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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaacaggtgtgctaaccaatattacgtgattgttcttctgagcaatactcatgtctttaatgcttgagattttttttggggggggggggtgagagcagGTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAGGGTCTTGTACTTTTGGCAGACGAG

Basic information

species Physcomitrella patens
transcript PP1S7_123V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S7_123V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 9
------------------ttaaacaggtgtgctaaccaatattacgtgattg---ttcttctgagcaatactcatgtctttaa---------tgcttgagattttttttgggggg--------ggggggtgaga--gcagGTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAGGGTCTTGTACTTTTGGCAGACGAG
                  ||  | || |  | |  | || |  | ||| ||    ||  |   | ||   ||  |    | |          | |||  ||  || | |||  |         |||   | |    |||||| || |||||||| |||||||||||  ||||| | || |||||| |||| |||||||| ||| ||||||| |||
gtaagcaataatcagtgctttgatagctaggtttgcaaagagcatgtgtttaaattttcttcaaacagggcttcttggatgagaagatggtttacttctgaccttctatggttgaattttcttgggttttcatgttgcagGTTCTTTCTGAGGACAACCAGCGAGACATTGTGGAATTCTGCAAGAAAGAAGGTCTTGTTCTTCTGGCAGATGAG
















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|162192249|gb|FC367774.1|FC367774
EST:     CCAATGTTCGGGCTCTGGTTGTCATCAATCCTGGAAATCCAACCGGCCAG                         GTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAG
genomic: CCAATGTTCGGGCTCTGGTTGTCATCAATCCTGGAAATCCAACCGGCCAGgtttgattta ... gtgagagcagGTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAG
EST: gi|162177329|gb|FC353486.1|FC353486
EST:     CCAATGTTCGGGCTCTGGTTGTCATCAATCCTGGAAATCCAACCGGCCAG                         GTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAG
genomic: CCAATGTTCGGGCTCTGGTTGTCATCAATCCTGGAAATCCAACCGGCCAGgtttgattta ... gtgagagcagGTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAG
EST: gi|100415274|gb|BY975235.1|BY975235
EST:     CCAATGTTCGGGCTCTGGTTGTCATCAATCCTGGAAATCCAACCGGCCAG                         GTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAG
genomic: CCAATGTTCGGGCTCTGGTTGTCATCAATCCTGGAAATCCAACCGGCCAGgtttgattta ... gtgagagcagGTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAG

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), 35 (downstream exon)
Score: 16

TGAAATGAATGAGCTCAAGCAGCAGCTCAAAGCTGCTCGTGATGCAGGCACCAATGTTCGGGCTCTGGTTGTCATCAATCCTGGAAATCCAACCGGCCAGgtttgattta ... gtgagagcagGTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAGGGTCTTGTACTTTTGGCAGACGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatactcatgtctttaatgcttgagattttttttggggggggggggtgagagcagGTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAGGGTCTTGTACTTTTGGCAGACGAG
           ctttaat  putative branch site (score: 16)
                    ttgagatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaacaggtgtgctaaccaatattacgtgattgttcttctgagcaatactcatgtctttaatgcttgagattttttttggggggggggggtgagagcagGTGCTCTCTGAGGAGAACCAGCGAGATGTTGTGCAGTTTTGCAAGGAAGAGGGTCTTGTACTTTTGGCAGACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG