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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctgtgtttatattcgttgtggtatatagtgatacttgtcagtgaaacttggcgcctggaataatccactaaactctacttggaaactctcattgtagGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC

Basic information

species Physcomitrella patens
transcript PP1S507_6V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 12
-attctgtgtttatattcgttgtggta--tatagtgatacttg--tcagtgaaacttggcgcctggaataatccactaaactctacttggaaactctcattgtagGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC
  |||||   | |  |      | |||  | |||  |   |||    |||   |  ||         ||  ||||| ||  ||||  |      | |   | ||||||||| ||||| ||  |||| || || || ||||| || ||||||||||||||||| || |||||||| || ||||| ||||| |||||| ||||| | 
agttctgaact-acctgtaggatagtaactctagctagcattggactagttttatgtgaaattgatgatt-tccaccaatatctaacttt---ttttttctatagGTATGTCGATGTTATTCTGCAGCTGATAGACAAAGCAGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTCACCAACAATGAAGAT

upper sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
--attctgtgtttatattcgttgt--ggtatatagtgatacttgtcagtgaaactt-ggcgcctggaataatccactaaactctacttggaaactctcattgtagGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC
     ||||    |  |  |||||  | | | |    ||  |  |   || || || | | ||    |   |   ||| |    | ||| |     |   ||||||||||| ||||| ||  | ||||| || || |||||||| ||||||||||||||||| || |||||||| || ||||| |||||||| ||| | ||| ||
aacaactgtagcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgctatatctgatttgta-----tttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC

upper sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
--attctgtgtttatattcgttgtggtatatagtgatacttgtcagtgaaacttggcgcctggaataatccactaaactctacttggaaactctcattgt--agGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC
  |  |  | |||   | |       |   | |  ||  |  ||||   |||||   |  ||   ||||      |    ||    |  |  |   || |  |||||||| ||||| ||  | ||| | || || || || ||||||||||| ||||||||||| |||| |||||| || ||||||||||| ||| ||||| ||
tcaccccatatttcagtacaaaaaattcccttgatatcttgatcag---aacttattgt-tgatgtaatatgtatactgatatcatgtcatcccttttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC

upper sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 12
attctgtgtttatattcgttgtggtatatagtgatacttgtcagtgaaacttggcgcctggaataatccactaaactctacttggaaactctcattgt--agGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC
       |      |||  |     | |||    |  |  |   | | |  |      ||   ||||      |    ||    |  |  |   || |  |||||||| || || ||  | ||| | || || || || || |||||||| || |||||||| |||| |||||| || ||||||||||| ||| ||||| ||
--gtcacgccatatttcagtacaaaaaatacccttgatatttgatcagaacttattgttgatttaatatgtacactgatatcatgccatcccttttatacagGTATGTTGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC

upper sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 12
attctgtgtttatattcgttg--tggtatatagtgatacttgtcagtgaaacttgg----cgcctggaataatccactaaactctacttggaaactctcattgtagGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC
     ||| ||  ||| |  |  ||| |   | || | | |||    | |||  |     |  |||     ||    |    | || |    || | |||| | ||||||||||| || ||  | ||  | || || || || || |||||||| ||||||||||| |||| ||| ||||| ||||||||||| ||| ||||| ||
-----gtgctttcattggaaggttggaagcaattgttgcctgttgaagcaacaagatcttctactgtttatatatgttgtcatgtattcttcaattgtcat-gcagGTATGTGGACGTGATCCTACAGTTGATTGACAAGGCAGGAGATTTTGTCAGTGATGACATATGGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGAC

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), 23 (downstream exon)
Score: 3

TATCTTACCAAAGCAGACTTTGGTATCCGAGAAGAGCTCGCATTGAAAGCTGCCATTCTCTCAGAAAGTTTTGCCACCGATCTTGATTGgtaccattat ... ctcattgtagGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacttggcgcctggaataatccactaaactctacttggaaactctcattgtagGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC
                       cactaaa  putative branch site (score: 3)
                                           ctctcatt  putative PPT
                aataat  TA-rich tract