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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTGGCTTCATTGGAAGGCTAGAAGAGCAAAAGGGGTCAGACATACTTGCAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTGgtttgtagttttttcatggtatttgcaagcctgcttatgcgtgtgttggtacag

Basic information

species Selaginella moellendorffii
transcript EFJ24731
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24731 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA16G02110.1 (Glycine max), 5'ss of exon 10
TATTGGCTTCATTGGAAGGCTAGAAGAGCAAAAGGGGTCAGACATACTTGCAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTGgtttgt----agttttttcatggtatttgcaagcctgcttatgcgtgtgttggtacag--------------------------------------------------
|||||| |||||||| ||||| ||||||||||| || || || || |||||||||||  |  || | ||||| || ||  | || ||  || | |  || ||  ||    | |      | |  |   | || |    ||   |     ||   |||                                                   
TATTGGTTTCATTGGTAGGCTTGAAGAGCAAAAAGGTTCTGATATTCTTGCAGAAGCTATTCCCCAATTTATCAAGGAGAATGTTCAGTTGGTAGCCCTAgtaagtataaaatgaaaaaaagaaagaagtaaacgcaatttctcaacccttctcacataaaaaaaggattaagaaatctcattcaaggatgatattctattgtcttag

upper sequence: EFJ24731 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: PP1S33_144V6.1 (Physcomitrella patens), 5'ss of exon 9
TATTGGCTTCATTGGAAGGCTAGAAGAGCAAAAGGGGTCAGACATACTTGCAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTGgtttg-tagttttttcatggtatttgcaagcctgcttatgcgtgtgttggtacag-------------------------------------------------------------------------------
| |||| ||||||||||| || ||||| ||||||||||| |||||||| ||||| || ||    |||||  | |  || || || || || ||||||||||| ||   | ||| || || ||| |    |  |    |  |   |     |  |                                                                                
TTTTGGATTCATTGGAAGACTGGAAGAACAAAAGGGGTCTGACATACTGGCAGAGGCTGTAAAGGATTTCCTGATGGATGATGTTCAGCTCATTGTGCTGgtatggctgctttctcctgttatctctctgggtttcgaaacagctaagaatgaataagtctgtggtcgattacacatcatatcactagaaatggtggttttttgttttttgaatgttttctcttcggttgacag
















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|169049787|gb|FE457801.1|FE457801
EST:     CAGAAGCAGTGGCCGATTTTATAGACGAAGACGTGCAACTGATTGTGCTG                         GGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
genomic: CAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTGgtttgtagtt ... gttggtacagGGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
EST: gi|169026890|gb|FE434241.1|FE434241
EST:     CAGAAGCAGTGGCCGATTTTATAGACGAAGACGTGCAACTGATTGTGCTG                         GGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
genomic: CAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTGgtttgtagtt ... gttggtacagGGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
EST: gi|169067448|gb|FE473968.1|FE473968
EST:     CAGAAGCAGTGGCCGATTTTATAGACGAAGACGTGCAACTGATTGTGCTG                         GGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
genomic: CAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTGgtttgtagtt ... gttggtacagGGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
EST: gi|169030301|gb|FE440026.1|FE440026
EST:     CAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTG                         GGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
genomic: CAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTGgtttgtagtt ... gttggtacagGGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
EST: gi|169081218|gb|FE488753.1|FE488753
EST:     CAGAAGCAGTGGCCGATTTTATAGACGAAGACGTGCAACTGATTGTGCTG                         GGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
genomic: CAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTGgtttgtagtt ... gttggtacagGGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
EST: gi|169078316|gb|FE490349.1|FE490349
EST:     ACGAAGACGTGCAACTGATTGTGCTG                         GNGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAA
genomic: ACGAAGACGTGCAACTGATTGTGCTGgtttgtagtt ... gttggtacagG-GTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAA
EST: gi|169047392|gb|FE456225.1|FE456225
EST:     CAGAAGCAGTGGCCGATTTTATAGACGAAGACGTGCAACTGATTGTGCTG                         GGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT
genomic: CAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTGgtttgtagtt ... gttggtacagGGTACCGGGAAGAAAACATATGAAGAGCAGCTGAAGCAGTTGGAAATCAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTGGCTTCATTGGAAGGCTAGAAGAGCAAAAGGGGTCAGACATACTTGCAGAAGCAGTGGCCGATTTTATAAACGAAGACGTGCAACTGATTGTGCTGgtttgtagttttttcatggtatttgcaagcctgcttatgcgtgtgttggtacag

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA