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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcacttacatctgcatgctcttgttatgcaaactcatttgaataggtatatagaactggattagttagtgaataggtattttattgtgtttttgttctatgtctcttatggctacagGACAATCTTTCTGCAATTGATATTCTTTCCGCATGCAACCTTGTGAACTATTTTGGAAAGATGGTTCTTGGTGGTTCTGGTGTTGGCCAGATTACTCTCT

Basic information

species Arabidopsis thaliana
transcript AT5G54260.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G54260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g54340.1 (Oryza sativa), 3'ss of exon 5
gtacatcacttacatctgcatgctcttgttatgcaaactcatttgaataggtatatagaactggattagttagtgaataggtattttattgtgtttttgttctatgtctcttatggctacagGACAATCTTTCTGCAATTGATATTCTTTCCGCATGCAACCTTGTGAACTATTTTGGAAAGATGGTTCTTGGTGGTTCTGGTGTTGGCCAGATTACTCTCT
              | || |   ||| ||| ||  |     ||   || | ||| ||    |    |  |  |||   || | || |  ||  || |||  |     ||||     ||  |||| ||||| ||||||||||||||||| || || ||||| ||||| || |||||||| |||||||  |||||||| |||||||||||  | ||  |  |||
-------------gtatg-agaatctcgttctgacattctgttattatggttat-tatgctta---tgatgggtgc-cagcttttctcatgcattcttgccc-----ctct-----ctgtagGATAATCTCTCTGCAATTGATATTCTCTCAGCCTGCAATCTTGTAAATTATTTTGGGAAGATGGACCTTGGTGGCTCTGGTGTTGGTGAAATAGCAGTCT

upper sequence: AT5G54260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G106056_T03 (Zea mays), 3'ss of exon 5
gtacatcacttacatctgcatgctcttgttatgcaaactcatttgaataggtatatagaactggattagttagtgaataggtattttattgtgtttttgttctatgtctcttatggctacagGACAATCTTTCTGCAATTGATATTCTTTCCGCATGCAACCTTGTGAACTATTTTGGAAAGATGGTTCTTGGTGGTTCTGGTGTTGGCCAGATTACTCTCT
|||      ||   |||  |   ||||   ||   || |   |||  ||  ||||  ||| | |  |      |||||    | ||| ||   || |   | ||| | |||   | ||  |||| ||||| ||||| || ||||||||||| || ||||| ||||| || ||||||||||||||||  |||||||| ||||| ||||| |||||  |  | |
gtatgggtgttgtttct-tactttcttaccatctgaatt---ttgtgtatttatactgaagttgtgtttacgatgaatgccaactttctt---ttatgaatttatatttct---gactgtagGATAATCTCTCTGCTATCGATATTCTTTCGGCTTGCAATCTTGTAAATTATTTTGGAAAGATGGACCTTGGTGGCTCTGGCGTTGGTCAGATAGCAGTTT

upper sequence: AT5G54260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0014g03680.t01 (Vitis vinifera), 3'ss of exon 4
gtacatcacttacatctgcatgctcttgttatgcaaactcatttgaataggtatatagaactggattagttag-tgaataggtattttattgtgtttttgttctatgtctcttatggctacagGACAATCTTTCTGCAATTGATATTCTTTCCGCATGCAACCTTGTGAACTATTTTGGAAAGATGGTTCTTGGTGGTTCTGGTGTTGGCCAGATTACTCTCT
               |||  |   | |  |||  | |     |  | |   |   ||  ||||| ||  |  | ||  |  |||   | | ||||||| || ||     |  | |||  ||||||||| ||||||||  ||||||||||||| |||||||| || |||||||||||||| || ||||||||||| |||||||||||||| || || |||||||
---------------ctgtttttacctaatatatatatatcctccagtt--ttcttaagactggttttttgggatgtgttagtaccat-tagtgttttggtcct-----tactgtggtgacagGACAACCTTTCTGCTGTTGATATTCTTTCGGCATGCAATCTGGTGAACTATTTTGGGAAAATGGTTCTTGGAGGTTCTGGTGTTGGTCAAATCACTCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttagtgaataggtattttattgtgtttttgttctatgtctcttatggctacagGACAATCTTTCTGCAATTGATATTCTTTCCGCATGCAACCTTGTGAACTATTTTGGAAAGATGGTTCTTGGTGGTTCTGGTGTTGGCCAGATTACTCTCT
                                       tctcttat  CT-rich tract
              tattttattgtgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatcacttacatctgcatgctcttgttatgcaaactcatttgaataggtatatagaactggattagttagtgaataggtattttattgtgtttttgttctatgtctcttatggctacagGACAATCTTTCTGCAATTGATATTCTTTCCGCATGCAACCTTGTGAACTATTTTGGAAAGATGGTTCTTGGTGGTTCTGGTGTTGGCCAGATTACTCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG