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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACGACAAACAGCTTATGTGGCTATAAGATTGTGACTGGTCAACCATCAGACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCAATGAGAGgtgagagtttttccttgccacttaaaacttggcctacgtttatggaagctgggttgcacctgtttgataatccgtatccagtatacttcttgtgtttgtc...

Basic information

species Physcomitrella patens
transcript PP1S47_196V6.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_196V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv10s0003g00670.t01 (Vitis vinifera), 5'ss of exon 12
ATACGACAAACAGCTTATGTGGCTATAAGATTGTGACTGGTCAACCATCAGACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCAATGAGAGgtg-agagtttttccttgccacttaaaacttggcctacgtttatggaagctgggttgcacctgtttgataatccgtatccagtatacttcttgtgtttgtc----
|| | ||||| || |||||||| || ||||| |||||||||||||||||||| | | || ||||| || |||| | || || |||| |||||||| | || || ||| | | | | | | | | | || | | || | | |||| | | | |
ATGCCACAAATAGTTTATGTGGTTACAAGATAGTGACTGGTCAACCATCAGATAGGCTCGGGGAGGACTTCTCAGAATATTACAAGGACTTCACTGAGAGgtttactattattttttgtctt-----gcctttctttcttgaagaaatcatgtggaccttctactaggcaatctagagaacacagaacaacaaaggacactaaaa
















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|162241354|gb|FC416985.1|FC416985
EST:     ATTTCAATGAGAG                         ATTGACTGTAGTAGAGGAGCTGGCGAAGGCAGCCAACAAGAAATTAACGCA
genomic: ATTTCAATGAGAGgtgagagttt ... tcgtattcagATTGACTGTAGTAGAGGAGCTGGCGAAGGCAGCCAACAAGAAATTAACGCA
EST: gi|162202250|gb|FC377586.1|FC377586
EST:     GACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCAATGAGAG                         ATTGACTGTAGTAGAGGAGCTGGCGAAGGCAGCCAACAAGAAATTAACGCA
genomic: GACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCAATGAGAGgtgagagttt ... tcgtattcagATTGACTGTAGTAGAGGAGCTGGCGAAGGCAGCCAACAAGAAATTAACGCA
EST: gi|208347797|gb|DC921124.1|DC921124
EST:     TTTCAATGAGAG                         ATTGACTGTAGTAGAGGAGCTNGCGAAGGCAGCCANCAAGAAATTAACGCA
genomic: TTTCAATGAGAGgtgagagttt ... tcgtattcagATTGACTGTAGTAGAGGAGCTGGCGAAGGCAGCCAACAAGAAATTAACGCA
EST: gi|37833862|gb|BJ591874.1|BJ591874
EST:     TTTTGCAGAGCTCTTTAAAGATTTCAATGAGAG                         ATTGACTGTAGTAGAGGAGCTGGCGAAGGCAGCCCACCAAGAAATTAACGC
genomic: TTTTGCAGAGCTCTTTAAAGATTTCAATGAGAGgtgagagttt ... tcgtattcagATTGACTGTAGTAGAGGAGCTGGCGAAGGCAG-CCAACAAGAAATTAACGC
EST: gi|162179887|gb|FC355958.1|FC355958
EST:     GACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCAATGAGAG                         ATTGACTGTAGT
genomic: GACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCAATGAGAGgtgagagttt ... tcgtattcagATTGACTGTAGT
EST: gi|162177458|gb|FC353719.1|FC353719
EST:     GACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCAATGAGAG                         ATTGACTGTAGTAGAGGAGCTGGCGAAGGCAGCCAACAAGAAATTATCGCA
genomic: GACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCAATGAGAGgtgagagttt ... tcgtattcagATTGACTGTAGTAGAGGAGCTGGCGAAGGCAGCCAACAAGAAATTAACGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACGACAAACAGCTTATGTGGCTATAAGATTGTGACTGGTCAACCATCAGACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCAATGAGAGgtgagagtttttccttgccacttaaaacttggcctacgtttatggaagctgggttgcacctgtttgataatccgtatccagtatacttcttgtgtttgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT