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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAAATGTTCGAGATATATTTGAAAAGgtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttcttcaattgcag

Basic information

species Arabidopsis thaliana
transcript AT1G03000.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G03000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os04g52690.1 (Oryza sativa), 5'ss of exon 10
GACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAAATGTTCGAGATATATTTGAAAAGgtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttct-tcaattgcag
 ||||||||||| ||||| || || |||||||| ||||||||||| || ||||||||| ||||||| || ||||| |||||  | || || ||||| ||||||| ||  ||||   |  || ||  |    ||||    ||   |       || ||||   | |    | |||| ||||   |||
AACAGAGTGCTCTTTAAACTTTCTTAGTGTAAAAGGTCCAGAATTGATTAACATGTATGTTGGAGAATCGGAGAAGAATGTAAGGGACATTTTTGAGAAGgtaaattg-atttacacaaccatacaattgccataagatgtgcatat-----atgcttacggttgcaactcttctgtcaacctcag

upper sequence: AT1G03000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G445617_T01 (Zea mays), 5'ss of exon 10
GACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAAATGTTCGAGATATATTTGAAAAGgta----agttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttcttcaattgcag
 || || ||||| || || || || || || || ||||||||| | || ||||||||| ||||||| ||||||||||||||||| ||||| ||||| ||||||    | ||| |   |    |   |  | ||| | |    ||| |||  ||| | ||   |        |||     |||       
AACTGAATGCTCATTGAACTTTCTTAGCGTCAAAGGTCCAGAACTGATAAACATGTATGTTGGAGAATCAGAGAAAAATGTTCGGGATATTTTTGAGAAGgtacagaatttacacagccatgtaattgtgtgaaacgtgcatagtttttttttcagttttccac-------tgtcaatctcag------

upper sequence: AT1G03000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G058141_T02 (Zea mays), 5'ss of exon 1
GACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAAATGTTCGAGATATATTTGAAAAGgtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttcttcaattgcag
 ||||| ||||| || || || || || || || ||||||||| | || ||||||||| ||||||| ||||||||||||| ||| ||||| ||||| ||||||    | | ||       ||  | |   |  |     ||   |  || |  || ||     ||| |       |||||  |||
AACAGAATGCTCATTGAACTTTCTTAGCGTCAAAGGTCCAGAACTGATAAACATGTATGTTGGAGAATCAGAGAAAAATGGTCGGGATATTTTTGAGAAGgta---cagaatttacacagccatgtaattgtgtgaaacgtgcataattttttttttt---tcagttttccactgtcaatctcag

upper sequence: AT1G03000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA19G39580.1 (Glycine max), 5'ss of exon 10
GACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAAATGTTCGAGATATATTTGAAAAGgta-agttatatttc-----ttcttccctaggaga---agcatattgagtctttggttctgattcttaaactagtgtgttttcttcaattg-cag---------------------------------------
 |||||||||||||||||||| || ||||| || ||||| ||| | ||||||||||| ||||||||||| || || ||||||||||| || ||  | |||||| | | ||||| |     || ||  |||    |     ||  ||||||   ||  | ||   |||    || ||||   |   || ||  |||                                       
TACAGAGTGCTCCTTAAATTTTCTTAGTGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGAATGTTCGAGACATTTTCCAGAAGgtataataatattccggatttttttatctaaataatttctcaatttgagtaaatgtgtttgtgccttt--ttactgtgaactaaacagttttcagaacagattttgataaaatgaacttcaaaataattcacag

upper sequence: AT1G03000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA03G36930.1 (Glycine max), 5'ss of exon 15
GACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAAATGTTCGAGATATATTTGAAAAGgta-agttatatttc---ttcttccctaggagaagcatattgagtct--ttggttctgattcttaaact--agtgtgttttcttcaattgcag-----------------------------------------
                            || || ||||| ||| | ||||||||||| ||||||||||| || || ||||||||||| || ||  | |||||| | | |||||||   |||||   |   |  |   | |  |||    ||   | |  || |    ||    ||||   ||  || ||                                             
---------------------------CGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGAATGTTCGAGACATTTTCCAGAAGgtataataatatttcagtttcttttatctaaataatttctcaagttaaattaaatgtatttgtgtctctttgctgtgaactcaacagtttttagaacagattttgatccaaatgaaattcaaaataattcacag

upper sequence: AT1G03000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 5'ss of exon 10
GACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAAATGTTCGAGATATATTTGAAAAGgtaagttatatttcttcttccctaggagaagcatattgagtct--ttggttctgatt---cttaaactagtgtgtttt----cttcaattgcag
 |||||||||||| | ||||| || |||||||| || || ||| | |||||||||||||| ||||| |||||||||||||||||||| || ||| | |||||||   |||||  |   |   ||| |        ||   |||     ||| || ||   || | | |  ||||   |    | ||  ||| ||
AACAGAGTGCTCCCTCAATTTTCTGAGTGTAAAAGGGCCTGAACTGATCAACATGTATATAGGAGAATCAGAGAAAAATGTTCGAGACATTTTTCAGAAGgtaaag-atattcttatgtgattagaatgccttgttttgctctaacatgttttggttgacctcacaattctgtgacattgggcatcctttgtag

upper sequence: AT1G03000.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S68_6V6.1 (Physcomitrella patens), 5'ss of exon 11
GACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAAATGTTCGAGATATATTTGAAAAGgtaagttat----------atttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtg-tgttttcttcaattgcag----
 || |||||| | || || || || ||||| || ||||| ||  | ||||||||||| ||||||||||||||||| ||||| |||||||||||| |||||||    |||          |  ||| || | | | |        || ||     |  ||     |||| |  ||  | ||  |  |    | |       
CACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGAATGTGCGAGATATATTTCAAAAGgttcagtatttacccagacacatctgctactcaaagtttcatgaatggaaaagctattttgatctctttagttaacgctgactgatcttttcgtgaaagg

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAAATGTTCGAGATATATTTGAAAAGgtaagttatatttcttcttccctaggagaagcatattgagtctttggttctgattcttaaactagtgtgttttcttcaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA