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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgatgatttactgtcagaatttgatcctccatctttttcttacatgtagaggtatcgtgaatattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG

Basic information

species Physcomitrella patens
transcript PP1S99_260V6.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
-----------------aatgatgatt-tactgtcagaatttgatcctccatctttttcttacatgtagaggtatcgtgaatattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG
                  | | | ||| | | || | | | | || ||| ||   |   | | |||||    |||  | ||  ||   ||||  | | ||      | ||      ||| | || ||||| || |||||||||||||||||||||| ||| || ||||||||||| ||||| || || |||||| | ||||||   || ||| | || 
gtaagatggatttggatgagggtaattattcggttacagtatcatgctcaatggataattaagatgtat---tatattaaagttt--cttatgacactttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 15
-----------------aatgatgatt-tactgtcagaatttgatcctccatctttttcttacatgta-gaggtatcgtga-atattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG
                  | | | ||| | |  | | | | | || ||   |  ||     || | || || ||||  |   | | |   ||||  |   ||      | ||      ||| | || ||||| || |||||||||||||||||||||| ||| || ||||||||||| ||||| || || || ||| | ||||||   || ||| | || 
gtaagttggatatggatgagggtaattattcctttacagtatcatgcttggtgcttggtggacgtttaagatgtattatattaaagtttcttatgacattttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGATTCAGAAAA

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
-------------aatgatgatttactgtcagaatttgatcctccatctttttcttacatgtagaggtatc--gtgaa----tattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG
                   |  | | | |   | ||| ||  || ||   |   | |  |  ||| ||||    | ||    |||| |  | ||| ||  ||| || || |     ||| || || ||||||||||| ||||||||||||||||| | ||| || ||||||||||| ||||| || || || ||| | ||||||   || ||| | |||
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
-------------aatgatgatttactgtcagaatttgatcctccatctttttcttacatgtagaggtatcgtgaatattgatttatctccccttttctctttt-tgatgt---tagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG
                   |  | | | |   | ||| ||  || ||   |   | | |||||             |||| |  | ||| ||  ||| ||||   | || |   ||| || || ||||||||||| |||||||||||||| || | ||| || ||||||||||| |||||  | || || ||| | ||||||   || ||| | |||
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacatgtcttcctatttgtcttccattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA06G06980.1 (Glycine max), 3'ss of exon 14
aatgatgatttact-gtcagaatttgatcct--ccatctttttcttacatgtagaggtatcgtgaatattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG
  |  |||  |||| |||  |||   ||       || | |||| |||    | || ||| |      || |  ||   |   |   || || |       ||||| || |||||||||||  |||||||||| ||| | ||||| ||||||||| |||| ||||| ||    || ||  | ||||||   ||  |   ||| 
-gttttgagctactagtctcaatacaattggaataatttgtttcctactaaca-agttattgcag---tttaactaatgctgataaacttttct-------agGCTTTTTTCTTGCGGAACTGGTAAAGATGGGGAGCCATATCTTGTGGAATGGGATGAAAGTGAAGGATATATAAAAAGAACATACAAGGGACTTAAGAAA

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
---------------------------------------------------------------------------------------------------aatgatgatttactgtcagaatttgatcctccatctttttcttacatg-tagaggtatcgtgaatattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG
                                                                                                   | |  |  |||  |  || | | || | ||     |      ||  ||  |||    | || | || |   | |  |    ||| ||||| ||  | | ||  | |||||||| ||||||||||||||||| || |||| | |||| ||||||||||| ||||| || ||||| ||| |||| ||    || ||  | |||
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttcttcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 14
-aatgatgatttactgt-cagaatttgatcctccatct-----ttttcttacatgtagaggtatcgtgaatattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG
    |||| | ||   | ||   |||  |  |   |||     | |||||   | |||   ||   |  ||| | |||    ||   | || ||||         ||||| |||||||| ||||||||||||||||| || ||| | || || |||||||||||||| || || || || || |||||||| | ||||||  |||| 
atgagatggtctatcatgcaattttttgttattagtcttgtattcttcttctttttagttttaatttatatagttattagaatcttgtattgtcttcc-------agGCTTTTCTCTTGTGGAACAAGTAAAGATGGTGAATCTCACCTAGTTGAATGGAATGAGAGCGAAGGAGCTATTAAACGGACATATTTAGGTTTTAGGAAA

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: 35 (upstream exon), 25 (downstream exon)
Score: 5

AGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTACAATGGCTTACAGTGCTGATGGCACTAGgtatgtagaa ... ttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtagaggtatcgtgaatattgatttatctccccttttctctttttgatgttagGCTCTTCTCTTGCGGAACAAGTAAAGATGGAGAGTCTTATCTGGTGGAATGGAATGAGAGTGAGGGTGCAATCAAGCGGACATACTCAGGTTTCCGGAAG
                  tattgatttatctccc  CT-rich tract
              tgaatattgatttat  TA-rich tract