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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttccaactgcagtagttttactcgcgtggtagcacatttcatgtttattgctttttatttattcatttataaattcaattatctatttgttttgcagACTCCCAATACGACAAACAGCTTATGTGGCTATAAGATTGTGACTGGTCAACCATCAGACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCA

Basic information

species Physcomitrella patens
transcript PP1S47_196V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_196V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv10s0003g00670.t01 (Vitis vinifera), 3'ss of exon 11
tctttccaactgcagtagttttactcgcgtggtagcacatttcatgtttattgctttttatttattcatttataaattcaattatctatttgttttgcagACTCCCAATACGACAAACAGCTTATGTGGCTATAAGATTGTGACTGGTCAACCATCAGACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCA
| | | | |||| | || | ||| | || | || | | ||| | ||| |||| |||| ||| | || ||| | ||||| || |||||||| || ||||| |||||||||||||||||||| | | || ||||| || |||| | || || ||||
-----------gttattgatccactctgattttacctt-cgtcacatccttttgcctggatcagtactattaaatattgttggatct---tgttgcacagGCCCCAAATGCCACAAATAGTTTATGTGGTTACAAGATAGTGACTGGTCAACCATCAGATAGGCTCGGGGAGGACTTCTCAGAATATTACAAGGACTTCA
















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|162179887|gb|FC355958.1|FC355958
EST:     CTACTTATGTGGAGTGTCTACTATATGCCTTTCATGAATTGGCCCACAAG                         ACTCCCAATACGACAAACAGCTTATGTGGCTATAAGATTGTGACTGGTCAA
genomic: CTACTTATGTGGAGTGTCTACTATATGCCTTTCATGAATTGGCCCACAAGgttacattat ... tgttttgcagACTCCCAATACGACAAACAGCTTATGTGGCTATAAGATTGTGACTGGTCAA
EST: gi|162186312|gb|FC361620.1|FC361620
EST:     CTACTTATGTGGAGTGTCTACTATATGCCTTTCATGAATTGGCCCACAAG                         ACTCCCAATACGACAAACAGCTTATGTGGCTA
genomic: CTACTTATGTGGAGTGTCTACTATATGCCTTTCATGAATTGGCCCACAAGgttacattat ... tgttttgcagACTCCCAATACGACAAACAGCTTATGTGGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttattgctttttatttattcatttataaattcaattatctatttgttttgcagACTCCCAATACGACAAACAGCTTATGTGGCTATAAGATTGTGACTGGTCAACCATCAGACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCA
                                           tttgtttt  CT-rich tract
 tttttatttattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttccaactgcagtagttttactcgcgtggtagcacatttcatgtttattgctttttatttattcatttataaattcaattatctatttgttttgcagACTCCCAATACGACAAACAGCTTATGTGGCTATAAGATTGTGACTGGTCAACCATCAGACCGTTTAGGAGAGGATTTTGCAGAGCTCTTTAAAGATTTCA

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