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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttagggcttgttccgttggaatgtatttgagttttcctttttgtctgtttttttcgccttcttatgtcgttgaggttcgccaagttgttttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCAAAGTCTTTTCTTTTGCAGTGGACGCTGGCCTGCAGACATGGACTCTAGA

Basic information

species Physcomitrella patens
transcript PP1S55_276V6.1
intron # 1
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|208348584|gb|DC913256.1|DC913256
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|100448146|gb|CJ972445.1|CJ972445
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|100441256|gb|BY962545.1|BY962545
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|18375339|gb|BJ206917.1|BJ206917
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|18372844|gb|BJ204446.1|BJ204446
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|208347059|gb|DC901866.1|DC901866
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|18329779|gb|BJ161785.1|BJ161785
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|100418045|gb|BY993309.1|BY993309
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|208387699|gb|DC937264.1|DC937264
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|100448769|gb|CJ973068.1|CJ973068
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|100386374|gb|BY988041.1|BY988041
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
EST: gi|100373539|gb|BY948973.1|BY948973
EST:     GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAG                         GCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA
genomic: GGTTGTTGATTTAGCGTCGCATTTTGTATCCAAAGCGTTCTTCAGACAAGgtactgagat ... tttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtttttttcgccttcttatgtcgttgaggttcgccaagttgttttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCAAAGTCTTTTCTTTTGCAGTGGACGCTGGCCTGCAGACATGGACTCTAGA
                                            ttttgtttc  CT-rich tract
                                            ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttagggcttgttccgttggaatgtatttgagttttcctttttgtctgtttttttcgccttcttatgtcgttgaggttcgccaagttgttttgtttcagGCTTTTTGCGTTCAGGGGTTAGTGTTTCTTATCACGAAGGCGAAAGGAGCAAAGTCTTTTCTTTTGCAGTGGACGCTGGCCTGCAGACATGGACTCTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA