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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttccttgttttcgaatgcacctcatttttatttttttattgattcgatgcttgtagtattttgagttccggatggcagtgagtgtgtgaactgagtttgtgacaaattgtcttatttcagGCGGCTCGTGCTTTGGCTAATCTAGCTGCTCATGGTGATAGCAACGGTAATAATGCTGCTGTTGGACAAGAGGCTGGTGCATTGGAAGCTCTTGTTCAGC

Basic information

species Arabidopsis thaliana
transcript AT3G60350.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G48840.1 (Glycine max), 3'ss of exon 4
gtatttccttgttttcgaatgcacctcatt-tttatttttttattgattcgatgcttgtagtattttgagttccggatggcagtgagtgtgtgaactgagtttgtgacaa--attgtcttatttcagGCGGCTCGTGCTTTGGCTAATCTAGCTGCTCATGGTGATAGCAACGGTAATAATGCTGCTGTTGGACAAGAGGCTGGTGCATTGGAAGCTCTTGTTCAGC
                         | ||| || | || | | ||  ||| |  |||||    | |  | |   |||||  ||||| |  ||  |    | ||   | ||  | |||   || |||||| |||||||| ||||||||  ||||||| ||||| ||||| ||| |||| ||||| |||||||||||||| || |||||  | || ||||| ||||| |
-------------------------tgattcttcagttgtatgttttttcaaatcttgt--cctctccattgagggatgtaagtgaattggtctaggatgattaacataactactgttaaatatcagGCTGCTCGTGCATTGGCTAACTTAGCTGCCCATGGAGATAGTAACAGTAACAATGCCGCTGTTGGACAAGAAGCAGGTGCTCTTGATGCTCTCGTTCAAC

upper sequence: AT3G60350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 5
gtatttccttgttttcgaatgcacctcatttttatttttttattgattcgatgcttgtagtattttgagttccggatggcagtgagtgtgtgaactgagtt-tgtgacaaattgtcttatttcagGCGGCTCGTGCTTTGGCTAATCTAGCTGCTCATGGTGATAGCAACGGTAATAATGCTGCTGTTGGACAAGAGGCTGGTGCATTGGAAGCTCTTGTTCAGC
                       | ||| || ||| |||||    ||    | ||      |||  | | | |  |||  | |  ||||| ||  ||| |    | || |  | |   |  |||||| ||||| || ||||||||  ||||||| ||||| ||||| ||| |||| |||||||| ||||||||||| || |||||  | || ||||||||||| |
------------------tgattcttcagttgtatgttttttaaaatcttgtcctctc--cattgagggatgcacatg--aattggtgtggga--tgattaacataactacct-ttaaacatcagGCTGCTCGGGCATTGGCTAACTTAGCTGCCCATGGAGATAGTAACAGTAACAATGCTGCCGTTGGACAAGAAGCAGGTGCCCTTGAGGCTCTTGTTCAAC

upper sequence: AT3G60350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0021g01810.t01 (Vitis vinifera), 3'ss of exon 5
gtatttccttgttttcgaatgcacctcatttttatttttttattgattcgatgcttgtagtattttgagttccggatggcagtgagtgtgtgaactgagt-ttgtgacaaattgtcttatttcagGCGGCTCGTGCTTTGGCTAATCTAGCTGCTCATGGTGATAGCAACGGTAATAATGCTGCTGTTGGACAAGAGGCTGGTGCATTGGAAGCTCTTGTTCAGC
                     || ||    |||     | | |||  |  |   | | |  || |||  |    ||  |   |  || ||  || | | | | |||||   |      ||  ||||| || ||||| ||||||||| | ||||||||||| ||||||||| | || ||||||||||||||||||||||| |||||| | ||||| ||||| |  |
---------------------cagcttgcatttgcacatgt-ttgtgtttacattagca-catattgtatatatga-agtgatctgt-tgctaattaattgtcgtgacttctgagtacataccagGCTGCACGTGCCTTGGCTAATTTGGCTGCTCATGGAGATAGCAACAGCAACAATGCTGCTGTTGGACAAGAGGCAGGTGCACTTGAAGCACTTGTGCTAC

upper sequence: AT3G60350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S13_130V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------gtatttccttgttttcgaat--gcacctcatttttatttttttattg---attcgatgcttgtagtattttgagttcc--ggatggcagtgagtg--tgtgaactgagtttgtgacaaattgtcttatttcagGCGGCTCGTGCTTTGGCTAATCTAGCTGCTCATGGTGATAGCAACGGTAATAATGCTGCTGTTGGACAAGAGGCTGGTGCATTGGAAGCTCTTGTTCAGC
                     |  ||   || || ||||  |    |  ||||  |   |    ||    | |   | |||||     |  ||||    |||  ||     |||  | | |    || |  ||| |   ||  |  || ||||| || || || ||||| ||||| ||  ||||||| || ||||||||||||||||||||||| || |  ||||| || ||| | |||||||| || |  |
gtgcggggcaatcagactctgaggtcgcggtgttggaatcggagtttggttttcgtggatgaggtgcacgtccagaggttgtatgggctgtagtttttgggagagcttgtggtggttctcagtacaggtcttgaaatcgtgattgtttgcagGCAGCGCGCGCCTTGGCCAATCTCGCCACTCATGGAGACAGCAACGGTAATAATGCTGCTGTGGGGCGGGAGGCAGGCGCACTTGAAGCTCTCGTGCGCC

upper sequence: AT3G60350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ24586 (Selaginella moellendorffii), 3'ss of exon 4
gtatttccttgttttcgaatgcacctcatttttatttttttattgattcgatgcttgtagtattttgagttccggatggcagtgagtgtgtgaactgagtttgtgacaaattgtcttatttcagGCGGCTCGTGCTTTGGCTAATCTAGCTGCTCATGGTGATAGCAACGGTAATAATGCTGCTGTTGGACAAGAGGCTGGTGCATTGGAAGCTCTTGTTCAGC
                                                                         | ||     |   | |||   ||||  |  | ||    |   |  || ||||| || || ||  | || |||||||| ||||| ||||||||||| || ||||||||||| || || |  ||||| ||||| || || || || ||  || 
----------------------------------------------------------------------gtagaattttcttacatttgtatgctga--tcataactccctaattctttgcagGCTGCCCGAGCGCTTGCAAATCTAGCAGCTCACGGTGATAGCAATGGGAATAATGCTGCAGTAGGGCGGGAGGCGGGTGCGTTAGAGGCGCTGGTAAAGT

upper sequence: AT3G60350.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ24022 (Selaginella moellendorffii), 3'ss of exon 4
gtatttccttgttttcgaatgcacctcatttttatttttttattgattcgatgcttgtagtattttgagttccggatggcagtgagtgtgtgaactgagtttgtgacaaattgtcttatttcagGCGGCTCGTGCTTTGGCTAATCTAGCTGCTCATGGTGATAGCAACGGTAATAATGCTGCTGTTGGACAAGAGGCTGGTGCATTGGAAGCTCTTGTTCAGC
                                                                         | ||     |   | |||   ||||  |  | ||    |  ||  || ||||| || || ||  | || |||||||| ||||| ||||||||||| || ||||||||||| || || |  ||||| ||||| || || || || ||  || 
----------------------------------------------------------------------gtagaattttcttacatttgtctgctga--tcataactccctaactctttgcagGCTGCCCGAGCGCTTGCAAATCTAGCAGCTCACGGTGATAGCAATGGGAATAATGCTGCAGTAGGGCGGGAGGCGGGTGCGTTAGAGGCGCTGGTAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccggatggcagtgagtgtgtgaactgagtttgtgacaaattgtcttatttcagGCGGCTCGTGCTTTGGCTAATCTAGCTGCTCATGGTGATAGCAACGGTAATAATGCTGCTGTTGGACAAGAGGCTGGTGCATTGGAAGCTCTTGTTCAGC
                                            tcttatttc  CT-rich tract
                                      aaattgtcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttccttgttttcgaatgcacctcatttttatttttttattgattcgatgcttgtagtattttgagttccggatggcagtgagtgtgtgaactgagtttgtgacaaattgtcttatttcagGCGGCTCGTGCTTTGGCTAATCTAGCTGCTCATGGTGATAGCAACGGTAATAATGCTGCTGTTGGACAAGAGGCTGGTGCATTGGAAGCTCTTGTTCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG