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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACATCCCTATTTTTATCCCGTGAAGGTGTCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattttccatctaaacttcaagaacaaaaaaagtagctctagctgtggggattctggtgtgattgtcaacacgtgaactttactcaaagaaacag...

Basic information

species Physcomitrella patens
transcript PP1S165_119V6.2
intron # 11
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|67723570|gb|BJ973829.1|BJ973829
EST:     GAGGTTAGCAACCGTCGCAGTGCTTGATATGNANTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: GAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|37852401|gb|BJ610409.1|BJ610409
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|37844002|gb|BJ602010.1|BJ602010
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|162267952|gb|FC444033.1|FC444033
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|208397887|gb|DC916642.1|DC916642
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|162160889|gb|FC337459.1|FC337459
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|37852940|gb|BJ610948.1|BJ610948
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|67698003|gb|BJ958236.1|BJ958236
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|208397217|gb|DC920860.1|DC920860
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|162153012|gb|FC330042.1|FC330042
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|162153011|gb|FC330041.1|FC330041
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
EST: gi|37847708|gb|BJ605716.1|BJ605716
EST:     TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCAT                         ATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT
genomic: TCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGT

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: 32 (upstream exon), 28 (downstream exon)
Score: 11

GCACATCCCTATTTTTATCCCGTGAAGGTGTCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattt ... tgtgttgcagATGGGCTTTCTTGTGATTACGTCCCACCCGGCTACCAGGTTTCTCAGTTGTGCGAAGCGCTTCGTTATTTGATCGCTTTTTGCTGTGACTAAAGCTTTTG




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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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACATCCCTATTTTTATCCCGTGAAGGTGTCGGAGGTTAGCAACCGTCGCAGTGCTTGATATGAATTGATATATCTCATgtaagtattttccatctaaacttcaagaacaaaaaaagtagctctagctgtggggattctggtgtgattgtcaacacgtgaactttactcaaagaaacag

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