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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTAGGGCGGGGGAAATACAGTGAGGTTTTTGAAGGTGTTCACGCCGTGAACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGAAAAAAAAGgtaccaagcttcggtacccaacattcttcatctgatgcattttgcatccttgatagagccagtcgtttatggttttccagcaatttcttgggcaagcttt...

Basic information

species Physcomitrella patens
transcript PP1S63_208V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 2
AGTAGGGCGGGGGAAATACAGTGAGGTTTTTGAAGGTGTTCACGCCGTGAACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGAAAAAAAAGgtaccaagcttcggtacccaacattcttcatctgatgcattt-tgcatccttgatagagccagtcgtttatggttttccagcaatttcttgggcaagcttt
 || ||  ||||||||||||||||||| || ||||||||||||  |    || |||||   || || ||||||||  |||| || |||||||| || |||||   |  | |  ||   |       ||    | || | ||| || |   |||          |  | | | | ||      | ||| | |       || 
GGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACCGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGaaggtgagagccatgtgtgagcgttgacgttttctttattcttttgtgaagttttggattttgttcttatgtcttggttgggtttactttttcgattcgagtt-

upper sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 2
AGTAGGGCGGGGGAAATACAGTGAGGTTTTTGAAGGTGTTCACGCCGTGAACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGAAAAAAAAGgta--ccaagcttcggt----acccaacattcttcatctgatgcattttgcatccttgatagagccagtcgtttatggttttccagcaatttcttgggcaagcttt
 || ||  ||||||||||||||||||| || ||||||||||||  |  | || |||||   || || ||||||||  |||| || |||||||| || |||||     | |  | ||     ||     ||||||  | ||| |  ||| | ||  ||| |        | | || |||||      | |||       ||      
GGTGGGTAGGGGGAAATACAGTGAGGTGTTCGAAGGTGTTCACTGCACGGACGGTGAGAAATGTGTCATTAAGATCCTGAAACCCGTGAAGAAGAAGaaggtgagttatgtgtgggcgttgacgttttattctttttgtgacgt-tttggaatttttgttccgatgtcttggttgtggttacttttcgattcgagtttcat-----

upper sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 5'ss of exon 2
AGTAGGGCGGGGGAAATACAGTGAGGTTTTTGAAGGTGTTCACGCCGTGAACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGAAAAAAAAGgtaccaagcttcggtacccaacattcttcatctgat-gcattttgcat--ccttgatagagccagtcgtttatggttttccagcaatttcttgggcaagcttt-----
||| ||  |||| |||||||||||||||||||||||| |  | |     |||| |||  | |||||  | |||||| | || || || || ||||| ||||||  |  |||  ||   |     ||||  | | |  | | |||| ||   | | |  | |  |    ||||    | |  |    |  ||        | ||     
AGTTGGAAGGGGAAAATACAGTGAGGTTTTTGAAGGTATAAATGTGACAAACAATGAAAGATGCGTAGTCAAGATTCTTAAACCTGTCAAAAAAAAGAAGgtattatactt--gtcttc-----tcttggtttaagagtagtttgtataggcctaagtgggatatatatttacatgtgtata-tgttcactcattttgaccttatcta

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|162177346|gb|FC352879.1|FC352879
EST:     ACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGNNNNNNNNG                         ATCAAAAGAGAAATCAAGATCCTGCAAAACCTCTGTGGGGGTCCCAATATT
genomic: ACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGAAAAAAAAGgtaccaagct ... acttcgacagATCAAAAGAGAAATCAAGATCCTGCAAAACCTCTGTGGGGGTCCCAATATT
EST: gi|22133071|gb|BQ827530.1|BQ827530
EST:     ACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGNNNNNNNNG                         ATCAAAAGAGAAATCAAGATCCTGCAAAACCTCTGTGGGGGTCCCAATATT
genomic: ACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGAAAAAAAAGgtaccaagct ... acttcgacagATCAAAAGAGAAATCAAGATCCTGCAAAACCTCTGTGGGGGTCCCAATATT
EST: gi|162151402|gb|FC327531.1|FC327531
EST:     ACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGNNNNNNNNG                         ATCAAAAGAGAAATCAAGATCCTGCAAAACCTCTGTGGGGGTCCCAATATT
genomic: ACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGAAAAAAAAGgtaccaagct ... acttcgacagATCAAAAGAGAAATCAAGATCCTGCAAAACCTCTGTGGGGGTCCCAATATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTAGGGCGGGGGAAATACAGTGAGGTTTTTGAAGGTGTTCACGCCGTGAACAGTGAGCGTTGCGTTATTAAGATTTTGAAGCCAGTGAAGAAAAAAAAGgtaccaagcttcggtacccaacattcttcatctgatgcattttgcatccttgatagagccagtcgtttatggttttccagcaatttcttgggcaagcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA