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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctctttgcactcgctgtgacctggaggcgtttgtttcgttgaccatccaagtttcgctaagcctttctgtaatacaccactgaaactttgtgaaaaatacctattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGGAGAAAGCTACATTCACGATATCCCCAGAAAATGCTTATGGAGAAGCTGG

Basic information

species Physcomitrella patens
transcript PP1S109_70V6.1
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|208368642|gb|DC940021.1|DC940021
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
EST: gi|100365372|gb|BY966565.1|BY966565
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
EST: gi|162221593|gb|FC397610.1|FC397610
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
EST: gi|100447939|gb|CJ972238.1|CJ972238
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
EST: gi|67570816|gb|BJ943640.1|BJ943640
EST:     GATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTT
genomic: GATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGG-TCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTT
EST: gi|67573557|gb|BJ946381.1|BJ946381
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
EST: gi|162173905|gb|FC349705.1|FC349705
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
EST: gi|18360372|gb|BJ192434.1|BJ192434
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
EST: gi|67716695|gb|BJ966955.1|BJ966955
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
EST: gi|162193217|gb|FC371524.1|FC371524
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
EST: gi|100362283|gb|BY947282.1|BY947282
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
EST: gi|162172470|gb|FC349139.1|FC349139
EST:     TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG                         GTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG
genomic: TGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGG

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: 34 (upstream exon), 34 (downstream exon)
Score: 69

TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAGgtaagctctt ... tattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGGAGAAAGCTACATTCACGATATCCCCAGAAAATGCTTATGGAGAAGCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaagcctttctgtaatacaccactgaaactttgtgaaaaatacctattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGGAGAAAGCTACATTCACGATATCCCCAGAAAATGCTTATGGAGAAGCTGG
                                           cctattct  CT-rich tract
                                  tgaaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctctttgcactcgctgtgacctggaggcgtttgtttcgttgaccatccaagtttcgctaagcctttctgtaatacaccactgaaactttgtgaaaaatacctattctgcagGTCAAGTGATCAAGGGATGGGATAAGGGCGTTGCAACCATGAAGAAGGGGGAGAAAGCTACATTCACGATATCCCCAGAAAATGCTTATGGAGAAGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG