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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGAGAAATGAGCTAGAGGAGCCTCGTAGCTCGGATGGGGATCACCTACCACGGCTTCAAAGTCTGCAGAGGATTCTCCAAGGAAGTGTTGCAGTGCAGgtgggtttttctcccataatatctgtgttatagattgtgttgtaaaacgtagaaatgctcatcatatgcctttccatggaaatatgcag

Basic information

species Arabidopsis thaliana
transcript AT4G16340.1
intron # 29
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16340.1 (Arabidopsis thaliana), 5'ss of exon 29
lower sequence: GRMZM2G462803_T04 (Zea mays), 5'ss of exon 7
TCTGAGAAATGAGCTAGAGGAGCCTCGTAGCTCGGATGGGGATCACCTACCACGGCTTCAAAGTCTGCAGAGGATTCTCCAAGGAAGTGTTGCAGTGCAGgtgggtttttctcccataatatctgtgtt--atagattgtgttgtaaaacgtagaaatgctcatcatatgcctttccatgg--aaatatgcag--------------
  |||||||||| ||||| || || || || || || || ||||| || ||| ||||||||||  |||| ||||| |||||||||||||| || ||||||||| |  |   ||   |  |  | |  ||    |||||     ||   ||       |||||||  | |  |||    |||  || | |   |              
ATTGAGAAATGAACTAGAAGAACCACGGAGTTCTGAAGGTGATCAACTCCCAAGGCTTCAAAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAGgtgaggctgaatctactttttgcagaattcggaagatttatgagtgtcactaccgtttgctcattttcttgcttcttttggccaattcttttgacatcaccatgcag

upper sequence: AT4G16340.1 (Arabidopsis thaliana), 5'ss of exon 29
lower sequence: GRMZM2G110406_T01 (Zea mays), 5'ss of exon 9
TCTGAGAAATGAGCTAGAGGAGCCTCGTAGCTCGGATGGGGATCACCTACCACGGCTTCAAAGTCTGCAGAGGATTCTCCAAGGAAGTGTTGCAGTGCAGgtgggttt----ttctcccataatatctgtgttatagattgtgttgtaaaacgtagaaatgctcatcatat-gcctttccatggaaatatgcag--------------
  |||||||||||||||| || || || || || || || ||||| || ||| ||||||| ||  |||| ||||| |||||||||||||| || ||||||||| |  |      || |   |  ||  |     |  || |  |||| |  |       |||||||  | | |  |||  |   || | |   |              
ATTGAGAAATGAGCTAGAAGAACCACGGAGTTCTGAAGGTGATCAACTCCCAAGGCTTCAGAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAGgtgaggctgaatcccttctgcagaattggaaaggtctatgggtttgtca--ctatcgtttgctcattttcttgtttttttagctaattcttttgatgctgccatgcag

upper sequence: AT4G16340.1 (Arabidopsis thaliana), 5'ss of exon 29
lower sequence: Vv11s0016g00100.t01 (Vitis vinifera), 5'ss of exon 29
TCTGAGAAATGAGCTAGAGGAGCCTCGTAGCTCGGATGGGGATCACCTACCACGGCTTCAAAGTCTGCAGAGGATTCTCCAAGGAAGTGTTGCAGTGCAGgtgggtt-----------tttctcccataatatctgtgttatagattgtgttgtaa--aacgtagaaatgctcatcatatgcctttccatggaaatatgcag
  |  | |||||||| || |||||||| ||||| || |||||||| || ||||| || ||||| || ||||| || |||||||| ||||||||||| || ||| |||           ||| |         | ||| ||     ||   ||||||  |  || |  |  |  | |  ||   || |    |  ||| |   
ATTACGCAATGAGCTTGAAGAGCCTCGCAGCTCTGAAGGGGATCAACTCCCACGCCTCCAAAGCCTACAGAGAATACTCCAAGGCAGTGTTGCAGTTCAAgtgagttgcatggacccctttttgtttcccgttttgtttttcctttttccttgtaaccactgttgtcaatccaaaccaatattttgcttatgtcataaga--

upper sequence: AT4G16340.1 (Arabidopsis thaliana), 5'ss of exon 29
lower sequence: PP1S60_296V6.1 (Physcomitrella patens), 5'ss of exon 27
TCTGAGAAATGAGCTAGAGGAGCCTCGTAGCTCGGATGGGGATCACCTACCACGGCTTCAAAGTCTGCAGAGGATTCTCCAAGGAAGTGTTGCAGTGCAGgtgggtttt---------tctcccataatatctgtgttatagattgtgttgtaaaacg--tagaaatgctcatcatatgcctttccatggaaata-tgcag
  |   |   |||||||| || |  |||      || || || || || ||  || | |||||||||||  |||| || ||||||||||| ||||||||||||  | ||            ||| ||| |    |   ||   || | ||||  | |   |||    | ||||  ||     ||   |     || |||| 
CTTAGCAGGGGAGCTAGATGACCACCGTTTGAATGAAGGTGACCATCTCCCTAGGTTGCAAAGTCTGCAACGGATACTGCAAGGAAGTGTCGCAGTGCAGgtgaatcttgggagtgctcagcccttaacaataattgcatgctttatattgtgtatcagttagtgtaggtcattgtactttctttatttcccctactgca-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGAGAAATGAGCTAGAGGAGCCTCGTAGCTCGGATGGGGATCACCTACCACGGCTTCAAAGTCTGCAGAGGATTCTCCAAGGAAGTGTTGCAGTGCAGgtgggtttttctcccataatatctgtgttatagattgtgttgtaaaacgtagaaatgctcatcatatgcctttccatggaaatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA