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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagctgcaaccatccttgttttgataactgcattatcaagttccattatttgataaacgcgagtttctgagttatattaagaatgcctttttgacgccaagtatccttttgttactgctgctttctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGCACAAGGAGCAACTGTGAATGTGAAGCCCAACCTACAGATTATTGCCGAT

Basic information

species Physcomitrella patens
transcript PP1S391_38V6.2
intron # 5
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|162185334|gb|FC360908.1|FC360908
EST:     ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAG                         GTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
genomic: ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAGgtaaaagctg ... tctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
EST: gi|162149735|gb|FC326786.1|FC326786
EST:     ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAG                         GTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
genomic: ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAGgtaaaagctg ... tctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
EST: gi|162244098|gb|FC424364.1|FC424364
EST:     ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAG                         GTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
genomic: ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAGgtaaaagctg ... tctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
EST: gi|162214538|gb|FC391505.1|FC391505
EST:     ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAG                         GTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
genomic: ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAGgtaaaagctg ... tctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
EST: gi|162188769|gb|FC364055.1|FC364055
EST:     ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAG                         GTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
genomic: ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAGgtaaaagctg ... tctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
EST: gi|162244099|gb|FC424365.1|FC424365
EST:     ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAG                         GTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
genomic: ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAGgtaaaagctg ... tctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
EST: gi|162149736|gb|FC326787.1|FC326787
EST:     ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAG                         GTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
genomic: ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAGgtaaaagctg ... tctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
EST: gi|162184383|gb|FC359129.1|FC359129
EST:     GGCGGTGTTCGATGGCAACGTCAAGGTGAACAG                         GTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
genomic: GGCGGTGTTCGATGGCAACGTCAAGGTGAACAGgtaaaagctg ... tctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
EST: gi|208363177|gb|DC954363.1|DC954363
EST:     ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAG                         GTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
genomic: ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAGgtaaaagctg ... tctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
EST: gi|162214537|gb|FC391504.1|FC391504
EST:     ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAG                         GTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC
genomic: ACTCACAGGTTAGGTCAGGCGGTGTTCGATGGCAACGTCAAGGTGAACAGgtaaaagctg ... tctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaatgcctttttgacgccaagtatccttttgttactgctgctttctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGCACAAGGAGCAACTGTGAATGTGAAGCCCAACCTACAGATTATTGCCGAT
          ttttgac  putative branch site (score: 3)
                                       ctgctttct  putative PPT
                            ttttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagctgcaaccatccttgttttgataactgcattatcaagttccattatttgataaacgcgagtttctgagttatattaagaatgcctttttgacgccaagtatccttttgttactgctgctttctgttgcagGTTTGCACAGCAGACAGATGCGGGGCAATTGAGTCGAAGTTTGTTACTAGCACAAGGAGCAACTGTGAATGTGAAGCCCAACCTACAGATTATTGCCGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC