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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggaaactaagtccactgaaaggtgcacttaattcatcctatctacttagagaatcacatgatgttggctgtctaaaactaacttcgaaagtgtgtgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC

Basic information

species Physcomitrella patens
transcript PP1S119_22V6.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S119_22V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G022563_T01 (Zea mays), 3'ss of exon 4
gggaaactaagtccactgaaaggtgcacttaattcatcct--atc-tacttagagaatcacatgatgttggctgtctaaaactaacttcgaaagtgtgtgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC
  | || | |||    | |||  |  |  |  ||  |  |  ||| ||||   | ||| | || ||||    ||  ||| |     |  | |    | || ||| |||||||   |||||||  | ||  | ||||| |||||||| ||   ||||||||||||||| |||||||| ||||| ||||| ||||| |||||  |
--gtaattcagtta--ttaaatatttatgtggttgttggtgaatcatactctcaaaatta-at-atgtcacttgaataata-----tatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC

upper sequence: PP1S119_22V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G111677_T01 (Zea mays), 3'ss of exon 2
gggaaactaagtccactgaaaggtgcacttaattcatcct--atc-tacttagagaatcacatgatgttggctgtctaaaactaacttcgaaagtgtgtgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC-------------------
  | || | |||    | |||  |  |  || ||  |  |  |||  |||   | ||| | || |||     ||  ||| |     |  | |    | || ||| |||||||   |||||||  | || || ||||| |||||||| ||    |||||||||||||| |||||||| ||||| ||||| ||||| |||||  |                   
--gtaattcagtta--ttaaatatttatgtagttgttggtgaatcacactcttaaaatta-at-atgccacttgaataata-----tatgcatacttttgtaggcggaggtttttagaatgtcttagtagttggtgcagatgctctttcaaactacgtggattggacagACAGAGGTACATGCATTCTTTTTGGTGATGCTGCTGGTGCTGTGTTGGTACAG

upper sequence: PP1S119_22V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA18G44350.1 (Glycine max), 3'ss of exon 4
gggaaactaagtccactgaaaggtgcacttaattcatcctatctacttagagaatcacatgatgttggctgtctaaaactaacttcgaaagtgtgtgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC-
                       || | ||  ||  |  | ||  ||| || | |  |   || | ||     | |       ||     |||  ||||||||| || |  || ||||| || ||  | || ||||||||||| || ||||| || |||||||| ||||||||||| |||||||| ||||| |||||  | 
---------------------tatgaa-ttggttatttttgtcagctt-gatagttcctaaatatggggaaaatcattgccctttattgtgtgaatgcaggAGGTGGATTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTCTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGCT

upper sequence: PP1S119_22V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 4
gggaaactaagtccactgaaaggtgcacttaattcatcctatctacttagagaatcacatgatgttggctgtctaaaactaacttcgaaagtgtg--tgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC
                      ||     |     ||  |   |   | || |||  |   || |  | ||   |  | |  | |  |  |||||  | ||||||| || |  || ||||| || ||  | || ||||||||||| || ||||| || |||||||| ||||||||||| |||||||| ||||| |||||  |
----------------------gtatgaattggctatttttgttgtcttgataattcctaaatat--gttgaaaatcattgccctttattgtgtgagttcagGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC

upper sequence: PP1S119_22V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv00s0233g00060.t01 (Vitis vinifera), 3'ss of exon 4
gggaaactaagtccactgaaagg-tgcacttaattcatcctatctacttagagaatcacatgatgttggctgtctaaaactaacttcgaaagtgtgtgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC
  | |||||  |    ||   || || | | |  |   | |   | |||         |||| |     |     ||  |||  |  | || |   ||||||||| || |   | ||||| |||||| | || || |||||||| || || || || ||||||||||| |||||||| |||||||| ||||| |||||  |
--gtaactagtttgtttgcttggctgtagtaaggttccctttcttgcttc--------catggttcatacaactgaactctacttgtgcaaat---tgcagGAGGTGGGTTTCATAATGTTCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGC

upper sequence: PP1S119_22V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv02s0154g00140.t01 (Vitis vinifera), 3'ss of exon 4
gggaaactaagtccactgaaagg-tgcacttaa-ttcatcctatctacttagagaatcacatgatgttggctgtctaaaactaacttcgaaagtgtgtgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC
  | |||||  |    ||   || || | | |  |||    | | |  |  | |  ||| |  |      |||   ||  |||  |  | || |   |||||| || || |   | ||||| |||||| | || || |||||||| || || || || ||||||||||| |||||||| |||||||| ||||| |||||  |
--gtaactagtttgtttgcttggctgtagtaaggttccctttctttcttccgtggttcatacaa------ctg---aactctacttgtgcaaat---tgcagGCGGTGGGTTTCATAATGTTCTTGTGATTGGAGCTGATGCTCTTTCTCGCTATGTTGATTGGACTGATAGAGGGACCTGTATTCTCTTTGGGGATGCTGC

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: 17 (upstream exon), 19 (downstream exon)
Score: 1

CAGAAGTTGCTGGGATGCCATAATGCCTTAGCTTTCGATTTGACGGCCGCATGTAGTGGCTTTGTTCTGGGACTTGTGACGGCCACTCGCTTTATTAGAGgtactgtttc ... gtgtgtgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagagaatcacatgatgttggctgtctaaaactaacttcgaaagtgtgtgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC
                               aactaac  putative branch site (score: 1)
                            taaaactaa  TA-rich tract