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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtgacatcttttaaggtgctgcttcgtaactaactagctttggttctacag

Basic information

species Selaginella moellendorffii
transcript EFJ20767
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 2
ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtgacatcttttaaggtgctgct-tcgtaactaactagctttggttc--tacag-----------------------------------------
  | || ||||| ||||| || |||||||||||||| |  |||||||||||||| ||| | ||||| |||||||| || |||||||| || || ||||||||  || |    | | ||| |    ||   || | | |  | |  |||  | |  | ||                                          
CTTGACTCATCCTGAGCTATATGAGGACATTGGAATAAGGCCTCCCAAGGGAGTAATATTATATGGGGAACCTGGCACAGGCAAAACTCTACTTGCAAAGgtttgtctctt-tttcttaggacattgaagtcttgaattcccatgtttactccatttcaaattcaattcattaataaactagtaacttaataaatgctagt

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 2
ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtgacatcttttaag---gtgctgcttcgtaactaactagctttggttctacag-------------------------------------------------------------------------------------------------------------------------------
  | || ||||| ||||| || ||||||||||| ||||  ||||| |||||||| ||||| ||||| ||||||||||| || ||||| || || ||||||||  |||     || || | |   || |    |  | | |  |  || || ||| |                                                                                                                                   
CTTAACACATCCTGAGCTATATGAGGACATTGGGATCAGGCCTCCGAAGGGAGTTATACTATATGGGGAACCTGGAACAGGGAAAACTCTACTCGCAAAGgtttgtgctgattccttgaggacagttccaagtttttatttccatgccttagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaacttttgaacgctgtag

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 2
ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtgacatcttttaaggtgctgcttcgtaactaactagctttggttctacag----------------------------------------------------------------------------------------------------------------------------------
  | || ||||| ||| |||| || |||||||| ||||  || ||||||||||| ||| | |||||||||||||||||||| ||||| || || || ||||| ||||      |||  |||           |   |||      || ||  ||  |                                                                                                                                  
CTTGACTCATCCTGAGTTGTATGAAGACATTGGGATCAGGCCACCCAAGGGAGTCATATTATATGGCGAACCTGGAACTGGAAAAACTCTACTCGCCAAGgtcagtgctcaggcttgcaagcatacaagatatctgtaatattgcttagtgttattgggtcaggcttcgatcctcaatgatatttgcctttgtctatgtttatctgaattatgcattatttttttctactctccagttttcaaatagcatgtacttgggcagtgactacttgaaactgtttctgcag

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G056569_T01 (Zea mays), 5'ss of exon 2
ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtgacatcttttaaggtgctgcttcgtaactaactagctttggttctacag------------------------------------------------------------------------------------------------------------------
  | || || || |||||||| || |||||||| || |  |||||||||||||| ||| | ||||| ||||||||||| || ||||| || || || ||||| ||| |    ||||  |||          || | ||  | ||||  ||  | |||                                                                                                                  
CTTGACTCACCCTGAGCTGTATGAAGACATTGGTATTAGGCCTCCCAAGGGAGTCATATTATATGGAGAACCTGGAACAGGAAAAACTCTTCTTGCCAAGgtcagtattctgtcttgcaagtatacaagatgtcaatatattgctt-agtattgcaggggcaggctttgatatctgcctttgtctatgtttatccaaattacactctttttctacttttcagttttcaaatagcatgtacttgggtagtgattacttgaaactgtctgcag

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA19G35510.1 (Glycine max), 5'ss of exon 2
ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaag-------tgtgacatctttta--aggtgctgcttcgtaa--ctaac-tagctttggttctacag-------------------------------
 || |||||||| || ||||| || |||||||| ||||| ||||| |||||||| ||  | || ||||||||||||||||| || ||| | || || |||||  |       || |   |||| ||   || | ||     |||  || || |   |||  |||  ||                                
CCTGACGCATCCTGAACTGTATGAAGACATTGGTATCAAGCCTCCTAAGGGAGTCATTTTATACGGCGAACCTGGAACTGGGAAGACGTTGCTAGCTAAGgtgtgcattttttggggtttcttatatggggcgatggaatataatcctgacatgttttttattcctcattttctctgtttaataacatggagtttgaaat

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 5'ss of exon 2
ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtg-acat----cttttaaggtgctgcttcgtaactaactagctttggttctacag--------------------------------------
 || || ||||| || ||||| ||||||||||| ||||| ||||| ||||| || ||||| ||||| || |||||||| || || ||  | || ||||||||  || |  | ||     |  ||     ||| | | | || |  || ||    || || |                                       
TCTAACACATCCTGAACTGTATGAGGACATTGGTATCAAGCCTCCTAAGGGGGTCATACTATATGGAGAGCCTGGAACAGGAAAGACCTTGCTTGCAAAGgtgtgtattcatatttgcttcctatcaaactggtgcattacaatttatctgccattttatatctctgattgtgccatcctctttttcctttcattttggt

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 2
ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtg----tgacatcttttaaggtgctgc--ttcgtaactaactagctt-tggttctacag------------------------------------
  | || ||||| |||||||| || |||||||| ||||| || ||||||||||| ||  | ||||| ||||| || ||||| ||||| || || || ||||||| |     || ||     | || |  ||   ||| | |||  ||| ||| |   | |||||                                    
GTTGACACATCCGGAGCTGTATGAAGACATTGGTATCAAGCCCCCCAAGGGAGTTATTTTGTATGGTGAACCCGGCACTGGGAAAACTCTTCTTGCTAAGgtaaatacgtttggcaaagggtgagatcatgtaattcttgacttgctaccttgtctctgtacagagaagttctgctttgctaacaaggtgacctttgttg

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|169060660|gb|FE467398.1|FE467398
EST:     GAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAG                         GCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAG
genomic: GAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtga ... ggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAG
EST: gi|169040853|gb|FE447904.1|FE447904
EST:     AGTGATACTTTATGGCGAACCTGGTACTGGCAAAACGCTCCTGGGCAA-G                         GCTGTTGCAAACTCCACATCTGCAAACGT-CTTGCGTGTTGTTGGCAGCG
genomic: AGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGG-CAAAGgtaagtgtga ... ggttctacagGCTGTTGCAAACTCCACATCTGCAA-CGTTCTTGCGTGTTGTTGGCAGCG
EST: gi|169034211|gb|FE445051.1|FE445051
EST:     GAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAG                         GCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAG
genomic: GAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtga ... ggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAG
EST: gi|169060659|gb|FE467397.1|FE467397
EST:     GGAACTGGCAAAACGCTCCTGGCAAAG                         GCTG-TGNCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGA
genomic: GGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtga ... ggttctacagGCTGTTG-CAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGA
EST: gi|169065782|gb|FE474372.1|FE474372
EST:     GAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAG                         GCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAG
genomic: GAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtga ... ggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 24 (downstream exon)
Score: 27

ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtga ... ggttctacagGCTGTTGCAAACTCCACATCTGCAACGTTCTTGCGTGTTGTTGGCAGCGAGCTTATTCAAAAGTATTTGGGAGACGGTCCTAAGCTTGTTAGGGAGCTCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTACGCATCCAGAGCTGTACGAGGACATTGGAATCAAACCTCCCAAGGGAGTGATACTTTATGGCGAACCTGGAACTGGCAAAACGCTCCTGGCAAAGgtaagtgtgacatcttttaaggtgctgcttcgtaactaactagctttggttctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG