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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

atctggccatgcagcaatgcatggcgatcggctatggattcctgacgaaattctcgcctgtctccccAGCTCGTGACGAGGGAGGAGGGATTGGAGCTCTACGAGGACATGATCCTCGGGCGCTGCTTCGAGGATATGTGCGCCCAGATGTACTACCGCTCCAAGAT

Basic information

species Selaginella moellendorffii
transcript EFJ29991
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29991 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S199_145V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------------atctggccatgcagcaatgcatg-gcgatcggctatggattcctgacgaaattctcgcctgtc---tccccAGCTCGTGACGAGGGAGGAGGGATTGGAGCTCTACGAGGACATGATCCTCGGGCGCTGCTTCGAGGATATGTGCGCCCAGATGTACTACCGCTCCAAGAT--
                                                                         |  ||   |    |  |   || | | | || |  ||  |  |||||  |||   |  ||     |   ||| | |||||||  || || ||  ||||||| |||||||||||| |  | |||||  |||||||||| |||||||| |||||||||||| |    |||||  
gtgagtggacgtggaggtgactgcgggcgtggattgggttggttggttggttggattggggtgggagctgcattggggatttttgacggttggtgtgtggttgggtgggggat--tgacgcgattgatgattgcgggattggcagTTGGTGACGAAAGATGAAGGGCTGGAGCTGTACGAGGACATGGTGTTGGGGCGGAGCTTCGAGGACATGTGCGCGCAGATGTACTACAGGGGGAAGATGT
















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|169048543|gb|FE454425.1|FE454425
EST:     CC-CCTAAAGATCGCCGAC---G
genomic: CCTCC-AAAGATCGCCGACATAG
EST: gi|169069942|gb|FE480376.1|FE480376
EST:     TCCTCCAAAGATCGCTG--AT-G
genomic: TCCTCCAAAGATCGCCGACATAG
EST: gi|169068681|gb|FE477984.1|FE477984
EST:     CC-CCTAAAGATCGCCGAC---G
genomic: CCTCC-AAAGATCGCCGACATAG
EST: gi|169042955|gb|FE452309.1|FE452309
EST:     CC-CCTAAAGATCGCCGAC---G
genomic: CCTCC-AAAGATCGCCGACATAG
EST: gi|169065002|gb|FE475074.1|FE475074
EST:     CC-CCTAAAGATCGCCGAC---G
genomic: CCTCC-AAAGATCGCCGACATAG
EST: gi|169098946|gb|FE501719.1|FE501719
EST:     CC-CCTAAAGATCGCCGAC---G
genomic: CCTCC-AAAGATCGCCGACATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaatgcatggcgatcggctatggattcctgacgaaattctcgcctgtctccccAGCTCGTGACGAGGGAGGAGGGATTGGAGCTCTACGAGGACATGATCCTCGGGCGCTGCTTCGAGGATATGTGCGCCCAGATGTACTACCGCTCCAAGAT
                           tcctgac  putative branch site (score: 2)
                                      ttctcgcctgtctccc  putative PPT
                                   aaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctggccatgcagcaatgcatggcgatcggctatggattcctgacgaaattctcgcctgtctccccAGCTCGTGACGAGGGAGGAGGGATTGGAGCTCTACGAGGACATGATCCTCGGGCGCTGCTTCGAGGATATGTGCGCCCAGATGTACTACCGCTCCAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG