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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtcaagtcatatatatacatacctacattttaaactcttttcgtagtgaagtggtgcaaatggaagatcttgactttccttgggtgataaattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGACAAAGTTACAGATTTCGCAG

Basic information

species Physcomitrella patens
transcript PP1S69_206V6.2
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|208360863|gb|DC934759.1|DC934759
EST:     CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACG                         GCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCACCAACATTGAAGATTGAC
genomic: CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACGgtcacactcc ... aattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
EST: gi|208363913|gb|DC939562.1|DC939562
EST:     CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACG                         GCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
genomic: CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACGgtcacactcc ... aattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
EST: gi|208392519|gb|DC933933.1|DC933933
EST:     CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACG                         GCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
genomic: CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACGgtcacactcc ... aattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
EST: gi|208360887|gb|DC934783.1|DC934783
EST:     CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACG                         GCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
genomic: CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACGgtcacactcc ... aattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
EST: gi|208358230|gb|DC934507.1|DC934507
EST:     CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACG                         GCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
genomic: CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACGgtcacactcc ... aattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
EST: gi|208384874|gb|DC907487.1|DC907487
EST:     CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACG                         GCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
genomic: CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACGgtcacactcc ... aattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
EST: gi|208377672|gb|DC932208.1|DC932208
EST:     CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACG                         GCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
genomic: CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACGgtcacactcc ... aattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC
EST: gi|208380943|gb|DC902973.1|DC902973
EST:     CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACG                         GCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAACAACATTGAAGATTGAC
genomic: CAATGGCGGAGGGCAACACCAGCTACCTCGGCCTCACTGCTATCATCACGgtcacactcc ... aattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgaagtggtgcaaatggaagatcttgactttccttgggtgataaattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGACAAAGTTACAGATTTCGCAG
                       tcttgac  putative branch site (score: 3)
                                        tgataaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtcaagtcatatatatacatacctacattttaaactcttttcgtagtgaagtggtgcaaatggaagatcttgactttccttgggtgataaattttgcagGCGGTGTTTCAGTTTTCGTTTTTCTGTGTTGCAGCAACATTGAAGATTGACAAAGTTACAGATTTCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA