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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttgtgcag

Basic information

species Arabidopsis thaliana
transcript AT3G11130.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 17
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttg-tgcag
 |||||||| ||| | || ||||| |||||||| |||||||| || ||||||||||||||||||||||||||||||||  | ||| | | | || |  ||||       || |  ||| ||   |  | ||||  || |   | | |||| ||| ||  |||   |   |  | || |  | || |||||
TGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGCTTGTACTTGCGAGCTCTCCAGgt-------cagtaccttttt--gttgttttggtttactt--ttttttttctttgcctgtctgtttaattaacattatattgtgatgcag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 17
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttg-tgcag
 |||||||| ||| | || ||||| |||||||| |||||||| || ||||||||||||||||||||||||||||||||  | ||| | | | || |  ||||       || |  ||| ||   |  | ||||  || |   | | |||| ||| ||  |||   |   |  | || |  | || |||||
TGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGCTTGTACTTGCGAGCTCTCCAGgt-------cagtaccttttt--gttgttttggtttact---ttttttttctttgcctgtctgtttaattaacattatattgtgatgcag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 15
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttgtgcag
 || ||||| ||  | || ||||| |||||||| ||||||||||| |||||| |||||||||| ||||||||||||||| | ||| | |   |  |  ||||       |  |  | | |  | | || | |  || ||   |    |||  | ||     |||     | || | ||   |  |||||
TGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCTGTGAAAAGGCTGGATTATACTTGCGTGCCCTCCAGgt-------cggtaacctttgcattgttttgg--ctgatctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 3
-----------------------------------GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttgtgcag
                                    | |||||| ||  | || ||||| |||||||| |||||||| || |||||| ||||| |||| ||||||||||||||  | ||| | | |                                                                                                  
GTTTTGGAGATAAACTTAGTGACTTACCCAAATGTTGTTGATGCCATTCTTGCTAATGgtatgttcagtcattatgatcgccctcgtattgcttagctgtgtgaaaaggctgggttgtacttgcgag-------------------------------------------------------------------------------------------------

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GRMZM2G591258_T01 (Zea mays), 5'ss of exon 9
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgct----caatgtcttctttaatattcttggcctaatagatgtattt------ttttttcccctctaacttcgtttccttttgctttgtgcag--
                                  |||||||| || |||||| |||||||||| ||||||||||||||  | ||| | | | |  |  ||||   | |     || ||       | |||| ||  || |  ||    | |||        ||      | |||    |  |   |  |  ||  | |   
---------------------------------TCATTATGATCGCCCTCGTATTGCTCAGCTGTGTGAAAAGGCTGGGTTGTACTTGCGAGCCCTCCAGgtcagtaccttcgcattggtgcagctgatat-ctccgcttcgtattcttgtttaactaaccttacattttgtaatgcagcatttgtcggtgtttcgaaacc

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 16
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctca--atgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaac-ttcgtttccttttgctttgtgcag
 ||||||||||| || || ||||| |||||||||||||||||||| |||||| ||||||| ||||||||||| ||||| |||||  | | | ||||  | ||  |  ||||  |  | |  |||| ||||  |||  |  |   |  |         |  ||||     |  || |  | |  || ||||||
TGCTGATGCAATTTTGGCTAATGGAATGTTCAGCCATTATGACCGTCCTCGTATTGCTCAACTTTGTGAAAAAGCTGGTCTTTATGTGCGAGCTTTGCAAgtaatgactcaccaaatgtgttttattattactggttttcttatttaacccaaaagccttctcttttactgattacactatttttggtgcag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 16
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctca--atgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaac-ttcgtttccttttgctttgtgcag
 ||||||||||| || || ||||| |||||||||||||||||||| |||||| ||||||| ||||||||||| ||||| |||||  | | ||||||  | ||  |  ||||  |  | |  |||| | ||  |||  |  |   |  |         |  ||||    ||  || | || |  || ||||||
TGCTGATGCAATTTTGGCTAATGGAATGTTCAGCCATTATGACCGTCCTCGTATTGCTCAACTTTGTGAAAAAGCTGGTCTTTATGTGCGATCTTTGCAAgtaatgactcaccaaatgtgttttattcttactggttttcttatttaacccaaaggccttctcttttattgattacattatttttggtgcag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA14G06340.2 (Glycine max), 5'ss of exon 17
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctcaatgtcttctttaatattcttg-gcctaatagatgtattttttt---ttcccctctaacttcgtttccttttgctttgtgcag
 ||||||||||| || || ||||| |||||||||||||||||||| |||||| |||| || ||||||||||| ||||| |||||  | | | ||||  | ||     |||      |   ||  ||||||||  | |  |  ||||   | ||    |    | || | ||  || | || | ||| ||||||
TGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAACTTTGTGAAAAAGCTGGCCTTTATGTGCGAGCTTTGCAAgtaaggactctccaaatgtgttt-tattcttgcactttctctatgttaatcttaaaatcaaacccttaattgattgcattattcttggtgcag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 17
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtt----tttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttgtgcag
 ||||||||||| || || ||||| |||||||||||||||||||| |||||| |||| |||||||| ||||| || || |||||  | | | ||||  | ||      |  |  ||||| || | |  |     |  |   ||    || ||    |    ||  |   ||  || | || | ||| ||||||
TGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAGCTTTGCGAAAAAGCGGGCCTTTATGTGCGAGCTTTGCAAgtaaggactctccaaatgtgttttattctcgcactttctctatgttagtcttaaagtcaaaccctttg-ttgattgcattattcttggtgcag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 17
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtt-------tttgctcaatgtcttctttaatattcttggccta----atagatgtatt---tttttttcccctctaacttcgtttccttttgctttgtgcag
 || ||||| || ||||||||||||||||| ||||||||||| || || ||  |||| |||||||||||||| ||||| |||||  | | | |  |  ||||        ||    ||||   || | |  |||| ||  |||     || | |  ||    ||  ||   | |||   ||      ||| |  |||||||||
TGCAGATGCTATATTAGCAAATGGGATGTTTAGCCATTATGATCGTCCACGGATTGCCCAGCTTTGTGAAAAAGCTGGTCTTTATGTGCGAGCCCTTCAGgtgaaattggttcttgcaattcattttattttattttttaccttttttattgttacatgaaattaattatacgtcttggttaaaacacttatattttgtgcag

upper sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: PP1S270_53V6.1 (Physcomitrella patens), 5'ss of exon 17
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcg--tttccttttgctttgtgcag-------------------------------------------------
 || ||||| || ||  | ||||| || ||||  ||||||||||| |||||  |||||||||||||||| ||||||||  | || || |   || |  ||||||      |||    |   || | |  | | | |  || |      ||||| ||| ||  ||||       || | | |  ||| |||                                                  
CGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTTGTGAGAAGGCTGGCGTGTATATGCGTGCTATGCAGgtttaga---aattcgcttgctagtgtaat-gacattttataccatactttttatccgctgcaactataaacctcgtctagaattgagcataactactttacacgacttaaatcgccgcgttgatgttttatcacttcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGACTTTACATCCAATCTTTAAAGgtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA