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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgtatgaaggaagggcatcattatatgtcttttatgccactcacttatactcctcacgaatcatgcatattgctacgtcttttggacatccttttctgattttccttgacctgtcttgtcgttcag

Basic information

species Arabidopsis thaliana
transcript AT4G26570.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 5'ss of exon 3
TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgtatgaaggaagggcatcattatatgtc----ttttatgccactcacttatactc--ctcac-gaatcatgcatattgctacgtc-ttttggacat-----ccttttctgattttccttgacctgtcttgtcgttcag
| |||||||| ||  | ||||| || || ||||| || ||||| || |||||||||||||||||||| ||||| || |||||||| ||  |    | | ||  |    | |    |||| |  |    | ||    |    | |  |  | ||  ||   |  | ||  || || || |     |  |  |||| | |  ||| ||  |    | || |||
TCAGCGTGAGCGAGGTCGAGGCGCTGTACGAGCTCTTCAAGAAGATAAGCAGTGCTGTGATTGATGACGGGCTGATTAACAAGgt-tggtgtggagtcctctgttcgcgccacgattttgtatcgtagaattgggattgattgattggttgattgatgaaggcatgttattgtgaacctgtatgcaatcactgactgtgtttgtccgttgaccttgtgcag

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G112672_T02 (Zea mays), 5'ss of exon 2
TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgt--atgaaggaagggcatcattatatgtcttttatgccactc-----acttatactcctcacgaatcatgcatattgctacgtcttttggacatccttttc-tgattttcct---tgacctgtcttgtcgttcag-------------------
|||||||||| ||  | |||||  | ||||| ||||| ||||| ||||||||||||||||||||||||||||| || ||||||||   ||   ||  |       | | | |||||| | |   |      |   ||||  ||  |      |   |||    ||         ||| | |   | ||||  |  |   | | |||  |||| |  |                     
TTAGCGTGAGCGAGGTCGAGGCATTGTATGAACTGTTCAAGAAGATCAGCAGTGCTGTGATTGATGATGGGCTGATCAACAAGgtttgtgggtgattgctgctgctttctttcttttcttctcttaggaaaatgaatacaactttcttgctttatgtatgtacacaatacacatacaccatacacatgatcgtgatgagtaatctgggttgtggcgctcttgtcctggcatcctgcag

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G007555_T01 (Zea mays), 5'ss of exon 3
TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgt--atgaaggaagg--gcatcattatatgtcttttatgccactcacttatactcctcacgaatcatgcatatt---gctacgtcttttggacatccttttctgattttccttgacctgtcttgtcgtt-cag
| |||||||| ||  | |||||||| || |||||||| ||||| || ||||||||||| || ||||||||||| || ||||||||   ||| ||  |   |   || | | |   | |||||  |     |  |  |    | |     ||||| |    |  | |     ||       | |  |   | | |||| | ||||   || || |||
TCAGCGTGAGCGAGGTCGAGGCTCTGTACGAGCTGTTCAAGAAGATAAGCAGTGCTGTCATCGATGATGGGCTGATTAACAAGgtcagtgatgggtgattggtccactgtttagttcttatgtaatctcttattgttgtgtatggtatgtgcatttgtgggtgatggtcaatgcctgagatatattagctgttcttg-cttgtcacctctttgcag

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G173424_T01 (Zea mays), 5'ss of exon 3
TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgtatgaaggaagggcat----cattatatgtcttttatgccactcacttatactcctcacgaatcatgca--tattgctacgtcttttgg-acatccttttctgattttccttgacctgtcttgtcgttcag-------------------
| |||||||||||  | ||||| || || |||||||||||||  |||||||| || || |||||||||||||| || ||||||||  | |    | |  |    || ||  ||  | |||||  |     |  || || |   |     ||||  | | | |    || || | |      | | ||||  ||  || |     | |  ||||                     
TCAGCGTGAGTGAGGTCGAGGCGCTGTACGAGCTGTTTAAGAGGATCAGCAGCGCCGTCATTGATGATGGGCTGATTAACAAGgtcggcaatgggtgtctggttcactacttggttcttatgtaatctcttattaatctttgtggtatgtgcaagtgtggatggtcctgttagtatgcttgtgtgtgatggtcaatg-ctgagatggctgttcttgcttgtcacctctgcgcag

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G44580.1 (Glycine max), 5'ss of exon 3
TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgtatgaa-ggaagggcatcattatatgtcttttatgccactcacttatactcctcacgaatcatgcatattgc-tacgtcttttggacatccttttctgattttccttgacctgtcttgtcgttcag
| || || ||||||||||| || ||||| ||||| || || || || ||||||||||| ||||| |||||| | || |||||||| ||   |    | |||    | |  |  | | |    |  | || || |  |||| | |   || | || | |   |     | | || | | ||| |||                         
TCAGTGTAAGTGAAATAGAAGCACTCTACGAGCTCTTCAAAAAGATTAGCAGTGCTGTAATTGACGATGGGTTGATTAACAAGgtttgtctgttttgtcattggaaaacattgtgttttgggcata-ttgtatt--tcactagttgagcctttttcatcaatgaaaagaaaatacatatctcatta------------------------

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 5'ss of exon 2
TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgtatgaaggaagggcatcattatatgtcttttatgccact---cacttatact-cctcacgaatcatgcatattgctacgtcttttggacatccttttctgattttccttgacctgtcttgtcg-ttcag-------------------------------------------------------------------------
  || || ||||||||||| || || ||||| ||||||||||| |||||||||||||| ||||||||||| || || ||||||||    |   |  |  |   ||  | |  |  | | |  |   |  | ||| |   |  |   |   | ||     | |  || |   | ||| |      | |||      | | |  ||    |||                                                                           
--AGTGTAAGTGAAATAGAAGCACTTTATGAACTGTTTAAGAAGATCAGCAGTGCTGTAATTGATGATGGCCTCATCAACAAGgtg---acatactgttttcctacttatactgaaagtctgtaggctatcatattgttttgcagtttcaggatgacattgctcctctgttatatcttagcacaaatttagcaatcttcttgtgaaaattccattattaatttgaagtactgatactttcttactattgtgttttgttggtggattctttaaatcccatattgcag

upper sequence: AT4G26570.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 5'ss of exon 2
TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgtatgaaggaagggcatcattatatgtcttttatgccactcacttatactcctcacgaatcatg-catattgctacgtcttttggacatccttt------tctgattttccttgacc-tgtcttgtcgttcag-----------------------
|||| || |||||||| ||||| || || |||||||||||||| |||||||| |||||||||||||| || || || ||||||||    ||  | |  || |||  || | |     |      |  | |  |  |    |  ||   || ||   ||  ||| |||    ||          | || | || |   ||  |   | ||  || |                        
TTAGTGTAAGTGAAATCGAGGCACTATACGAGCTGTTTAAGAAGATCAGCAGCGCTGTGATTGATGACGGTCTGATCAACAAGgttcatagataagctattattcaatttataggcagtattggaaatctgattgtagtaatgcacctcacatgaataaatctcttgattctctcccattccatttgttgtttcccaactatagttagtaattgatgtttctacggtaccatattacag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86019690|gb|DR315436.1|DR315436
EST:     TGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG                         GAAGAATTTCAGTTAGCCTTTGTTCAAGACAAATAAAAAAGAGAGCTTGTT
genomic: TGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgtatgaagga ... tgtcgttcagGAAGAATTTCAGTTAGCCTT-GTTCAAGACAAATAAAAAAGAGAGCTTGTT
EST: gi|86019689|gb|DR315435.1|DR315435
EST:     TGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAG                         GAAGAATTTCAGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTT
genomic: TGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgtatgaagga ... tgtcgttcagGAAGAATTTCAGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTT
EST: gi|164219803|gb|ES071629.1|ES071629
EST:     TGATGATGGGCTAATAAACAAG                         GAAGAATTTCAGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTT
genomic: TGATGATGGGCTAATAAACAAGgtatgaagga ... tgtcgttcagGAAGAATTTCAGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAGCGTGAGTGAAATAGAGGCTCTCTATGAGCTGTTTAAGAAAATCAGCAGTGCTGTGATTGATGATGGGCTAATAAACAAGgtatgaaggaagggcatcattatatgtcttttatgccactcacttatactcctcacgaatcatgcatattgctacgtcttttggacatccttttctgattttccttgacctgtcttgtcgttcag

- - - - - - - - - - - - - - - - - - - AAGAAA