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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattgtgttaatctgctgtattgactttgcttcgtagtgaaactaattgagtttatttctggaacag

Basic information

species Arabidopsis thaliana
transcript AT3G05530.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 5'ss of exon 4
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattgtgttaatctgctgtattgactttgcttcgtagtgaaactaat-tgagtttatttctggaacag-----------------------------------------------------------------------------------------------
 || ||  | || || || ||||| ||  ||||||| || |||||||| |||||||| || || || ||||||||||||||||| || || ||||| ||||||| | | |||  |   | |    || || |   || ||  || | |  |  || | | ||   |||| |  | | |||                                                                                               
AGACACGCTACCTTCAGAATATGATTCACGGGTTAAGGCAATGGAGGTAGATGAAAAGCCTACAGAGGATTACAATGACATTGGTGGCCTTGAGAAACAGgtatttatttactttaaagatctaatgatgaa--aacattagttaggatggtcaccattctgttgttatgtaagtagcagtaacttcatttccatatctcataagtgttcatcagttgctgtttgttcattgttatctgctctcttatgttctacttttatattgtctaatgcag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 5'ss of exon 4
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattgtgttaatctgctgtattgactttgcttcgtagtgaaactaattgagtttatttct----ggaacag-------------------------------------------------------------------------------------------------------
||| ||  ||||||| |||||||| ||  | || || || |||||||| ||||||||||| || || || |||||||| |||||||| || || |||||||||  ||  |       |||| |     |  | ||    |  || | | || || || |       || |||    |||| |                                                                                                        
GGACACACTGCCATCAGAGTATGATTCACGAGTAAAGGCAATGGAGGTGGATGAAAAACCCACAGAGGACTACAATGATATTGGAGGTCTTGAAAAGCAGgtacattgcttaataaatgttgaa--agttcagtgttcctttttggaactggaaatattgacaaccatctctttagggaataatagagcaatttgtatcgcttcatgcatcaagcatgttacatttccatccatcttttccttttcataatttatcattctttccatcctattttattgaatatag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 4
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgta---tgtttat---------------accattgtgttaat-ctgctgtattgactttgcttcgtagtgaa-actaattgagtttatttctggaacag-----
 ||||| ||||| || |||||||||||  ||||||| || ||||| || ||||| ||||| ||||| ||||||||||||||||| ||||| ||||| ||||||   || ||                 ||  || | | |   || ||||  ||  |||| | | | |  |  |   | | |  | || | ||| | |      
AGATACATTGCCTTCAGAGTATGACTCACGGGTTAAGGCAATGGAAGTAGATGAGAAACCTACTGAGGATTACAATGACATTGGCGGACTTGAGAAACAGgtaatttgctttccagaactgggggttaactgttatatcagcactactgttgtggatttgttacattgcaagcaagcagtaatatgatgtttggtataacacag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 4
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattgtgttaatctgctgtattgactttgcttcgtagt---gaaactaat---tgagtttatttctgg-aacag
||||||| |||| ||||||||||| ||||| ||||| |||||||| || |||||||| ||||| || ||||||||||||||||| ||| |||||||||||||  | ||      |||   |||| |  || |     ||   || |  ||   | || | ||   | || | |||||    |||||
GGATACCCTGCCTTCCGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACAGAGGATTACAATGACATTGGCGGATTAGAGAAGCAGgtgagctttggttcttgccataatttattgaagcactttcttttgggggttaggtaattgatctctcaggtcatttcaatcaacag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 4
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattgtgttaatctgctgtattgactttgcttcg--tagtgaaactaat---tgagtttatttctggaacag---------------
|||||||||||| || |||||||| ||||| ||||| |||||||| || |||||||| ||||| || || |||||||||||||| ||| |||||||||||||  | ||      |||  ||||| |  || |  | | ||| || |  |||| ||   |||   | || | |||||   |||                 
GGATACCTTGCCTTCTGAGTATGATTCTAGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACCGAGGACTACAATGACATTGGTGGATTAGAGAAGCAGgtgagctttggttcttgccttaatttattgaa--gcccttgtttgggttagttaatgcaatctctcaggtcatttcaataacttggtcttcctcaacag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G42110.1 (Glycine max), 5'ss of exon 2
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgta-----tgtttatac-cattgtgttaatctgctgtattgac----tttgcttcgtagtga-aactaattgagtttatttctggaacag----------------------------
                                     ||||||||||| |||||||| ||||| || || |||||||||||||| ||  ||||||||||||||     |  |||    || | | | |||   || | |        ||| |||| || | | || ||  | |     | ||||  |  |                            
-------------------------------------GCCATGGAGGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtactctataattacgggcaatttatcaatgcactctttctttctttttttcttcttatttacaattaggtaacagggtctctgatagtgtgatcaataacttggtctctgccaacag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 4
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattg------tgttaatctgctgtattgactttgcttcgtagtga--aactaattgagttt---atttctggaacag---------------------
|||| || |||| || |||||||| ||  | ||||| |||||||| || |||||||| ||||| || || |||||||||||||| ||  |||||||||||||    |   |  |  |      | |  ||   || | |    ||| |||  |    |  |  |||  | | ||   ||     || ||                      
GGATGCCCTGCCTTCTGAGTATGATTCACGAGTTAAGGCCATGGAAGTTGATGAAAAGCCAACGGAGGACTACAATGACATTGGTGGTTTAGAGAAGCAGgtgcactataattaccgacaatttatcgatgcactctttctctttttcttatttacaattaggtaacagggcttccgatgatgtgatcaataacttggtctttgccaacag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 4
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattgtgt-taatctgctgtattgact-ttgcttcgtag-----tgaaact----aattgagtttatttctgg----aacag
 ||||| |||||||| |||||||| ||| | || || || |||||||| |||||||||||||| ||||| |||||||| || ||||| || |||||||||| | ||||  |   |||||  || | |   | | ||  | ||||||    |     ||| |||    | |  |  ||   |||      |||||
AGATACTTTGCCATCTGAGTATGATTCTCGAGTAAAGGCTATGGAGGTTGATGAAAAACCAACAGAAGACTACAATGATATCGGAGGGCTGGAGAAGCAGgcaagttt-caattttgtgcatattttatggaagtggttgttgcttgtccgatttttgatactttcaactaaaacttgcctctaattacaacag

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|164030247|gb|ES018045.1|ES018045
EST:     ACATTGGAGGACTAGAGAAGCAG                         ATCCAAGAGCTTGTAGAGGCAATTGTGCTTCCCATAGACGCACAAGGAACG
genomic: ACATTGGAGGACTAGAGAAGCAGgtatgtttat ... tctggaacagATCCAAGAGCTTGTAGAGGCAATTGTGCTTCCCAT-GACGCACAAGGAACG
EST: gi|163979437|gb|ES014396.1|ES014396
EST:     ACATTGGAGGACTAGAGAAGCAG                         ATCCAAGAGCTTGTAGAGGCAATTGTGCTTCCCATGACGCACAAGGAACGT
genomic: ACATTGGAGGACTAGAGAAGCAGgtatgtttat ... tctggaacagATCCAAGAGCTTGTAGAGGCAATTGTGCTTCCCATGACGCACAAGGAACGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATACCTTGCCATCCGAGTATGACTCTAGGGTTAAAGCCATGGAGGTCGATGAAAAACCAACTGAAGATTACAATGACATTGGAGGACTAGAGAAGCAGgtatgtttataccattgtgttaatctgctgtattgactttgcttcgtagtgaaactaattgagtttatttctggaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC