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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactggatgtattattttagtttttggagctgttagttttaaacctcaccgatgcagactggcacatttcgatgttactttgattgtaagatttgtttgaattagaggggactgttgctgatgtaatttctggatgtttcatctcgaactccttttattgcagCTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAACCGCTGAGGCGCTGGCCATGGGCAAGATCGTTGTCTGCGCAGATCATCCT

Basic information

species Physcomitrella patens
transcript PP1S123_79V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S123_79V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ09054 (Selaginella moellendorffii), 3'ss of exon 6
gtaagactggatgtattattttagtttttggagctgttagttttaaacctcaccgatgcagactggcacatttcgatgttactttgattgtaagatttgtttgaattagaggggactgttgctgatgtaatttctggatgtttcatctcgaactccttttattgcagCTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAACCGCTGAGGCGCTGGCCATGGGCAAGATCGTTGTCTGCGCAGATCATCCT
                                                                                                              | |  || ||   ||  |   |  ||| || ||  |  ||     ||    |||||||||||| || || ||||| |||||| | ||||||||||||||||| || || || ||||| ||||||||||| ||||||||||| ||||| |||||||| 
--------------------------------------------------------------------------------------------------------------gtgctctcttttggacttggata-tggttgcttactaacgggtctctc---ttgcagCTATAAGGTGTTTATCAATCCAAGCGTGAGCGATGTGGTGTGCACGACGACGGCAGAGGCACTGGCCATGGGAAAGATCGTTGTTTGCGCCGATCATCCG
















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|19789560|gb|BQ041380.1|BQ041380
EST:     GCCTTGGATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGG                         CTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAAC
genomic: GCCTTGGATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGGgtaagactgg ... tttattgcagCTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAAC
EST: gi|18335134|gb|BJ167152.1|BJ167152
EST:     GATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGG                         CTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAAC
genomic: GATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGGgtaagactgg ... tttattgcagCTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAAC
EST: gi|162239939|gb|FC414829.1|FC414829
EST:     GCCTTGGATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGG                         CTATAAAGTTTTCATCAACCCTAGCATAAGCGATGTGGTGTGCACAACAAC
genomic: GCCTTGGATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGGgtaagactgg ... tttattgcagCTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAAC
EST: gi|67578331|gb|BJ950498.1|BJ950498
EST:     GCCTTGGATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGG                         CTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAAC
genomic: GCCTTGGATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGGgtaagactgg ... tttattgcagCTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAAC
EST: gi|162228853|gb|FC404698.1|FC404698
EST:     GCCTTGGATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGG                         CTATAAAGTTTTCATCAACCCTAGCATAAGCGATGTGGTGTGCACAACAAC
genomic: GCCTTGGATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGGgtaagactgg ... tttattgcagCTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAAC
EST: gi|162157797|gb|FC334068.1|FC334068
EST:     GCCTTGGATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGG                         CTATAAAGTTTTCATCAACCCTAGCATAAGCGATGTGGTGTGCACAACAAC
genomic: GCCTTGGATTTTCATCCAGGGAGAGATCATGCTGATGCCTCCCTCCATGGgtaagactgg ... tttattgcagCTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggactgttgctgatgtaatttctggatgtttcatctcgaactccttttattgcagCTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAACCGCTGAGGCGCTGGCCATGGGCAAGATCGTTGTCTGCGCAGATCATCCT
       tgctgat  putative branch site (score: 3)
                                        ctccttttatt  putative PPT
            atgtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagactggatgtattattttagtttttggagctgttagttttaaacctcaccgatgcagactggcacatttcgatgttactttgattgtaagatttgtttgaattagaggggactgttgctgatgtaatttctggatgtttcatctcgaactccttttattgcagCTATAAAGTTTTCATCAACCCAAGCATAAGCGATGTGGTGTGCACAACAACCGCTGAGGCGCTGGCCATGGGCAAGATCGTTGTCTGCGCAGATCATCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA