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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatgaatactgactgggttctgtttgattggctcatgcaactcaattgacag

Basic information

species Arabidopsis thaliana
transcript AT2G38840.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g58240.1 (Oryza sativa), 5'ss of exon 7
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatgaatactgactgggttctgtttgattggctcatgcaactcaattgacag
 | |||||||||||||| ||| ||||||| |||||||||||| |||| |||||||| |||||||||||||           | ||| | | ||| || |    |    ||  || ||| | | |  ||| ||    |||      |||      |||| |    |   |||
GTGCGTGAAGCTGATATATCTAGGCTCTCATTTGCTGTTGAGATTGCAGAAGAATTCTATGGAAGgtttg-----------tttgcctctttgtattttcatttgcagtttgct-cctttcttatcactaacaattttcctgaaaattttgatgtgcatcatggtgagcag

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os07g08400.1 (Oryza sativa), 5'ss of exon 7
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatga-atactgactgggttctgtttgattggctcatgcaactcaattgacag
|| |||||||||||||| ||| | ||||| |||||||||||  |||| |||||||| ||||||||||||||    || | |  | | | | ||     |  ||| | | |   ||||||  | |  | || ||    ||     |  |  |          |  | |  |||
ATTCGTGAAGCTGATATATCTAGACTCTCATTTGCTGTTGAAATTGCTGAAGAATTCTATGGAAGgtttgct---ttctgccattcctatttggagcttacaattt-actaagtgcctccttaatgttctaacaaaatttccacttttctgtcggcatttgttgactc-cag

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G305254_T06 (Zea mays), 5'ss of exon 7
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatgaatactgac--tgggttctgtttgattggctcatgcaactcaattgacag------------------------------------------------------------------------------
 | |||||||||||||| ||| |||| || ||||| |||||  |||| ||||| || |||||||||||||| || || |  | ||| |||||||    ||  |||| ||    |   |||  ||| ||| ||  |      | |||  ||   |  ||||  |   |   |||                                                                              
GTACGTGAAGCTGATATATCTAGGCTTTCATTTGCCGTTGAAATTGCTGAAGAGTTCTATGGAAGgtttgctcatttcttttgtgcctttctgt----ttccatataatcattttgatctg-gaacactaacatttatcctttttttgttatatgctgcacttttgtgagcagagtgaaggtaatactccagtttcatgaattataaggctgtaaaataggaacatggatatttttttgatggaaatgctt

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G305254_T04 (Zea mays), 5'ss of exon 7
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatgaatactgac--tgggttctgtttgattggctcatgcaactcaattgacag--------------------------------------------------------------------------------
 | |||||||||||||| ||| |||| || ||||| |||||  |||| ||||| || |||||||||||||| || || |  | ||| |||||||    ||  |||| ||    |   |||  ||| ||| ||  |      | |||  ||   |  ||||  |   |   |||                                                                                
GTACGTGAAGCTGATATATCTAGGCTTTCATTTGCCGTTGAAATTGCTGAAGAGTTCTATGGAAGGtttgctcatttcttttgtgcctttctgt----ttccatataatcattttgatctg-gaacactaacatttatcctttttttgttatatgctgcacttttgtgagcagagtgaaggtaatactccagtttcatgaattataaggctgtaaaataggaacatggatatttttttgatggaaatgcttat

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G305254_T07 (Zea mays), 5'ss of exon 6
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatgaatactgac--tgggttctgtttgattggctcatgcaactcaattgacag-------------------------------------------------------------------------------
 | |||||||||||||| ||| |||| || ||||| |||||  |||| ||||| || |||||||||||||| || || |  | ||| |||||||    ||  |||| ||    |   |||  ||| ||| ||  |      | |||  ||   |  ||||  |   |   |||                                                                               
GTACGTGAAGCTGATATATCTAGGCTTTCATTTGCCGTTGAAATTGCTGAAGAGTTCTATGGAAGgtttgctcatttcttttgtgcctttctgt----ttccatataatcattttgatctg-gaacactaacatttatcctttttttgttatatgctgcacttttgtgagcagagtgaaggtaatactccagtttcatgaattataaggctgtaaaataggaacatggatatttttttgatggaaatgctta

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G019361_T01 (Zea mays), 5'ss of exon 7
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatgaatactgac--tgggttctgtttgattggctcatgcaactcaattgacag--------------------------------------------------------------------------------------
 | |||||||||||||| ||| |||| || |||||  ||||  |||| |||||||| |||||||||||||  || || |    ||| ||||||| | |||    || ||    |   |||  ||| ||| ||  |   |  | |||  ||   |  ||||  |   |   |||                                                                                      
GTACGTGAAGCTGATATATCTAGGCTTTCATTTGCCATTGAAATTGCTGAAGAATTCTATGGAAGGTTTGTTCATtttt--cgtgcctttctgtttggtt----ataatcattttgatctg-gaaaactaacatttattctttttttgttatatgctgcatgtttgtgagcagagtgaaggtaacactgcatttgcgtgacttataagcctgcaataggaacatggatagttttttaatggaaatgcttgtttcttcag

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G019361_T02 (Zea mays), 5'ss of exon 7
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatgaatactgac--tgggttctgtttgattggctcatgcaactcaattgacag------------------------------------------------------------------------------------
 | |||||||||||||| ||| |||| || |||||  ||||  |||| |||||||| |||||||||||||  || || |    ||| ||||||| | |||    || ||    |   |||  ||| ||| ||  |   |  | |||  ||   |  ||||  |   |   |||                                                                                    
GTACGTGAAGCTGATATATCTAGGCTTTCATTTGCCATTGAAATTGCTGAAGAATTCTATGGAAGGTTTGttcattttt--cgtgcctttctgtttggtt----ataatcattttgatctg-gaaaactaacatttattctttttttgttatatgctgcatgtttgtgagcagagtgaaggtaacactgcatttgcgtgacttataagcctgcaataggaacatggatagttttttaatggaaatgcttgtttcttc

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA02G16130.1 (Glycine max), 5'ss of exon 9
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatgaatactgactgggttctgtttg-attggctcatgcaactcaattgacag
|| ||||||||||| || ||||| ||||| ||||| ||||||||||| |||||||||||||| ||||||||    |  |   ||   | | |||      |||||| ||           |    | ||  |    | || ||   ||||  |  |  |||           
ATACGTGAAGCTGACATCTCTCGACTCTCTTTTGCGGTTGAGCTTGCTGAAGAATTTTATGGGAGgtttgcatcttgatgaactttttatttgttaataataatattatcttgaattatcaatgttgctctccttatccttttaatattgctttgtaaaacctct-------

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA10G03660.1 (Glycine max), 5'ss of exon 9
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatgaatactgactgggttctgtttg-attggctcatgcaac-tcaattgacag---------------------------------------------------------------------------------
|| ||||| ||||| || ||||| ||||| ||||| ||||||||||| |||||||||||||| ||||||||    |  |   ||   | | |||      || ||| ||           |    | ||  |    | || ||   ||||  |  |  ||| ||  |||   |                                                                                 
ATACGTGAGGCTGACATCTCTCGACTCTCTTTTGCGGTTGAGCTTGCTGAAGAATTTTATGGGAGgtttgcatcttgatgaactttttatttgttaataatagtattatcttgaattatcaatgttgctctccttatccttttaatattgctttgtaaaacatcttttgggggataaattgtagttattaactttgtttgtttgattcacaaattctgcacatactaaatttgcaactacggtgtgttgaacag

upper sequence: AT2G38840.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv07s0141g00110.t01 (Vitis vinifera), 5'ss of exon 7
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgt---ttaatatgattgcctgcctctatgaatactgactgggtt-ctgtttgattggctcatgcaactcaattgacag-----------------------------
|| |||||||| || ||||||||  | || ||||||||||||||||| |||||||| |||||||||||     | ||  | | ||      | | ||||     | |    ||   | |   |||   | ||   ||      | ||| |||| |      || |   || |||                              
ATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAGgttgctaaatttcaattatgttaccgtattttgtagaccagtcaagttattttcaaatattgcttctttatgcaccatttttttattgccatcactaatttgtttcacattgtgtcttcaaatgttatgtggcaaatag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAGgtttgcccaattgtactctgcatttctgtcttgtttaatatgattgcctgcctctatgaatactgactgggttctgtttgattggctcatgcaactcaattgacag

- - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG