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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtattagttatattcatcaactcaattgataggtgttgttgctgtcgtctgaatttacgtgttgaaattcttactgctgctaacggaattttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGTTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCT

Basic information

species Physcomitrella patens
transcript PP1S119_137V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S119_137V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA01G29420.1 (Glycine max), 3'ss of exon 3
---------gta-ttagttatattc-atcaactcaattgataggtgtt----gttgctgtcgtctgaatttacgtgttgaaattcttactgctgctaacggaattttact--cgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGTTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCT
         ||  ||| || |   | ||         | | |||||||     ||| | |  | | | |||  |  || |  || |      ||||       |||| ||   | || | ||| |     |||||||||||  | || | ||| ||||| ||||| ||||| || || || || || ||||||||||||||||| ||||||||||||
gtaagctttgtgcttaattttgccccatttgtatttgttacaggtgtttatgattgttcttttattattttgtgattttagcttatggggtttgctgtgtttttttttctaatgaagGCAAACTGGTAACATGTACAAGAATGTGAAGAGGAAGATTGAGAGAGGTGTTGCCTTCCCGACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCT

upper sequence: PP1S119_137V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA03G07420.1 (Glycine max), 3'ss of exon 3
gtattagttatattca--tcaactcaattgataggtgt-tgttgctgtcgtctgaatttacgtgttgaaattcttactgctgctaacggaattttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGTTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCT
|||    || |  | |  |   | | |||  || |||| || |  |    |    ||||  |  || |  || |   || ||||   |   ||||| | | || | ||| |   | |||||||||||  | || | ||| || || ||||| ||||| || || || || || ||||||||||||||||| ||||||||||||
gtaagttttgtgcttaagttttccccatttgtatgtgtatgatttttcttttattatttgtggttttagcttatgggtg-tgctg-tgttgttttaat-gaagGCAAACTGGTAGCATGTACAAGAATGTGAAGAGGAAGATAGAGAGAGGTGTTGCCTTCCCTACATGTGTGTCTGTGAACAACACTGTCTGTCACTTCTCT

upper sequence: PP1S119_137V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv08s0217g00020.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------------gtattagt-tatattcatcaactcaattgataggtgttgt-tgctgtcgtctgaatttacgtgttgaaa-----ttcttactgctgcta------acggaattt--------tactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGTTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCT
                                                                      |||| |  |||    ||  | |  ||| | |  | |||| |  ||| |  |  ||||  |    ||||     ||  |  |  || ||      |  |  |||        |    |||| | ||| |    ||||||||||||| |||| ||||| ||||| || || ||||| ||||| |||||| | ||||| ||||||||||| ||||| || |||
gtgagccttctttttttacatagacattatattatgttgaatatttttttgataggcataatatgttcaatatttgagtatgccgatgtattttatttagatttcttgtgttttgttgggttgatttttgcaaagaaaaaggctttatcatattgttataatctataggttttgttgtttatgtatgcagGCAAACTGGCAATATGTACAAGAACGTTAAGAAGAAGATTGAGAGGGGTGTTGCCTTTCCAACTTGCATTTCTGTTAACAACACTGTCTGTCATTTTTCT

upper sequence: PP1S119_137V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv06s0004g06870.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------gtattagttatattcatcaactcaattgatagg--------tgttgtt--gctgtcgtctgaatttacgtgttgaaattc----------ttactgctgctaacggaattt-----tactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGTTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCT
                                   | || | || | ||  | |  | ||  ||||          | |||||  ||  | || ||  ||||  || ||  |||           ||  |||| || | |  ||||     |    | || | ||| |    | ||||||| ||  | || ||||| || || || || ||||||||||| |||||| | || || ||||||||||| ||||||||||| 
gtatgatatgatatgataaattttgtttttctgaagcataatttttgtttttgagttaaagagataatgtatcttcttttgtttggcattagtttgtgtttatttggtgggatttgatatgggttttgatgctacttaagtgatttggttgtggctgtagGCAAACTGGGAATGTGTACAAAAATGTCAAGAAGAAGATCGAGAGGGGTGTTGCATTTCCGACTTGCATTTCAGTAAACAACACTGTTTGTCACTTCTCA

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|67569798|gb|BJ942622.1|BJ942622
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA                         TCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
EST: gi|208397136|gb|DC908150.1|DC908150
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA                         TCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
EST: gi|100439250|gb|BY980169.1|BY980169
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA                         TCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
EST: gi|100384797|gb|BY950787.1|BY950787
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA                         TCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
EST: gi|162183958|gb|FC359328.1|FC359328
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA                         TCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
EST: gi|100445208|gb|BY982837.1|BY982837
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA                         TCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
EST: gi|67719527|gb|BJ969786.1|BJ969786
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA                         TCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
EST: gi|162161202|gb|FC337265.1|FC337265
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA                         TCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
EST: gi|100397823|gb|BY990419.1|BY990419
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA                         TCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
EST: gi|67716276|gb|BJ966536.1|BJ966536
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGA                         TCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGT
EST: gi|18365978|gb|BJ198056.1|BJ198056
EST:     GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTNGCGA                         TCTAACAGCAGGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAG
genomic: GGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGG-TATGTACAAGAACTTTAAAAAGAAAATTGACAGAG

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), 27 (downstream exon)
Score: 9

AGGCTTTGCAAGCAGTCCTGGCAGCATGTGCGCCAGGATTCAAGATTGTCGACCTGTGCGAGAAGGGCGACAGCGTGATTCGCGAgtgagttggc ... ttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGTTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtctgaatttacgtgttgaaattcttactgctgctaacggaattttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGTTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCT
                                tgctaac  putative branch site (score: 9)
                                           ttttactc  putative PPT
                   aaattctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattagttatattcatcaactcaattgataggtgttgttgctgtcgtctgaatttacgtgttgaaattcttactgctgctaacggaattttactcgcagTCTAACAGCAGGTATGTACAAGAACTTTAAAAAGAAAATTGACAGAGGAGTTGCATTTCCCACTTGCGTATCTGTGAACAACACTGTATGTCACTTCTCT

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