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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacag

Basic information

species Physcomitrella patens
transcript PP1S66_174V6.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 13
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacag
|   ||||| ||||   | ||||| ||||| ||||||||||| ||||| || || |||||| |||||||||| || || || |   | || || |||||||||    || | |  |||   |  | |||  ||  ||  | | ||  | |||   | |||   |  | |  |   |                           
CTCAGTGGCATCTTCAGCCAATCTTTGGGCCCTTATTATGGACGCGGGAACTGGGTTCACATCCCAAGTTTATGAACTCTCACCAATATTTCTTCATAAGgta--ctcttactc-ttgagcaaagattcc-ctcttttctctggagcgttctgagttgcctattcttgtacttttag--------------------------

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: LOC_Os05g11140.2 (Oryza sativa), 5'ss of exon 12
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacag------------------------------------------------------------------------------
    |||||||||||| |||||||||||||| | || |||||||| || || ||||| ||  | ||||| || ||||| |||||   ||| || || ||||| |||  | |    |  | ||||  | ||  |||||  |  || | | ||   |    |   | | |  ||||  || || ||      |   | |||  |                                                                               
TTCAGTGGCTTCTTGTTCAAATCTGTGGGCTTTAATAATGGATGCTGGCACTGGATTTACTTCTCAAGTATATGAGCTTTCTCAACATTTTCTTCACAAGgtgagtaattaaaattattatagtagtactctttgtt--tcctgcatgctcctatccttctcatccatcggtggctatcaatattacagcttacactctcaataatagctaagtgtgatttacatggtttcacactgctatgttccaattgttttgatatgctcgcctatgatgctcttag

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GRMZM2G116086_T01 (Zea mays), 5'ss of exon 13
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgat--tgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacag
    || || ||||   | ||||| |||||||| ||||||||||| ||||| || |||||| ||||||| || || ||||| |   | ||||| ||||||||| |  |||  |  |  ||  ||||| || | ||         |  |      || |     | |  |||  || |  |||                       
TTCAGTAGCATCTTCAGCCAATCTTTGGGCTCTCATTATGGATGCAGGGACTGGTTTCACATCCCAAGTATATGAACTGTCACCCATATTCCTTCATAAGgtatggtctcgattctcatgcatagtgctttttctaagcaaggctacatttataagctacaagtgtcttttcttgcactttag----------------------

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA06G09190.1 (Glycine max), 5'ss of exon 12
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaag-tgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcat-tggtattctacag----------------------------------------------------
|||||||||||||||| | ||||| ||||| || ||||||||||| || || || |||||||| |||||||| || || ||||   | ||||| || |||||  | |  |   || ||     |||    |    ||    | |    ||| |  | |   |   | | |       || |   |     | | ||||| |||                                                      
CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACAGCACAAGTTTATGAACTCTCTCCCTTCTTCCTTCACAAGgttggctagtttatgttttagctgtggcattatgcgtgtgatgttggtgatatcatagtatcatgtttgtaactattatcattttatctgtatagtattttactaattttgttttgaacttaatgtagtctaacaaactcatgtttctttttaatag

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 12
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaa--attaacatggtcattg----gtattctacag----------------------------------------------------
|||||||||||||||| | ||||| ||||| || ||||||||||| || || || ||||| || |||||||| || |||||||     ||||| || |||||   ||||   | ||  ||||||| |   || |  ||  | ||  |    |  |      |  || | | |||||  |||| | |  |   ||    ||||| |||                                                      
CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACCGCACAAGTTTATGAACTGTCTCCCCACTTCCTTCACAAGgtt--tgctagtttatgttttagtggtg--gcattatgcatgtggtgttggtgatatcatattatcatctttggaactattatcgttttatctgtactgtattttactaattttgtttttaacttaacgtaggctaacaaactcacgtttctgtttaatag

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA04G09070.2 (Glycine max), 5'ss of exon 12
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaag-tgctcagtgattgtttagtg--tttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattg----gtattctacag----------------------------------------------------
|||||||||||||||| | ||||| ||||| || ||||||||||| || || || ||||| || |||||||| || || ||||     ||||| || |||||  | |  |   || ||     |||   || ||| ||| || || |    |||   ||     || ||||| ||    |||| | |  |   ||    ||||| |||                                                      
CAGTGTGGCTTCTTGTTCTAATCTTTGGGCACTCATTATGGATGCTGGCACTGGTTTCACCGCACAAGTTTATGAACTCTCTCCCCACTTCCTTCACAAGgttggctagtttatgttttagcggtggcattatgcgtgtggtgttggtgatatcctatta----tcatcttt-gtaactattatcgttttatctgtactgtattttactaattttgtttttaacttaacgtaggctaacaaactcacgtttctgtttaatag

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA08G47680.3 (Glycine max), 5'ss of exon 10
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatg-gtcattggtattctacag
  |||||||||||||| | ||||| ||||| |||||||||||||| || || || ||  ||   ||||||||  || |||| |   ||||| | || ||||| |    |   |||||  |     |   | | |||  | |       |  ||| |  |  | ||| | ||  |||  |  | || |    || |  | | |||
TTGTGTGGCTTCTTGTTCCAATCTCTGGGCCCTTATTATGGATGCAGGAACTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAGgtgaa-attatatgatttatgtaaatcagtacatgtcatat-------aattagctatctgttttcatatgatgaatcttgcctgtgattctgtttcttttcag

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA18G53810.1 (Glycine max), 5'ss of exon 12
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaac--atg-gtcattggtattctacag-
  |||||||||||||| | ||||| ||||| |||||||||||||| || || || ||  ||   ||||||||  || |||| |   ||||| | || ||||| |    |   |||||  |     |   | |||||  | |       |  ||| |  |  | ||| | ||  |||  |  |  ||| |    || |  | | ||| 
-TGTGTGGCTTCTTGTTCCAATCTCTGGGCCCTTATTATGGATGCTGGAACTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAGGtgaa-attatatgatttatataaatcagtacttgtcatat-------aattagctatctgttttcatatgatgaatcttgcccatgtgattctgtttcttttcagg

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA10G44050.1 (Glycine max), 5'ss of exon 12
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacag
  ||||| ||||||||   ||||| |||||||||||||||||||| || || || || ||||| ||||||||| || ||||     ||||| | || ||||| |          | | |   || | |||    |||  |||      ||||| ||          | |  |  || ||| |   || | || |  | | |||
TTGTGTGTCTTCTTGTTGCAATCTTTGGGCTCTTATTATGGATGCTGGAACTGGTTTTACAGCTCAAGTTTACAAGTTGTCAACCTTTTTCTTGCACAAGgtga----------aatatgctgtatgtcttgcagtttcttt-----aatctaatt-------ccatgtgattaaacttatccatgtgactgttgctttgcag

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA07G01890.1 (Glycine max), 5'ss of exon 12
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattg-tttagtgtttctgcttgt-tgtt-tttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacag
| |||| ||||| |||   || || |||||  | || |||||||| ||||| || ||||| ||||||||||||||||| || |   | || ||||||||||||| |    |   |||| |||  | |||||  |||| | || |||  | ||  |  |||   | |   ||       ||  |||||    |||       ||  |
CGGTGTTGCTTCATGTCAGAACCTATGGGCGTTAATCATGGATGCAGGGACAGGTTTCACTGCCCAAGTTTACGAGCTCTCACCCTTCTTTCTCCATAAGgtaaatttcaatccattgcttttatttttctatttgtgtattgtttagaagacatgcttgctacacactttcc-----aaccaacata-caattcacccaataatg

upper sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 5'ss of exon 12
CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacag
  |||| || |||||  ||||||||||||| |||||||||||||| || || || ||||||  ||||||||| || ||||| | | | ||| | || ||||| |       |||    |  ||| ||| |  || ||  ||       || |   |     |  |  |      || |||  ||  |  ||   |     |||
TTGTGTTGCATCTTGCTCAAATCTGTGGGCACTTATTATGGATGCTGGAACTGGTTTCACACACCAAGTTTATGAACTGTCACCTTTCTTCTTACACAAGgtgatattctggtgtccat--agt-tttttattttttaatt--agttaattttaataataataataataataataatttaggatcatttttctgacataccag

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|162189086|gb|FC365204.1|FC365204
EST:     CAGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAG                         GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCT
genomic: CGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctc ... tattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCT
EST: gi|162194954|gb|FC369032.1|FC369032
EST:     CAGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAG                         GAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCT
genomic: CGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctc ... tattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCT

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), 35 (downstream exon)
Score: 29

CAGTGTGGCTTCTTGTACAAATCTGTGGGCTCTTATTATGGATGCGGGGACGGGATTCACAGCCCAAGTTTACGAGCTGTCTCATGTTTTCCTCCATAAGgtaagtgctc ... tattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG




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