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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctagtatctattttcctgggtgtgtttggtgcatacttttgcaccgtgcattcaaagtgtggtgaaaactcttagtgaatcttgtttcgctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGAGGCGTGCTCATG

Basic information

species Physcomitrella patens
transcript PP1S47_97V6.1
intron # 16
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|19789030|gb|BQ041056.1|BQ041056
EST:     CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG                         GATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
genomic: CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTGgtaaattttc ... gctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
EST: gi|162199129|gb|FC375821.1|FC375821
EST:     CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG                         GATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
genomic: CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTGgtaaattttc ... gctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
EST: gi|37831033|gb|BJ589045.1|BJ589045
EST:     CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG                         GATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
genomic: CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTGgtaaattttc ... gctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
EST: gi|18341144|gb|BJ173177.1|BJ173177
EST:     CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG                         GATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
genomic: CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTGgtaaattttc ... gctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
EST: gi|18337417|gb|BJ169441.1|BJ169441
EST:     CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG                         GATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
genomic: CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTGgtaaattttc ... gctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
EST: gi|37828058|gb|BJ586070.1|BJ586070
EST:     CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG                         GATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
genomic: CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTGgtaaattttc ... gctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
EST: gi|162187556|gb|FC363818.1|FC363818
EST:     CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG                         GATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
genomic: CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTGgtaaattttc ... gctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
EST: gi|37836283|gb|BJ594291.1|BJ594291
EST:     CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG                         GATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
genomic: CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTGgtaaattttc ... gctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
EST: gi|162174579|gb|FC350234.1|FC350234
EST:     CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG                         GATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA
genomic: CTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTGgtaaattttc ... gctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtgcattcaaagtgtggtgaaaactcttagtgaatcttgtttcgctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGAGGCGTGCTCATG
                                            cgctgat  putative branch site (score: 4)
                                         tttcgct  CT-rich tract
      attcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctagtatctattttcctgggtgtgtttggtgcatacttttgcaccgtgcattcaaagtgtggtgaaaactcttagtgaatcttgtttcgctgatgcagGATCTTGATGCTGTGGAGGCCCTTATACAAGGGCTTGCTTTATTTCAAGGAGGCGTGCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - tggtgca