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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtactggtttataatgcttagtcataattttctcttgccctcatagcaatcctaattttacatatgttgtcccatagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC

Basic information

species Arabidopsis thaliana
transcript AT5G60040.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os04g41490.1 (Oryza sativa), 3'ss of exon 10
--gtcagtactggtttataatgct-tagtcataattttctcttgc--cctcatagcaatcctaattttacatatgttgtcccatagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
   | | |     || || |  ||  |  |   |  |     ||   |||||||    |||   |  |   | | ||    || |||| || || ||||| ||||||||  | ||||| ||||| || || ||||||||||||||||||||||||||||| |||||||||||  |||| || || |
gtataaattgctcttcattacactgcacccgctacatgaaaatgttacctcatattggtccct-tgctctttgtatttaatcacagGCTAGGATTATGCCCTGGAGAACACTAAGGTTTAACGAGTCTGTCTGTAACCCATATAATGCTGATTTTGATGGCGATGAGATGAATTTGCATGTTCCTC

upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA11G15530.1 (Glycine max), 3'ss of exon 8
gtcagtactggtttataatgcttagtcataattttctcttgccctcatagcaatcctaattttacatatgttgtcccat--agGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
    ||| |   ||| || |   | |    | ||      |   |     ||||   | |  ||  ||  || || |||  ||||||| || |||||||||||||| || || ||||| ||||| || |||||||||||||||||||| ||||||||||||||||||||| | || || ||||
----gtaatttcttaaaaagtgaaatgtagaattgtgagagattttgatccaattgcattaatatttaatttttcacatacagGCAAGGATTATGCCTTGGAGAACTTTAAGATTCAATGAATCTGTATGTAACCCATATAATGCTGACTTTGATGGTGATGAGATGAACTTACATGTCCCAC

upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv06s0004g03740.t01 (Vitis vinifera), 3'ss of exon 10
---gtcagtactggtttataatgct----tagtcataattttctcttgccctcatagcaatc--ctaattttacatatgttgtcccatagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
    | |  |||| |||  | ||      |||  || ||||    ||    |  || || |    ||| ||| | ||| |   |   |||||  | ||||||||||||||||| |||||||| || ||||| ||||| |||||||||||||| ||||||||||||||||| ||||| ||||| || ||||
gtgattaaaactgattttaagtgtacaaataggtatcatttgaagttctttttttaacatttaattaagttttcttatttatgcatgtagGCGCGGATAATGCCTTGGAGAACATTGAGGTTTAATGAATCAGTTTGCAACCCATATAATGCAGATTTTGATGGTGATGAAATGAATATGCATGTCCCAC

upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S26_192V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------------------------------------------------gtcagtactggtttataatgcttagtcata-attttctcttgccctcatagcaatcctaattttacatatgttgtccc-----atagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
                                                          |  || |  | |  | | ||| | ||  |  || |  | ||| |||    ||  |  || || |    |    | |       | |||||||||| ||||| ||| | ||| |  | || ||||| || ||||||||||| ||||||||||| || || |||||||| |||||  |||| || || |
gtaagatccttattcttttagattacatgataattttaaccttctttggaaatatgctgctag-atggatcaacattgcatcgtactggatgtatttttgtccttcctgccttgttatttctgttaacaccggcttttattacagGCAAGAATTATGCCATGGCGTACGCTTCGATTTAACGAGTCCGTTTGTAACCCGTATAATGCTGACTTCGACGGTGATGAAATGAATCTGCATGTTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataattttctcttgccctcatagcaatcctaattttacatatgttgtcccatagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
                           tcctaat  putative branch site (score: 2)
                                            ttgtccc  putative PPT
                              taattttacatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtactggtttataatgcttagtcataattttctcttgccctcatagcaatcctaattttacatatgttgtcccatagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG