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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgtggtgcactcttgatacttgcaacatactaaactatgaaaggactttactgaatatatgtggcgtaagcactggaagagttatgaatcaactaacttgttgaataatttgacctgatgttatatagaatgaagaatctttttcccaccgtattaatatcaatagtcttttaatttttatttgcagGGAGCAGTAAATTTTGCATTAATGATGTCTCAAATGGAAGGAGGTTCTCCAGTTGACTACAACACCATCACTGATCTTTTTCTTCAG

Basic information

species Arabidopsis thaliana
transcript AT3G08530.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 12
gttagtgtggtgcactcttgatacttgcaacatactaaactatgaaaggactttactgaatatatgtggcgtaagcactggaagagttatgaatcaactaacttgttgaataatttgacctgatgttatatagaatgaagaatctttttcccaccgtattaata-tcaatagtcttttaatttttattt---gcagGGAGCAGTAAATTTTGCATTAATGATGTCTCAAATGGAAGGAGGTTCTCCAGTTGACTACAACACCATCACTGATCTTTTTCTTCAG
                                                                                 |   |||||   | | | ||||||  |  |||| |||   | | ||   | |  ||    || ||| |   | |  |  |||  |   |    | | ||||| ||| |    |||||||| || || |||||||| |||||||| |||||||| ||||||| |||||| ||||||||||| ||||||||||| || ||||||
------------------------------------------------------------------------------gtaattggttattt-taagcaaacttgg-gcttaatgtga---ggtattcatttgtttggtacatgtttcttttatctcagaaatccttgcttcattgtcaatttgtatcttgaccagGGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 14
gttagtgtggtgcactcttgatacttgcaacatactaaactatgaaaggactttactgaatatatgtggcgtaagcactggaagagttatgaatcaactaacttgttgaataatttgacctgatgttatatagaatgaaga-atctttttcccaccgtattaatatcaatagtcttttaatttttatttgcagGGAGCAGTAAATTTTGCATTAATGATGTCTCAAATGGAAGGAGGTTCTCCAGTTGACTACAACACCATCACTGATCTTTTTCTTCAG
    ||| |    ||   ||    |   |  ||  |    | ||||    ||  ||    | | ||| ||     | |   |     |  |       ||  |   ||  ||| | |   |  | ||  | || ||    | ||    ||  ||  || |    |    ||   |||| ||||| |||||||||| || || ||||||||||||||||||||||||||||| ||||||   |||||||| |||||||| || |||||||| |||||||||
--gtgtgagagaaacctctgcagttcatacaatttttttatttgaac---ctgaaccatttctttgtagct----ccccttattgtctgcgtccttgttatatctgtgg-taact-gtttttgttttgaacagtatatgtacattaagttgacaatgtctgctgacagttaccattttcattttgatttgcagGGCGCTGTTAATTTTGCATTAATGATGTCTCAAATGGAGGGAGGTAGCCCAGTTGATTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 14
gttagtgtggtgcactcttgatacttgcaacatactaaactatgaaaggactttactgaatatatgtggcgtaagcactggaagagttatgaatcaactaacttgttgaataatttgacctgatgttatatagaatgaagaatctttttcccaccgtattaatatcaatagtcttttaatttttatttgcagGGAGCAGTAAATTTTGCATTAATGATGTCTCAAATGGAAGGAGGTTCTCCAGTTGACTACAACACCATCACTGATCTTTTTCTTCAG
                                        | ||| || |   |    | | ||| |    |||    |  |   |||     | ||| |  |  |||  ||  |   ||| ||  | | |    |    |    | ||  ||  || |    |    ||   |||| ||||| |||||||||| || || ||||||||||||||||||||||||||||| ||||||   |||||||| |||||||| || |||||||| |||||||||
---------------------------------------gtgtgagagaaacctctgcagtttatattatataattttttta---gttgaacctgaaccatttctttg--tagctcc-ccttattctctgtctccttgttatatctgttgacaatgtctgctgacagttaccattttcattttgatttgcagGGCGCTGTTAATTTTGCATTAATGATGTCTCAAATGGAGGGAGGTAGCCCAGTTGATTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 14
gttagtgtg-gtgcactcttgatacttgcaacatactaaactatgaaaggact----ttactgaatata-tgtggcgtaagcactggaagagttatgaatcaactaacttgttgaataatttgacctgatgttatatagaat-gaagaatctttttcccaccgtattaatatcaatag-----tcttttaatttttatttgcagGGAGCAGTAAATTTTGCATTAATGATGTCTCAAATGGAAGGAGGTTCTCCAGTTGACTACAACACCATCACTGATCTTTTTCTTCAG
    || || | | |  ||   || ||   |   ||||     |   |   ||    ||       | | ||| |  |||    |     | ||||  ||   || || ||   |||  | | ||   || | || |  | | | ||||  |  |         |   |  |||| |      | |||| |||||  |||  |||| || || |||||||||||||||||||| |||||||| |||||||  |||||||| ||||||||||| |||||||| |||||||||
----gtatgagagaatcctctgtagttcatattaactatttctttgtatttctcccattgtctgccacactgttggataattgattatcaaattatatattttctgacatgg-aaattctataact--atttcatctcaatttgcagaaattaatagttgtaaaaactaattcaacaactttcttttttcattttggtttctagGGTGCTGTTAATTTTGCATTAATGATGTCGCAAATGGAGGGAGGTTGCCCAGTTGATTACAACACCATAACTGATCTGTTTCTTCAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 14
gttagtgtggtgcactcttgatacttgcaacatactaaactatgaaaggactttactgaatatatgtggcgtaagcactggaagagttatgaatcaactaacttgttgaataatttgacctgatgttatatagaatgaagaatctttttcccaccgtattaatatcaatagtcttttaatttttatttgcagGGAGCAGTAAATTTTGCATTAATGATGTCTCAAATGGAAGGAGGTTCTCCAGTTGACTACAACACCATCACTGATCTTTTTCTTCAG
                                                                                    |  |   |||    |||||  ||   |  ||| | || |  ||  | | | | |    | | |   | |    |  ||  |        |||| |||||  |||  |||| || || |||||||||||||||||||| |||||||| |||||||  |||||||| ||||||||||| |||||||| |||||||||
------------------------------------------------------------------------------------acatggaaattctataactattt---ttttttcatctcaatttgcagaaattaatagttgtataaactaattcaagaacttt-----ctttttcattttggtttctagGGTGCTGTTAATTTTGCATTAATGATGTCGCAAATGGAGGGAGGTTGCCCAGTTGATTACAACACCATAACTGATCTGTTTCTTCAG

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 14
gttagtgtggtgcactcttgatacttgcaacatactaaactatgaaaggactttactgaatatatgtggcgtaagcactggaagagttatgaatcaactaacttgttgaataatttgacctgatgttatatagaatgaagaatctttttcccaccgtattaatatcaatagtcttttaatttttatttgcagGGAGCAGTAAATTTTGCATTAATGATGTCTCAAATGGAAGGAGGTTCTCCAGTTGACTACAACACCATCACTGATCTTTTTCTTCAG
                                        |||| |||   ||| || | | | ||  |  |   |          ||||||   || |   ||   |||    |   | | |  ||    | | || | ||  |||| |  |  | |            | | |||| ||||   ||||||||||| |||||||||||  ||||||||||||||||||| ||||||| |||  |||| |  || || || |||||||| |||||||||
---------------------------------------gtatgcaagcctttttct-agtgtttgcagattttcctt--------ttatga---aattg--ttccagaaaggatcagcttaaattt---caaattggataaaattttcctgagtgga------------ggcatttatttttgggttgcagGGAGCTGTAAATTTTGCGCTAATGATGTCTCAAATGGAGGGAGGTTGTCCCATTGATTTTAATACGATAACTGATCTCTTTCTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaatctttttcccaccgtattaatatcaatagtcttttaatttttatttgcagGGAGCAGTAAATTTTGCATTAATGATGTCTCAAATGGAAGGAGGTTCTCCAGTTGACTACAACACCATCACTGATCTTTTTCTTCAG
                                          tttttattt  CT-rich tract
                   tattaatatcaatagt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgtggtgcactcttgatacttgcaacatactaaactatgaaaggactttactgaatatatgtggcgtaagcactggaagagttatgaatcaactaacttgttgaataatttgacctgatgttatatagaatgaagaatctttttcccaccgtattaatatcaatagtcttttaatttttatttgcagGGAGCAGTAAATTTTGCATTAATGATGTCTCAAATGGAAGGAGGTTCTCCAGTTGACTACAACACCATCACTGATCTTTTTCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG