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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccatcctttgcctgtcatcgagttgaatccgtgatcatgtgttattagggacgtcattgtgagatgtttttattggtaatgacacagATTGAAAGCAACAATGCCAACGTCGATGATGCAATCATGCTTGACAAGGATGGGTTTGTGTCTGAAACCAATGCAACCAACATT

Basic information

species Arabidopsis thaliana
transcript AT5G27410.2
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA10G29770.1 (Glycine max), 3'ss of exon 15
-----------------------------------------------------------------------------------------gtaccatcctttgcctgtcatcgagttgaatccgtgatcatgtgttat----tagggacgtcattgtgagatgtttttattggtaatgacacagATTGAAAGCAACAATGCCAACGTCGATGATGCAATCATGCTTGACAAGGATGGGTTTGTGTCTGAAACCAATGCAACCAACATT
                                                                                          | |  |   | || | ||||     | |  | || ||  ||  | ||       | |  | ||    | |   | ||  |  |  ||  |||||||||| | || ||||| || |  ||||||||||||||||||||||| || || | ||| ||||||||||||||||| ||||| 
gtattttttttcctctcgtgaatttttacatgtaattattacagcaaattgtatcaggtaatgaataatatgcaaccatgtggaaacggatgcttttaatggcttttcatgctaat-atcctgtcattctgaataatatttcttgcagcttatcacaaaaaagtctt--tatttctgttacagATTGAAGGTAATAATGCAAAAGCAGATGATGCAATCATGCTTGACAAAGACGGTTATGTATCTGAAACCAATGCAACAAACATG

upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 14
----------gtaccatcctttgcctgtcatcgagttga-atccgtgatcatgtgttattagggacgtcattg-tgagatgtttttattggtaatgacacagATTGAAAGCAACAATGCCAACGTCGATGATGCAATCATGCTTGACAAGGATGGGTTTGTGTCTGAAACCAATGCAACCAACATT
          ||    |       |  |  ||  | | | ||||    |||  ||  ||     ||  ||||  | | || || |||||||   |    ||||||||| |||| ||||| || |  ||||||||||||||||| ||| | ||||| | | | || |||||||||||||| ||||||
aaaaaagagtgtgttgttaacactcctttgtcatgctaatatccagtctca-atgacatatcttactacattactaaaatattattattggcc-tagtgcagATTGAAGGCAATAATGCAAAAGCAGATGATGCAATCATGCTCGACCAAGATGGTTATTTATCAGAAACCAATGCAACTAACATT

upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA19G42530.1 (Glycine max), 3'ss of exon 14
-------------gtaccatcctttgcctgtcatcgagttgaatccgtgatcatgtgttattagggacgtcattgt-gagatgtttttattggtaatgacacagATTGAAAGCAACAATGCCAACGTCGATGATGCAATCATGCTTGACAAGGATGGGTTTGTGTCTGAAACCAATGCAACCAACATT
              | | | |  ||  ||||| |   | | |   | ||      ||  ||     ||  |||| |  | || |  |||||||   |    ||||||||| |||| ||||| || |  ||||||||||||||||| ||| | ||||| | | | || |||||||||||||| ||||||
taaaaagagtgtgttgctaacacttctctgtctt---gctaatatcctgtctcaatgacatattttactacatttttaaaatatcattattggcc-tagtgcagATTGAAGGCAATAATGCAAAAGCAGATGATGCAATCATGCTCGACCAAGATGGTTATTTATCAGAAACCAATGCAACTAACATT

upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 24
----gtaccatcctttgcctgtcatcgagt-tgaatccgtg---------atcatgtgttattagggacgtcattgtgagatgtttttattggtaatgacacagATTGAAAGCAACAATGCCAACGTCGATGATGCAATCATGCTTGACAAGGATGGGTTTGTGTCTGAAACCAATGCAACCAACATT
    ||   | || ||   |||| |   |  |  || | ||         || |||| || ||  |||  | |   | |  |  |  |||| |   ||  |||||| ||| | || ||||| || |  ||||||||||||||||||||||||||||| | ||| |||||||| ||||| || ||||||
tctggtggtagcccttcattgtccttatgcattcatacatgtacagatctattatgtcttgtt--ggattttaacttaaattagt--tatttggggtggtacagATAGAAGGGAATAATGCAAATGCTGATGATGCAATCATGCTTGACAAGGATGGTTATGTTTCTGAAACAAATGCTACAAACATT

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|116467245|gb|EG509837.1|EG509837
EST:     TAGATTCCAAGATTCATCGCAACAACCTCCTCAATAATATACTTGCAAAG                         ATTGAAAGCAACAATGCCAACGTCGATGATGCAATCATGCTTGACAAGGAT
genomic: TAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCAAAGgtaccatcct ... aatgacacagATTGAAAGCAACAATGCCAACGTCGATGATGCAATCATGCTTGACAAGGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcatgtgttattagggacgtcattgtgagatgtttttattggtaatgacacagATTGAAAGCAACAATGCCAACGTCGATGATGCAATCATGCTTGACAAGGATGGGTTTGTGTCTGAAACCAATGCAACCAACATT
                                  tttttattggtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccatcctttgcctgtcatcgagttgaatccgtgatcatgtgttattagggacgtcattgtgagatgtttttattggtaatgacacagATTGAAAGCAACAATGCCAACGTCGATGATGCAATCATGCTTGACAAGGATGGGTTTGTGTCTGAAACCAATGCAACCAACATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG