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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGAACTGCTGTTGGAGCCATTGGAGCTCAAAGTATTGGAGAACCTGGAACGCAGATGACCTTGAAAACTTTTCACTTTGCTGGAGTGGCTAGCATGAgtaagtctctctcgttgttctcttgcctttctaactgcctttgctttcaaag

Basic information

species Selaginella moellendorffii
transcript EFJ24638
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24638 (Selaginella moellendorffii), 5'ss of exon 20
lower sequence: LOC_Os04g41490.1 (Oryza sativa), 5'ss of exon 20
CCTGGAACTGCTGTTGGAGCCATTGGAGCTCAAAGTATTGGAGAACCTGGAACGCAGATGACCTTGAAAACTTTTCACTTTGCTGGAGTGGCTAGCATGAgtaagtctctctcgttgttctcttgcctttctaactgcctttgctttcaaag---------------------------------------------------
 | ||| |  |  |||| || ||||| ||||||||||||||||| |||||||| |||||||| ||||||||||| || ||||| ||||| |||||||||||||  ||        | |    || | |      |||| |||  ||| ||                                                     
GCCGGAGCATCAATTGGGGCAATTGGGGCTCAAAGTATTGGAGAGCCTGGAACTCAGATGACATTGAAAACTTTCCATTTTGCAGGAGTAGCTAGCATGAgta--tcctatatactatatggtt-cgtgaaagtctgcttttaattttaagaattactagcaggtcgttttggcctatttcctataatttatttactttagag

upper sequence: EFJ24638 (Selaginella moellendorffii), 5'ss of exon 20
lower sequence: GRMZM2G178236_T02 (Zea mays), 5'ss of exon 1
CCTGGAACTGCTGTTGGAGCCATTGGAGCTCAAAGTATTGGAGAACCTGGAACGCAGATGACCTTGAAAACTTTTCACTTTGCTGGAGTGGCTAGCATGAgtaag-tctctctcgttgttctctt---gcctttctaactgcctttgctttcaaag--------------------------------------------
 | ||| |  || ||||||| |||||||||||||||||||| || || || || ||||||||  ||||||| ||||| ||||| ||||| |||||||||||||   | | |  || || |           || || | | |  | || || |||                                             
GCAGGAGCATCTATTGGAGCAATTGGAGCTCAAAGTATTGGGGAGCCAGGGACTCAGATGACACTGAAAACATTTCATTTTGCGGGAGTAGCTAGCATGAgtatcctttttaccgctgcttcaggaaaatattactgaattctgtggcatttaaacatgctcaattaagatgcttcattttgtttttcagtttctttttc

upper sequence: EFJ24638 (Selaginella moellendorffii), 5'ss of exon 20
lower sequence: GLYMA11G15530.1 (Glycine max), 5'ss of exon 18
CCTGGAACTGCTGTTGGAGCCATTGGAGCTCAAAGTATTGGAGAACCTGGAACGCAGATGACCTTGAAAACTTTTCACTTTGCTGGAGTGGCTAGCATGAgtaagtctctctcgt---tgttctcttgcctttctaactgcctt---tgctttcaaag-------------------------------------------
 ||||| || ||||||| || | ||||||||| ||||||||||| ||||| || |||||||| ||||||||||| |||||||||||||| || ||||||||||    |   | |    |||| |||  | ||  |||   |       || ||    |                                           
GCTGGAGCTCCTGTTGGTGCAACTGGAGCTCATAGTATTGGAGAGCCTGGGACCCAGATGACTTTGAAAACTTTCCACTTTGCTGGAGTTGCAAGCATGAgtatcctttatttgaccatgttgtct-actttgataatcactaagggggcatttggtgggggataaatttttagtttcctgggaatgttagattggaaatc

upper sequence: EFJ24638 (Selaginella moellendorffii), 5'ss of exon 20
lower sequence: AT5G60040.1 (Arabidopsis thaliana), 5'ss of exon 21
CCTGGAACTGCTGTTGGAGCCATTGGAGCTCAAAGTATTGGAGAACCTGGAACGCAGATGACCTTGAAAACTTTTCACTTTGCTGGAGTGGCTAGCATGAgtaagtctctc-----tcgttgttctcttgccttt-cta-actgcctttgctttcaaag----------------------------------------
 |||| |||||  ||||  | || |||||||| ||||||||||||||||| || || ||||| |||||||||||||||||||||||||| || ||||||||||    | |      |   | || |||    ||  ||| |   |   |||||  | |                                         
GCTGGGACTGCAATTGGGACAATAGGAGCTCAGAGTATTGGAGAACCTGGGACACAAATGACTTTGAAAACTTTTCACTTTGCTGGAGTTGCGAGCATGAgtatccttgttgaaaatgcctattttctgaatttcgctataaaactagtgcttatacatatgagtagttggttgttttgatttcctgattctggttcag

upper sequence: EFJ24638 (Selaginella moellendorffii), 5'ss of exon 20
lower sequence: Vv06s0004g03730.t01 (Vitis vinifera), 5'ss of exon 1
CCTGGAACTGCTGTTGGAGCCATTGGAGCTCAAAGTATTGGAGAACCTGGAACGCAGATGACCTTGAAAACTTTTCACTTTGCTGGAGTGGCTAGCATGAgtaagtctctc-tcgttg---ttctcttg---cctttctaactg---cctttgctttcaaag------------------------------------------------------
 ||||||||||  |||| || ||||||||||| ||||||||||| ||||| || |||||||| || |||||||| ||||||||||| || || ||||||||||    | |   | |||     ||||||   ||||| |  | |   | ||||  |    ||                                                      
GCTGGAACTGCAATTGGTGCAATTGGAGCTCATAGTATTGGAGAGCCTGGGACACAGATGACATTAAAAACTTTCCACTTTGCTGGTGTTGCAAGCATGAgtatccttttaaccattgaaagactcttggcacctttttccccggggcttttgtctattgagtcttctgtattttttttttctggtcaccaatgtggtactttaactctgtattag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGGAACTGCTGTTGGAGCCATTGGAGCTCAAAGTATTGGAGAACCTGGAACGCAGATGACCTTGAAAACTTTTCACTTTGCTGGAGTGGCTAGCATGAgtaagtctctctcgttgttctcttgcctttctaactgcctttgctttcaaag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA