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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcctcagttgaacatcctgtgactttgaatgcctatgctttggttagatactcttatggacttgtttctccttgttaatactggtaaagctatcacacgtacacgacttgtccttgtggacataatctttcaaaattgcttatgatggttcgtttgtactgtagGAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG

Basic information

species Physcomitrella patens
transcript PP1S9_381V6.2
intron # 10
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|162159142|gb|FC334313.1|FC334313
EST:     AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAG                         GAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
genomic: AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAGgtatgtgcct ... tgtactgtagGAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
EST: gi|162164287|gb|FC342102.1|FC342102
EST:     AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAG                         GAATGTCATCGACCATCCGAATGAAGACAAATATCGA
genomic: AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAGgtatgtgcct ... tgtactgtagGAATGTCATCGACCATCCGAATGAAGACAAATATCGA
EST: gi|37848308|gb|BJ606316.1|BJ606316
EST:     AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAG                         GAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
genomic: AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAGgtatgtgcct ... tgtactgtagGAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
EST: gi|162164286|gb|FC342101.1|FC342101
EST:     AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAG                         GAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
genomic: AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAGgtatgtgcct ... tgtactgtagGAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
EST: gi|162153921|gb|FC329428.1|FC329428
EST:     AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAG                         GAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
genomic: AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAGgtatgtgcct ... tgtactgtagGAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
EST: gi|162165438|gb|FC340874.1|FC340874
EST:     AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAG                         GAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
genomic: AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAGgtatgtgcct ... tgtactgtagGAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
EST: gi|162245447|gb|FC421349.1|FC421349
EST:     AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAG                         GAATGTCATCGACCATCCGAAATGA-GACNAATATCG
genomic: AGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAGgtatgtgcct ... tgtactgtagGAATGTCATCGACCATCCGAA-TGAAGACAAATATCG

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), 34 (downstream exon)
Score: 17

CTGCAATGGCACGGCTGCAAAATGCCATAACCACTCTGAAGAGACAAGCAAGTCCTTCTGAAACCAATGCAACTATTCAAGTATTGTTCACTATTTTCAGgtatgtgcct ... tgtactgtagGAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccttgtggacataatctttcaaaattgcttatgatggttcgtttgtactgtagGAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG
                                       ttcgttt  CT-rich tract
            ataatctttcaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgcctcagttgaacatcctgtgactttgaatgcctatgctttggttagatactcttatggacttgtttctccttgttaatactggtaaagctatcacacgtacacgacttgtccttgtggacataatctttcaaaattgcttatgatggttcgtttgtactgtagGAATGTCATCGACCATCCGAATGAAGACAAATATCGACGCCTTCGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA