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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGTTGGAACTCTCCGTGGCTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTGgtacgtttctctccatctctctaactcacccacagaatcttcttgtcatttgttttgtttaaacattctacttttttcctggatgcag

Basic information

species Arabidopsis thaliana
transcript AT3G11500.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G083642_T02 (Zea mays), 5'ss of exon 3
GGTTGTTGGAACTCTCCGTGGCTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTGgtacgtttctctccatctctctaactcacccacagaatcttcttgtcatttgttttgtttaaacattctacttttttcctggatgcag
 ||| | || || || ||||| || || |||||||||||||| || ||||| |||||||| || ||||||||  |||||||||| || ||||| ||||||||| ||||   || |   ||  ||           | |    | || |  || |        |||  ||||| || ||||        
TGTTATCGGCACACTTCGTGGGTTCGACCAGTTCATGAATCTGGTGGTGGACAACACTGTGGAGGTCAATGGAAATGACAAAACAGATATTGGAATGGTGgtaagttttcttcta---ctgaaaggttatttggtacttgcttagtaacatgct-------gacagcctactattatcctcag-----

upper sequence: AT3G11500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G38130.1 (Glycine max), 5'ss of exon 3
GGTTGTTGGAACTCTCCGTGGCTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTGgtacgt----ttctctc----catctctctaactca--cccacagaatcttcttgtcatttgt---------tttgtttaaacattctacttttttcctg--gatgcag
||||||||| ||||||||||||||||| ||||| |||||| | ||||| || |||||||| ||||| |||||  |||| |||| |||||| |||||||||||  ||    |||| |       ||| |  || | |       |  || ||   || | | |          |   ||| ||  |  || |||||||||     |||||
GGTTGTTGGTACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctattcttttgcattgtcttttaaatttaagttgttaagatattgcagttaatagagcatgaacatggatttgaaattgataattttttcctcttattgcag

upper sequence: AT3G11500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G09150.1 (Glycine max), 5'ss of exon 3
GGTTGTTGGAACTCTCCGTGGCTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTGgtacgtttctctccatctctctaactcacccacagaatcttcttgtcatttgttttgt-ttaaacattctacttttttcctggatgcag
| ||||||| ||||||||||||||||| ||||| |||||| | ||||| || |||||||| ||||| |||||  |||| |||| |||||| |||||||||||  ||     ||    | |||   |   | |   |      |   |||   ||||   || |  ||| |||  |||| ||| |     
GATTGTTGGCACTCTCCGTGGCTTTGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctcttctcattttctttgtggtcaaggtatagcagtgagcatggattttaaattgataattttacccttttactgcag----

upper sequence: AT3G11500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G35490.1 (Glycine max), 5'ss of exon 3
GGTTGTTGGAACTCTCCGTGGCTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTGgtacgt--ttctctccatctctctaactcacccacagaatcttcttgt-catttgttttgtttaaacatt--ctacttttttcctggatgcag
||||||||| |||||||||||||| || ||||| |||||| | ||||| || |||||||| ||||| |||||  |||| |||| |||||| |||||||||||  ||  |  | | ||| ||  |         | || |  |  | |  |||     | ||||  | |||    | |||    ||   |||||
GGTTGTTGGTACTCTCCGTGGCTTCGACCAGTTTATGAATTTAGTTGTTGACAACACTGTGGAAGTGAATGGCAATGAGAAAAATGACATAGGGATGGTGgtgagtcctcttttgcatatcaatggtcatggtatagcagttaatagagcatggacatggtttttagattgataattttccctcttattgcag

upper sequence: AT3G11500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv08s0007g03130.t01 (Vitis vinifera), 5'ss of exon 3
GGTTGTTGGAACTCTCCGTGGCTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTGgtacgttt-ctctccatctc--tctaactcacccacagaatctt-cttgtcatttgttt-tgtt----taaacattctacttttttcc--tggatgcag---------------
||| ||||||||||| ||||| ||||| ||||||||||| || || ||||| |||||||| ||||| |||||  |||| |||||||| || || ||||||||| |||   | | |||||   | ||  |  | |  |  || ||  ||  ||||||  | || |    |||  |    |   |||| |  | ||||                  
GGTGGTTGGAACTCTTCGTGGGTTTGACCAGTTCATGAACCTGGTGGTGGACAACACTGTGGAAGTGAATGGAAATGAGAAAACTGATATAGGCATGGTGgtaggttaatttttcatcttgttttatttttctcttaatattttatttaccatttggatatgatactgtaattagctcagccttttgcaattgatgtcacaattgtacctgcag

upper sequence: AT3G11500.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S475_6V6.1 (Physcomitrella patens), 5'ss of exon 3
GGTTGTTGGAACTCTCCGTGGCTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTGgt-acgtttctctccatc---tctctaactcacccaca--gaatcttcttgtcatttgttttgtttaaacattctacttttttcctggatgcag---------------------------------------
 |||||||||   || ||||| ||||| ||||||||||| |||||  ||||||||||||||||  ||||||||| ||||| ||  || ||||| |||||||| | |  |||  || |    |||  |  | ||  | |  || | |     || | |||    |||     ||  |  | |||    ||| ||                                        
TGTTGTTGGAGTCCTGCGTGGATTTGACCAGTTCATGAACCTTGTACTGGATAACACTGTTGAGATCAATGGTGCTGACAGAAACGAGATTGGCATGGTGgtgaggcctctacccgttgtttcttgagttaacatatatcgattgtaacgctcctgtgtgcgttttccctttttcaaatcttttgaagatacatattgggacatctaatgagcaaatcgggtgttgtgtgcag

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|152038476|gb|AV823925.2|AV823925
EST:     ATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTG                         GTGATAAGAGGAAACAGCATTGTTACTGTTGAAGCTCTCGAACCAGTTGGA
genomic: ATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTGgtacgtttct ... ctggatgcagGTGATAAGAGGAAACAGCATTGTTACTGTTGAAGCTCTCGAACCAGTTGGA
EST: gi|164018221|gb|ES114982.1|ES114982
EST:     ACATTGGGATGGTG                         GTGATAAGAGGAAACAGCATTGTTACTGTTGAAGCTCTCGAACCAGTTGGA
genomic: ACATTGGGATGGTGgtacgtttct ... ctggatgcagGTGATAAGAGGAAACAGCATTGTTACTGTTGAAGCTCTCGAACCAGTTGGA
EST: gi|164213970|gb|ES086504.1|ES086504
EST:     AAAACTGACATTGGGATGGTG                         GTGATAAGAGGAAACAGCATTGTTACTGTTGAAGCTCTCGAACCAGTTGGA
genomic: AAAACTGACATTGGGATGGTGgtacgtttct ... ctggatgcagGTGATAAGAGGAAACAGCATTGTTACTGTTGAAGCTCTCGAACCAGTTGGA
EST: gi|164120803|gb|ES137795.1|ES137795
EST:     ATTGGGATGGTG                         GTGATAAGAGGAAACAGCATTGTTACTGTTGAAGCTCTCGAACCAGTTGGA
genomic: ATTGGGATGGTGgtacgtttct ... ctggatgcagGTGATAAGAGGAAACAGCATTGTTACTGTTGAAGCTCTCGAACCAGTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTGTTGGAACTCTCCGTGGCTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAAGTCAATGGTGATGACAAAACTGACATTGGGATGGTGgtacgtttctctccatctctctaactcacccacagaatcttcttgtcatttgttttgtttaaacattctacttttttcctggatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG