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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtagtggctatctgttttgttttgcgattcgttcatatatttattttttttctctgcctgtatctcatcatttcattgagagtttgattgtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACAAGGTGGATAAAGAGAAGCTGGTGGCTGGTACTCGAGTTGCACTAGACAT

Basic information

species Physcomitrella patens
transcript PP1S47_46V6.2
intron # 2
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|18356521|gb|BJ188580.1|BJ188580
EST:     CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCT                         TAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
genomic: CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCTgtaagtaatg ... gtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
EST: gi|18353546|gb|BJ185601.1|BJ185601
EST:     CGTGGGTCAAATCATCGGANAAGTGTTGAGGCAGCTGGATTCTGAACGCT                         TAATTGTGAAGGCGAGCAGTGGCCC
genomic: CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCTgtaagtaatg ... gtctgagcagTAATTGTGAAGGCGAGCAGTGGCCC
EST: gi|18330767|gb|BJ162773.1|BJ162773
EST:     CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCT                         TAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
genomic: CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCTgtaagtaatg ... gtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
EST: gi|100450689|gb|CJ974389.1|CJ974389
EST:     CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCT                         TAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
genomic: CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCTgtaagtaatg ... gtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
EST: gi|208398538|gb|DC912383.1|DC912383
EST:     CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCT                         TAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
genomic: CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCTgtaagtaatg ... gtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
EST: gi|18357042|gb|BJ189101.1|BJ189101
EST:     CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCT                         TAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
genomic: CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCTgtaagtaatg ... gtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
EST: gi|100405000|gb|BY991388.1|BY991388
EST:     CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCT                         TAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
genomic: CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCTgtaagtaatg ... gtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
EST: gi|162269527|gb|FC445083.1|FC445083
EST:     CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCT                         TAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
genomic: CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCTgtaagtaatg ... gtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
EST: gi|18344191|gb|BJ176230.1|BJ176230
EST:     CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCT                         TAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA
genomic: CGTGGGTCAAATCATCGGAGAAGTGTTGAGGCAGCTGGATTCTGAACGCTgtaagtaatg ... gtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttctctgcctgtatctcatcatttcattgagagtttgattgtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACAAGGTGGATAAAGAGAAGCTGGTGGCTGGTACTCGAGTTGCACTAGACAT
                                     gtttgat  putative branch site (score: 5)
                         atttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtagtggctatctgttttgttttgcgattcgttcatatatttattttttttctctgcctgtatctcatcatttcattgagagtttgattgtctgagcagTAATTGTGAAGGCGAGCAGTGGCCCACGGTATGTGGTTGGATGCCGCAACAAGGTGGATAAAGAGAAGCTGGTGGCTGGTACTCGAGTTGCACTAGACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG