttcaccgttttcactgtcatgtttattgaccttttcagtttgttattttttagttttt--ttagtctactcatggtgaatcaacattttacagGATGGTAATCCCAGGCTCTCCTGCTTTGGCCTTATGAAGAATAGCAGAGATGGCAAAAGCTATAGTACAAACTTGGCCTTCACCCCGCCAGAATACTTGA

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv03s0038g03270.t01 (Vitis vinifera), 3'ss of exon 3
----ttttgtgg-tttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttat----ttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
    | |  ||| || ||   |  || |      | ||  ||| |   |||||   | | | |        | ||| | ||    | ||  ||   |   | ||   ||||||| |||||||| || || ||||||||  | ||||| || || |||||||||||||| || ||||| ||||| || ||||| ||||| || ||  |||
gtgctataatggattcttttctcaaaattttaaagtttattatctac-tgttatacataatttgatgtttagctaggtgataatctaatattttgattggactttgtagGATGGTGACCCACGGCTTTCATGTTTTGGCTTGATGAAAAATAGTAGAGATGGGAAAAGTTATAGCACAAATCTTGCCTACACACCTCCGGAATATCTAA

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv08s0007g01520.t01 (Vitis vinifera), 3'ss of exon 4
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
                 |  | ||  | | | |    |||   | || | |  | | |    |  || |   |||||| |||  |   |    ||  ||||||||  | ||  | || || || ||||| || |||||||| || |||||||| || || |||||||||||| |||||| ||| ||||| ||||| || |
----------------gtatattatttttacctatcttgt---ttttcaatttatttttatgactggct--cttatttgtggggagtgg----ttgacagGATGGTAATCCCAGACTGTCTTGCTTTGGCCTTATGAAGAATAGTAGAGATGGCAAGAGTTACAGCACCAATTTGGCTTTCACCCCTCCAGAGTATTTGA

upper sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv18s0001g00180.t01 (Vitis vinifera), 3'ss of exon 3
--ttttgtggtttttcctttgaactagctctgcttgg--tatgtggatgttaactaa-agtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
      || |   ||    ||       |    |     ||| ||||    || ||  |||      |||   | ||   ||  |||||   |     ||| ||| |||| || ||||| || || || |||||  | ||||| || ||||||||||| ||||| |||||||| ||||| || || || |||||||||||  |||
taaccagtagacattttcctggttgtattgaaataaaactatctggagaccaattagtagtaatagcaacaagtggtaacttattggttggtt-----ttagcagAATGGTGATCCACGGCTTTCTTGCTTTGGTATGATGAAAAATAGCAGAGATGGAAAAAGTTACAGCACAAATCTTGCCTATACACCTCCTGAGTATCTAA

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: 22 (upstream exon), 14 (downstream exon)
Score: 1

GCGAGTTTCTTTGTATATTGCACAGGCTTTAGATCATTGTGCCAATAGTAATCTACGTTTGTACCATGATCTCAATGCCTACCGCGTCCTGTTTGATCAGgtatctcttt ... aatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA
  aactaaa  putative branch site (score: 1)
                          tttatttatggttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtggtttttcctttgaactagctctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttatttatggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC