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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttaagagttgaagcattatcaaatgctcaattgcttcggttgaatatttgcacatatcgaatctaggtgaccaaacatggtgtgaaactttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG

Basic information

species Physcomitrella patens
transcript PP1S223_50V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S223_50V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 4
----------gtgttaagagttgaagcattatcaaa-tgctcaatt----gcttcggttgaatattt---------gcacatatcgaatctaggtgacc--aaacatggtg---tgaa---actttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG
              | ||| ||  | | |   ||   |||  ||||    |||| ||    ||||           |   | || | |||  | | | |  ||  ||| ||   || |     |||   ||||| ||||||||||||||||||||||| |  || || || ||||||||     ||||     ||||   |||||    ||||  |
gtaagtatttaaactcagaatttgaacctctccactctgcaaaattcatagcttggggcagatatggaatgagggggactaaattgtatcaggataaacataattatgttgatttgcatgttttttctgcagGGAGCAATCATGGCGGTTGGAGCATCAGAACCAACCGTTGTTGCCACCAAGGATGGTCGGATTGGCATGAAGAGCCAGATGCAG
















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|162155717|gb|FC331330.1|FC331330
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|162185524|gb|FC361248.1|FC361248
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|37828398|gb|BJ586410.1|BJ586410
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|162155716|gb|FC331329.1|FC331329
EST:     CCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: CCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|208361643|gb|DC950331.1|DC950331
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|67692304|gb|BJ952537.1|BJ952537
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|162172649|gb|FC348030.1|FC348030
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|162180018|gb|FC356089.1|FC356089
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|37842788|gb|BJ600796.1|BJ600796
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|162190854|gb|FC368052.1|FC368052
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|208372257|gb|DC948060.1|DC948060
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|18335076|gb|BJ167094.1|BJ167094
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|162200375|gb|FC376660.1|FC376660
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|37836649|gb|BJ594657.1|BJ594657
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|208389164|gb|DC945740.1|DC945740
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|208365828|gb|DC951063.1|DC951063
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|18337537|gb|BJ169561.1|BJ169561
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|37851326|gb|BJ609334.1|BJ609334
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTNGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|162200361|gb|FC376659.1|FC376659
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACCGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|162174414|gb|FC350485.1|FC350485
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
EST: gi|208365900|gb|DC951079.1|DC951079
EST:     TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG                         GGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA
genomic: TTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGA

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: 30 (upstream exon), 24 (downstream exon)
Score: 3

GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATGgtgagtgaat ... ctttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatttgcacatatcgaatctaggtgaccaaacatggtgtgaaactttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG
                                          aaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttaagagttgaagcattatcaaatgctcaattgcttcggttgaatatttgcacatatcgaatctaggtgaccaaacatggtgtgaaactttgaacagGGTGCAATCATGGCGGTTGGAGCATCTGTTCCCACAGTCGTTGCCACAGGAAATGGCTTATTTGGAGCGAAGAATAGGATGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - caaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - ttgcaca