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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGTCGGCGACGACTTGTCCTGCTGCCATGGGATTTAGTTTTGCTGCTGGGACGACAGACGGGCCAGGAGCTTTTGACTTCAAGCAAGGAGACACTGACgtaagttgctgtattcattctcgatttggagctgacctgaaattacag

Basic information

species Selaginella moellendorffii
transcript EFJ09250
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ09250 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G180732_T01 (Zea mays), 5'ss of exon 6
ACAGTCGGCGACGACTTGTCCTGCTGCCATGGGATTTAGTTTTGCTGCTGGGACGACAGACGGGCCAGGAGCTTTTGACTTCAAGCAAGGAGACACTGACgtaagttgc-tgtattcattctcgatttggagctgacctgaaattacag---------------------------
 ||    | ||  || || || || |||||||| |||   ||||||||||| || ||||| || || |||||||||||||| || ||||||||     | ||   | || |  |   | |  |  |    || |   || | |    |                            
GCAAGTTGTGAAAACATGCCCAGCAGCCATGGGGTTTGCCTTTGCTGCTGGAACCACAGATGGTCCTGGAGCTTTTGACTTTAAACAAGGAGATGTCAAGgttgatcgcatcaaccaaatgaccttgacaagtttcactaacaccgtattgactggtttataccatctcttatcag

upper sequence: EFJ09250 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA14G01330.1 (Glycine max), 5'ss of exon 5
ACAGTCGGCGACGACTTGTCCTGCTGCCATGGGATTTAGTTTTGCTGCTGGGACGACAGACGGGCCAGGAGCTTTTGACTTCAAGCAAGGAGACACTGACgtaa--gttgct--gtattcattctcgatt-tggagctgacctgaaattacag-------------------------------------------
  ||   |  | ||| || |||||||| |||||||||   ||||||||||| || ||||| || || |||||||||||||| |||||||| ||   | | ||||   ||| |  |   | || ||    | |    ||| |||   |||                                               
TGAGGTTGTAAAGACATGCCCTGCTGCAATGGGATTTGCATTTGCTGCTGGAACAACAGATGGACCTGGAGCTTTTGACTTTAAGCAAGGTGATGATCAGgtaaccattgataagaccttatgcttacctattatcctggccttgtattcttaaatatctttgaaactctgcttattatttctaattgtatgtcag

upper sequence: EFJ09250 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA02G47420.1 (Glycine max), 5'ss of exon 5
ACAGTCGGCGACGACTTGTCCTGCTGCCATGGGATTTAGTTTTGCTGCTGGGACGACAGACGGGCCAGGAGCTTTTGACTTCAAGCAAGGAGACACTGACgtaagttgctgtattcattctcgatttggagctgacctgaaattacag--------------------------------------------------
  ||      | ||| || |||||||| |||||||||   ||||||||||| || ||||| || || |||||||||||||| |||||||| ||   | | ||||       ||     |   | ||     ||  ||||   ||  |                                                   
TGAGGTCATAAAGACATGCCCTGCTGCAATGGGATTTGCATTTGCTGCTGGAACAACAGATGGACCTGGAGCTTTTGACTTTAAGCAAGGTGATGATCAGgtaaccactgataagaccttatgcttacctactatcctggccttgtattcttaaatagctttgaaactctatgcttattatgtctaattgtatgtcag

upper sequence: EFJ09250 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: Vv06s0004g05890.t01 (Vitis vinifera), 5'ss of exon 5
ACAGTCGGCGACGACTTGTCCTGCTGCCATGGGATTTAGTTTTGCTGCTGGGACGACAGACGGGCCAGGAGCTTTTGACTTCAAGCAAGGAGACACTGACgtaa---gttgctgtattcattctcgatttggagctgacctga----aattacag----------------------------------------------------------------------------
  ||   |  |  || ||||| || || ||||| |||   |||||||| || || || || || || ||||||||||||||||||||||||||   | | ||||   |    |  |||| || | ||||      |    | |    |||||  |                                                                            
TGAGGTAGTAAAAACATGTCCCGCCGCAATGGGGTTTGCATTTGCTGCAGGAACAACTGATGGTCCTGGAGCTTTTGACTTCAAGCAAGGAGATGATCAGgtaacaagaatttcaattctttatggattccatattatttttataagaattatggattccacattttatgtgctatttgttgtaatgcatggccttcctgtgagataatttttttctatggtgttattcag

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|169073678|gb|FE481377.1|FE481377
EST:     GGACGACAGACGGGCCAGGAGCTTTTGACTTCAAGCAAGGAGACACTGAC                         GGAAATCCATTCTGGAAAGCTGTTCGTGACTTGCTGAGGAAACCAACCGAA
genomic: GGACGACAGACGGGCCAGGAGCTTTTGACTTCAAGCAAGGAGACACTGACgtaagttgct ... gaaattacagGGAAATCCATTCTGGAAAGCTGTTCGTGACTTGCTGAGGAAACCAACCGAA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGTCGGCGACGACTTGTCCTGCTGCCATGGGATTTAGTTTTGCTGCTGGGACGACAGACGGGCCAGGAGCTTTTGACTTCAAGCAAGGAGACACTGACgtaagttgctgtattcattctcgatttggagctgacctgaaattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA