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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATTGTGGAGCAGTTGACATCTGGCCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattccactgctctcctcatctttggttaaatttacttttcatttactgcgtttcgcatgaactggaggctactttttgcctatacgtagcagtaga...

Basic information

species Physcomitrella patens
transcript PP1S391_7V6.1
intron # 4
splice site 5'
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|162262140|gb|FC437909.1|FC437909
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|208375133|gb|DC956473.1|DC956473
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|162213711|gb|FC390326.1|FC390326
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|18344907|gb|BJ176948.1|BJ176948
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|37853276|gb|BJ611284.1|BJ611284
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|162213710|gb|FC390325.1|FC390325
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|18359874|gb|BJ191935.1|BJ191935
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|67694778|gb|BJ955011.1|BJ955011
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|67695494|gb|BJ955727.1|BJ955727
EST:     CCGTGGAATAATTTTATTTTTATTACATACCTTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCGTGGAATAATTTTATTTTTATTACATACC-TTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|162262139|gb|FC437908.1|FC437908
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTCGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|67572127|gb|BJ944951.1|BJ944951
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|162159565|gb|FC335743.1|FC335743
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|162159564|gb|FC335742.1|FC335742
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|67571446|gb|BJ944270.1|BJ944270
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
EST: gi|37834573|gb|BJ592585.1|BJ592585
EST:     CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAG                         GGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG
genomic: CCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAG

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: 10

GTGATTGTGGAGCAGTTGACATCTGGCCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattcca ... gttttctcagGGCGACCATGGAAGTCAGTGAAGATTCAACTTAAATCGAATTTCCCATCAGTGCAGCTAAATGCCTGGAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATTGTGGAGCAGTTGACATCTGGCCCGTGGAATAATTTTATTTTTATTACATACCTTGGATTAGTTGTTGAAGgcacattccactgctctcctcatctttggttaaatttacttttcatttactgcgtttcgcatgaactggaggctactttttgcctatacgtagcagtaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG