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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGGAGGGTGCCGGTACGGTGGAAGAAGTTGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagtgggttcagcctcgtaacatgctgcacatgaagttgtttaccattgtcgagcagatgcatcaatccgttgtgaatcactattgctgtgttgtaacgattgattgagtttgtgtgcactcaacttaagattagcgggtttggaacttgtggatatatctattcatacag

Basic information

species Physcomitrella patens
transcript PP1S47_50V6.1
intron # 3
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|208351815|gb|DC910369.1|DC910369
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|18342947|gb|BJ174983.1|BJ174983
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|100406897|gb|BY973921.1|BY973921
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|18351509|gb|BJ183561.1|BJ183561
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|100412056|gb|BY956393.1|BY956393
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|18355480|gb|BJ187539.1|BJ187539
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|162161504|gb|FC338711.1|FC338711
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|208357885|gb|DC902367.1|DC902367
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAGGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|100361332|gb|BY965788.1|BY965788
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|100361491|gb|BY984032.1|BY984032
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|100357893|gb|BY946627.1|BY946627
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|100426792|gb|BY977365.1|BY977365
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|100434852|gb|BY960844.1|BY960844
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|18351694|gb|BJ183746.1|BJ183746
EST:     TGGATCCGAGGTCACAGATGTANGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|67573857|gb|BJ946681.1|BJ946681
EST:     TGGATCCNAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|162273278|gb|FC449558.1|FC449558
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|18350946|gb|BJ182997.1|BJ182997
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
EST: gi|208389245|gb|DC933273.1|DC933273
EST:     TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAG                         GAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG
genomic: TGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGG

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: 15

GAATGGAGGGTGCCGGTACGGTGGAAGAAGTTGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagt ... attcatacagGAGTAATGGGGTCGTATGTCGAAGAGAAGTTGATCGATGCGGAGAAACTGGTGAAAATACCTGACGGAATTGAGTTCACCGTTGCTGCTGCTCTTATCCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATGGAGGGTGCCGGTACGGTGGAAGAAGTTGGATCCGAGGTCACAGATGTAGGAGTCGGAGACAGAGTGTGCTATGCAGgtacagcagtgggttcagcctcgtaacatgctgcacatgaagttgtttaccattgtcgagcagatgcatcaatccgttgtgaatcactattgctgtgttgtaacgattgattgagtttgtgtgcactcaacttaagattagcgggtttggaacttgtggatatatctattcatacag

- - - - - - - - - - - - - - - - - - - - - -  CAGATG