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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTAACCCCTCTGCACTTCGGGAAACCGTGGTGGAGGTGCCCAATACCACCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaactgtgttacttcctattgaggattgtgtattttcatgtgctttgcagaaaagtgtgtgttgatcttagtcagggcatctgaatattcattt...

Basic information

species Physcomitrella patens
transcript PP1S296_11V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S296_11V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ29753 (Selaginella moellendorffii), 5'ss of exon 6
CAGTAACCCCTCTGCACTTCGGGAAACCGTGGTGGAGGTGCCCAATACCACCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaactgtgtta-cttcctattgaggattgtgtattttcatgtgctttgcagaaaagtgtgtgttgatcttagtcagggcatctgaatattcattt
                            ||||| || ||||| |||    |||||||||||||||| ||||| ||||| || ||| ||||||| ||||||||   |      | | | ||   |   |  ||||   |||     | |  | |||||                                            
----------------------------GTGGTTGAAGTGCCTAATGTTTCCTGGGAAGACATTGGTGGTCTTGAGAACGTCAAGAGGGAGCTTCAAGAGgtgggtgtttgttatgagctggatgcggctgattccttatgccggtat-ttgtgcag--------------------------------------------
















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|22132961|gb|BQ827459.1|BQ827459
EST:     CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAG                         ACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
genomic: CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaac ... ggtttggcagACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
EST: gi|162179673|gb|FC355731.1|FC355731
EST:     CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAG                         ACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
genomic: CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaac ... ggtttggcagACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
EST: gi|162215375|gb|FC391871.1|FC391871
EST:     CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAG                         ACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
genomic: CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaac ... ggtttggcagACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
EST: gi|162170416|gb|FC347614.1|FC347614
EST:     CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAG                         ACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGGATG
genomic: CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaac ... ggtttggcagACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
EST: gi|162150014|gb|FC326545.1|FC326545
EST:     CTGGGAAGACATTGGAGGTCTGGAGAAATGT-AAGCGGGAGCTACAAGAG                         ACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
genomic: CTGGGAAGACATTGGAGGTCTGGAGAA-TGTTAAGCGGGAGCTACAAGAGgtacttaaac ... ggtttggcagACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
EST: gi|162163653|gb|FC339758.1|FC339758
EST:     CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAG                         ACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
genomic: CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaac ... ggtttggcagACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
EST: gi|162162587|gb|FC338681.1|FC338681
EST:     CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAG                         ACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
genomic: CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaac ... ggtttggcagACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
EST: gi|162157112|gb|FC333682.1|FC333682
EST:     CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAG                         ACTGTGCAATATCCAGTGGA
genomic: CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaac ... ggtttggcagACTGTGCAATATCCAGTGGA
EST: gi|162191519|gb|FC368445.1|FC368445
EST:     CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAG                         ACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG
genomic: CCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaac ... ggtttggcagACTGTGCAATATCCAGTGGAGCATCCTGAGAAGTTTGAGAAATTTGGAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTAACCCCTCTGCACTTCGGGAAACCGTGGTGGAGGTGCCCAATACCACCTGGGAAGACATTGGAGGTCTGGAGAATGTTAAGCGGGAGCTACAAGAGgtacttaaactgtgttacttcctattgaggattgtgtattttcatgtgctttgcagaaaagtgtgtgttgatcttagtcagggcatctgaatattcattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT