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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATGGCGGGAAGAGTATATGTGACTGACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAGgtatacattctgtcctctcttctttcaagtcgtgcgtaggatggctattggggggtttgtttgaaactgcaactttgagctacaagcactggactacttt...

Basic information

species Physcomitrella patens
transcript PP1S4_346V6.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S4_346V6.1 (Physcomitrella patens), 5'ss of exon 23
lower sequence: Vv13s0019g04770.t01 (Vitis vinifera), 5'ss of exon 20
AGCATGGCGGGAAGAGTATATGTGACTGACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAGgtatacattctgtcct-ctcttctttcaagtcgtgcgtaggatggctattggggggtttgtt-tgaaactgcaactttgagctacaagcactggactacttt-
   ||| |  | || | |||  ||  |||||||||||||||||||||||| ||||| ||| ||   |||||  | |||||    |   | |||| ||| | ||| | | |  |    ||     |||      ||| |   || ||  |  |  || |  || |         ||      
GAAATGACCAGCAGGGAATACTTGGATGACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAGgtcagtaagttttcctgctccttttttagggcaagtagcggccaa-tatcacattgttggccctgcaaaaggcatgttta--tatatatttcaacctgtcaaa

upper sequence: PP1S4_346V6.1 (Physcomitrella patens), 5'ss of exon 23
lower sequence: EFJ18263 (Selaginella moellendorffii), 5'ss of exon 20
AGCATGGCGGGAAGAGTATATGTGACTGACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAGgtatacattctgtcctctcttctttcaagtcgtgcgtaggatggctattggggggtttgtttgaaactgcaactttgagctacaagcactggactacttt
|| ||| | || ||||| ||||| |  || || |||||||||||||| |||||||||||||||    | ||  | |||||| | ||| |||  |    | | ||||      |  |   |  |  ||  |                                                
AGTATGACCGGGAGAGTCTATGTTAGCGATCACGATGCTGAAGAACCTGAAGATTTCATTGTTTCATTTACTTCTCAGgtagatattgtgtatt----tatgtcaaact---caaaacgtttcccttcag------------------------------------------------
















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|162184469|gb|FC359943.1|FC359943
EST:     ACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAG                         ATTGCTAGAAGGGATGAGGAAATGGCTGCCTATGTGCCACCATTAAAACGT
genomic: ACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAGgtatacattc ... cttttcgcagATTGCTAGAAGGGATGAGGAAATGGCTGCCTATGTGCCACCATTAAAACGT
EST: gi|37842367|gb|BJ600375.1|BJ600375
EST:     ACCAAGATGCTGAAGANCCAGAAGATTTCATTGTTGGTCTCACAACCCAG                         ATTGCTAGAAGGGATGAGGAAATGGCTGCCTATGTGCCACCATTAAAACGT
genomic: ACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAGgtatacattc ... cttttcgcagATTGCTAGAAGGGATGAGGAAATGGCTGCCTATGTGCCACCATTAAAACGT
EST: gi|162277703|gb|FC453542.1|FC453542
EST:     ACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAG                         ATTGCTAGAAGGGATGAGGAAATGGCTGCCTATGTGCCACCATTAAAACGT
genomic: ACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAGgtatacattc ... cttttcgcagATTGCTAGAAGGGATGAGGAAATGGCTGCCTATGTGCCACCATTAAAACGT
EST: gi|162184468|gb|FC359942.1|FC359942
EST:     ACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAG                         ATTGCTAGAAGGGATGAGGAAATGGCTGCCTATGTGCCACCATTAAAACGT
genomic: ACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAGgtatacattc ... cttttcgcagATTGCTAGAAGGGATGAGGAAATGGCTGCCTATGTGCCACCATTAAAACGT
EST: gi|162157650|gb|FC332972.1|FC332972
EST:     ACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAG                         ATTGCTAGAAGGGATGAGGAAATGGCTGCCTATGTGCCACCATTAAAACGT
genomic: ACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAGgtatacattc ... cttttcgcagATTGCTAGAAGGGATGAGGAAATGGCTGCCTATGTGCCACCATTAAAACGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCATGGCGGGAAGAGTATATGTGACTGACCAAGATGCTGAAGAACCAGAAGATTTCATTGTTGGTCTCACAACCCAGgtatacattctgtcctctcttctttcaagtcgtgcgtaggatggctattggggggtttgtttgaaactgcaactttgagctacaagcactggactacttt

- - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - AAGAAC