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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTTCGGAGGCTCGAATAGCAGAATGGCAGCCTTTATGGTGGCTGCCGTGGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacattagaaaaggctggattgtgttggaattgatttttgaccgtgaaaatggatttgaattacatcaatccaatgtatcgcatctgaagtacac...

Basic information

species Physcomitrella patens
transcript PP1S47_244V6.1
intron # 2
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|18374800|gb|BJ206378.1|BJ206378
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18366948|gb|BJ199028.1|BJ199028
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18326122|gb|BJ158121.1|BJ158121
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCGAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18374190|gb|BJ205768.1|BJ205768
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|100399062|gb|BY954180.1|BY954180
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18367539|gb|BJ199622.1|BJ199622
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18374946|gb|BJ206524.1|BJ206524
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18329595|gb|BJ161601.1|BJ161601
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18329333|gb|BJ161339.1|BJ161339
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18363432|gb|BJ195504.1|BJ195504
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18364334|gb|BJ196407.1|BJ196407
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|100446323|gb|CJ970622.1|CJ970622
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18371365|gb|BJ202967.1|BJ202967
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
EST: gi|18358406|gb|BJ190465.1|BJ190465
EST:     GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAG                         GAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC
genomic: GGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCC

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: 28 (upstream exon), 23 (downstream exon)
Score: 2

AGCTTCGGAGGCTCGAATAGCAGAATGGCAGCCTTTATGGTGGCTGCCGTGGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacat ... tttgtctcagGAGCACTCCTGTACTTGAAGCCCGAATTTCATCTGGATCAAACGCCTGCCCTTGAAGGAGAGGTTGTTGCTTCTACTCTAGTGGGCGCAGTCGCCGCTGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTTCGGAGGCTCGAATAGCAGAATGGCAGCCTTTATGGTGGCTGCCGTGGCCGCCATTGGAAACATGTTGCAAGGATGGGACGGTGGAGCCATTGCAGgtatggacattagaaaaggctggattgtgttggaattgatttttgaccgtgaaaatggatttgaattacatcaatccaatgtatcgcatctgaagtacac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG