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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgggctgatttctggtctatatggaatttgggaagggaaagttccttcgcaagcattgttaccatcagattatttatgtattggttgatagctgcaatgttcttcgagtggtgtattaggttagtatgtttctgatcgttaatttgtggatctacatcatacccctcaccaaatgtgcggtctaaattattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCGAGAGCGCAAGCTTAATCAG

Basic information

species Physcomitrella patens
transcript PP1S78_33V6.1
intron # 3
splice site 3'
intron type U2

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|18338507|gb|BJ170531.1|BJ170531
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
EST: gi|6167188|gb|AW145452.1|AW145452
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
EST: gi|162240059|gb|FC418823.1|FC418823
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
EST: gi|162240058|gb|FC418822.1|FC418822
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
EST: gi|208380076|gb|DC914626.1|DC914626
EST:     CCACTGCATGGATAGTTCATAATCAACATCTTGAA-CTTTTTCANGCCAG                         GCTAA-AGATACAGCACTCGAAT
genomic: CCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTT-CAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAAT
EST: gi|37821556|gb|BJ579622.1|BJ579622
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
EST: gi|208381716|gb|DC928379.1|DC928379
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
EST: gi|162256324|gb|FC432334.1|FC432334
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
EST: gi|18334929|gb|BJ166947.1|BJ166947
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
EST: gi|162256323|gb|FC432333.1|FC432333
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
EST: gi|15728433|gb|BI740785.1|BI740785
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
EST: gi|7287371|gb|AW599858.1|AW599858
EST:     ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAG                         GCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG
genomic: ACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCG

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: 33 (upstream exon), 34 (downstream exon)
Score: 4

ACTTGAGAATCTCGAGCTCATGCTGAATTATGGCACCACTGCATGGATAGTTCATAATCAACATCTTGAAGCTTTTCAAGCCAGgttgggctga ... attattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCGAGAGCGCAAGCTTAATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttgtggatctacatcatacccctcaccaaatgtgcggtctaaattattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCGAGAGCGCAAGCTTAATCAG
                                       gtctaaa  putative branch site (score: 4)
                                              ttattcc  CT-rich tract
                                        tctaaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgggctgatttctggtctatatggaatttgggaagggaaagttccttcgcaagcattgttaccatcagattatttatgtattggttgatagctgcaatgttcttcgagtggtgtattaggttagtatgtttctgatcgttaatttgtggatctacatcatacccctcaccaaatgtgcggtctaaattattccagGCTAAGAGATACAGCACTCGAATATCAGCGTGAGATTGAGATATTGAATCGAGAGCGCAAGCTTAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT