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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaagttgttgagtattcttttgattcagatgaaaaactttgcgctctcttcgatgcgttgaaggtaacctactgacgaagttcgttatctgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTCACTTTTGCGAATGATGGAAAACGCGTCAGA

Basic information

species Physcomitrella patens
transcript PP1S49_285V6.1
intron # 4
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|100388672|gb|BY970820.1|BY970820
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
EST: gi|100392123|gb|BY953205.1|BY953205
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
EST: gi|208377279|gb|DC932429.1|DC932429
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
EST: gi|100394360|gb|BY972030.1|BY972030
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
EST: gi|100416278|gb|BY975313.1|BY975313
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
EST: gi|208384727|gb|DC915274.1|DC915274
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
EST: gi|162215240|gb|FC390813.1|FC390813
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
EST: gi|208346693|gb|DC913339.1|DC913339
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
EST: gi|100408084|gb|BY955901.1|BY955901
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
EST: gi|67569115|gb|BJ941939.1|BJ941939
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
EST: gi|100382686|gb|BY986915.1|BY986915
EST:     GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATG                         GATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC
genomic: GTCCTGCTTACCATTCCCGAGCTAAATCCTGAAATGgtaagtcctc ... tgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttcgatgcgttgaaggtaacctactgacgaagttcgttatctgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTCACTTTTGCGAATGATGGAAAACGCGTCAGA
                         tactgac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaagttgttgagtattcttttgattcagatgaaaaactttgcgctctcttcgatgcgttgaaggtaacctactgacgaagttcgttatctgtggtgcagGATGTGTACAGAATAGGGACTTTGCTGGAACTCATACGAGAACTTGCGTTCACTTTTGCGAATGATGGAAAACGCGTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA