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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGGACTGCAATTGGGACAATAGGAGCTCAGAGTATTGGAGAACCTGGGACACAAATGACTTTGAAAACTTTTCACTTTGCTGGAGTTGCGAGCATGAgtatccttgttgaaaatgcctattttctgaatttcgctataaaactagtgcttatacatatgagtagttggttgttttgatttcctgattctggttcag

Basic information

species Arabidopsis thaliana
transcript AT5G60040.2
intron # 21
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G60040.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: LOC_Os04g41490.1 (Oryza sativa), 5'ss of exon 20
GCTGGGACTGCAATTGGGACAATAGGAGCTCAGAGTATTGGAGAACCTGGGACACAAATGACTTTGAAAACTTTTCACTTTGCTGGAGTTGCGAGCATGAgtatccttgttgaaaatgcctattttctgaatttcgctataaaactagtgcttatacatatgagtagttggttgttttgatttcctgattctggttcag--
|| ||  |  |||||||| |||| || ||||| ||||||||||| ||||| || || ||||| ||||||||||| || ||||| ||||| || ||||||||||||||  |  |  ||     |  |   | | |   | |||   ||    |||     | |     ||||    |||  | |  |   | |  || ||  
GCCGGAGCATCAATTGGGGCAATTGGGGCTCAAAGTATTGGAGAGCCTGGAACTCAGATGACATTGAAAACTTTCCATTTTGCAGGAGTAGCTAGCATGAgtatcct-atatactatatggttcgtgaaagtctgcttttaattttaagaattactagcaggtcgttttggcctatttcctataatttatttactttagag

upper sequence: AT5G60040.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G178236_T02 (Zea mays), 5'ss of exon 1
GCTGGGACTGCAATTGGGACAATAGGAGCTCAGAGTATTGGAGAACCTGGGACACAAATGACTTTGAAAACTTTTCACTTTGCTGGAGTTGCGAGCATGAgtatccttgttgaaaatgcctattttctgaatttcgctataaaactagtgcttatacatatgagtagttgg------ttgttttgatttcctgattctggttcag
|| ||  |  | |||||  |||| |||||||| |||||||| || || ||||| || |||||  ||||||| ||||| ||||| ||||| || ||||||||||||||| ||     ||| |        ||| |  ||  ||  ||   || | || | |||   | ||        |  ||||| ||| | | ||||  |||  
GCAGGAGCATCTATTGGAGCAATTGGAGCTCAAAGTATTGGGGAGCCAGGGACTCAGATGACACTGAAAACATTTCATTTTGCGGGAGTAGCTAGCATGAgtatcctttttaccgctgctt--caggaaaatattactg-aattctgtggcatttaaacatgctcaattaagatgcttcattttgtttttcagtttctttttc--

upper sequence: AT5G60040.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA11G15530.1 (Glycine max), 5'ss of exon 18
GCTGGGACTGCAATTGGGACAATAGGAGCTCAGAGTATTGGAGAACCTGGGACACAAATGACTTTGAAAACTTTTCACTTTGCTGGAGTTGCGAGCATGAgtatccttg--ttgaaaatgcc-tattttctgaatttcgctataaaactagtgcttatacatatgagtagttggttgttttg-atttcctgattctggttcag
|||||  || |  ||||  |||  |||||||| ||||||||||| |||||||| || ||||||||||||||||| ||||||||||||||||| |||||||||||||||   ||||  |||   | |  | |||   || |||       | |   |      || | |  || |||   | | | |    ||||     ||  
GCTGGAGCTCCTGTTGGTGCAACTGGAGCTCATAGTATTGGAGAGCCTGGGACCCAGATGACTTTGAAAACTTTCCACTTTGCTGGAGTTGCAAGCATGAgtatcctttatttgaccatgttgtctactttgataatcactaagggggcatttggtggggg-ataaatttttagtttcctgggaatgttagattggaaatc--

upper sequence: AT5G60040.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: EFJ13293 (Selaginella moellendorffii), 5'ss of exon 20
GCTGGGACTGCAATTGGGACAATAGGAGCTCAGAGTATTGGAGAACCTGGGACACAAATGACTTTGAAAACTTTTCACTTTGCTGGAGTTGCGAGCATGAgtatccttgttgaaaatgcctattttctgaatttcgctataaaactagtgcttatacatatgagtagttggttgttttgatttcctgattctggttcag
 |||| |||||  ||||  | || |||||||| ||||||||||||||||| || || ||||| |||||||||||||||||||||||||| || ||||||||||    | |      |   | || |||    ||  ||| |   |   |||||  | |                                         
CCTGGAACTGCTGTTGGAGCCATTGGAGCTCAAAGTATTGGAGAACCTGGAACGCAGATGACCTTGAAAACTTTTCACTTTGCTGGAGTGGCTAGCATGAgtaagtctctc-----tcgttgttctctcgccttt-cta-actgcctttgctttcaaag----------------------------------------

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

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGGACTGCAATTGGGACAATAGGAGCTCAGAGTATTGGAGAACCTGGGACACAAATGACTTTGAAAACTTTTCACTTTGCTGGAGTTGCGAGCATGAgtatccttgttgaaaatgcctattttctgaatttcgctataaaactagtgcttatacatatgagtagttggttgttttgatttcctgattctggttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA