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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagactccttaaattctatataaacgagttgtttgatgtcccctgtctcgtaatattctgatacatactgatgtctggcag

Basic information

species Arabidopsis thaliana
transcript AT1G25490.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 6
TGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagac--tccttaa--attctatataaacgagttgtttgatgtcccctgtctcgtaatattctga--tacatactgatgtctggcag
|||||| |||||||| ||||| || || || ||||| || ||||||||| || |||| | |||  ||||||| |||||||| || ||||||||||| |||||  | |    |||||  |     ||| |||  ||| | || ||     | |  |  |  |  || |  | |  ||||   |||| |||
TGAGGCGGAAGTGCGGATAGCGGCTGCAGGGAAAGTTACTAAGTTCTGTAGGATTTTAAGTCCTCAGCTTGCAATTCAGCATATTCTTCCTTGTGTCAAGgtgggccaacgcttaaccaaatattattaactggttttctgctgctgtttattcc-cagcaaactaacttgccaactg-catctg-cag

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G122135_T01 (Zea mays), 5'ss of exon 6
TGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagactccttaaattctatataaacgagttgtttgatgtcccctgtctcgtaatattctgatacatactgatgtc--tggcag
||||||||||||||||||||| || || |||||||| || |||||||| ||  | || |||||| ||||| | || || || || ||||| || || |||||  |        |||| |   |      |||| |   | |   |||  |   |||   ||  | ||| || ||  |  |   ||
TGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTAAATCCACAGCTTTCAATCCAACATATTCTTCCGTGCGTTAAGgtgggtgcaaagcaattattcgt---tttgttgctattttttttctgagtg--aattaactagttcatgctaattgcatttatag

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 6
TGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagactccttaaattctatataaacgagttgtttgatgtcccctgtctcgtaatattctgatacatactga-tgtctg-gcag
||||||||||||||| |||||||| || |||||||| || ||||| || ||  | || |||||  ||||  |  | || || || ||||| || || |||||  |        |||| | |  | || | ||  ||| | |      |||   | |    | |  ||| |  | ||  |   |||
TGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTAAATCCTCAGCTCTCAGTCCAACATATTCTTCCATGCGTTAAGgtgggggcaaagcaattat-tgaacaccatttcgttgctatttttcttctg--agtgaattaactcatgccaagtgcatctacag

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 6
TGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagactccttaaattctatataaacgagttgtttgatgtcccctgtctcgta-atattctgatacatactgatgtctggcag--------------------------------------------------------
|||||||||||| || |||||||| || ||||||||||||||||| || ||| |||| |||||||| ||||| |||||||| || ||||||||||||||||||    || ||  |    | || |   |     || || |  |   |    || | |  ||         |   || || ||                                                         
TGAGGCTGAAGTACGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTAAATCCAGATCTTGCAATTCAGCATATTCTTCCTTGTGTGAAGgtatacatctttggaaaagaaattat--aacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaacttttgcag

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 6
TGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagactcctt-------aaattcta-tataaacgagttgtt--tgatgtcccctgtctcgtaata-ttctgatacat-actgatgtctggcag-------------------------------------------
||||||||||||||| |||||||| || ||||||||||||||||| || ||| |||| |||||||| ||| | |||||||| || ||| ||||||||||||||    || ||       ||||| ||  | |   |  ||  |  | || | |   | ||  |  |  || || |   | | |   || ||  |                                            
TGAGGCTGAAGTGCGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTAAATCCAGATCTTTCAATTCAGCATATTCTTTCTTGTGTGAAGgtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaacttttgcag

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 6
TGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagactccttaaattctatataaacgagttgtttgatgtcccctgtctcgtaatattctgatacatactgatgtctg-gcag
||| |||||||| || || ||||| || || |||||||||||||| || ||| | || |||||||| ||| | |||||||| || |||||||| ||||||||  | ||| ||   ||   | |  |  | ||   |  | |    | | |    |   |   |||| |    |  |||  ||||
TGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTAAATCCAGATCTTTCAATTCAGCATATTCTTCCTTGCGTGAAGgt--gtctctttggttttggtcttga--aattcagtattctgaattatatttacaggctaaaatactttgcaagatctttgcag

upper sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 5
TGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgt----aagactccttaaattctatataaacgagttgtttgatgtcccctgtctcgtaatattctgatacata-ctgatgtctggcag-------------------------------------
|||||||||||| ||||||||||| || || ||||| || || ||||||| | | || |||||||| ||||| ||||| || || ||||| ||||| |||||    | |  |  | |||   | | |    |  || | | ||||| ||| |     |  |   |  ||   | || ||||    | |                                     
TGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTAAATCCAGAACTTGCAATTCATCATATTCTTCCCTGTGTAAAGgtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtag

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|125202643|gb|EL217597.1|EL217597
EST:     AGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAG                         GAATTATCATCGGATTCTTCTCAACATGTCCGCTCTGCTCTAGCTTCAGT
genomic: AGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagactcc ... tgtctggcagGAATTATCATCGGATTCTTCTCAACATGTCCGCTCTGCTCTAGCTTCAGT
EST: gi|86067631|gb|DR363388.1|DR363388
EST:     GGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAG                         GAATTATCATCGGATTCTTCTCAACATGTCCGCTCTGCTCTAGCTTCAGTA
genomic: GGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagactcc ... tgtctggcagGAATTATCATCGGATTCTTCTCAACATGTCCGCTCTGCTCTAGCTTCAGTA
EST: gi|47830292|gb|CK119976.1|CK119976
EST:     GGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAG                         GAATTATCATCGGATTCTTCTCAACATGTCCGCTCTGCTCTAGCTTCAGTA
genomic: GGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagactcc ... tgtctggcagGAATTATCATCGGATTCTTCTCAACATGTCCGCTCTGCTCTAGCTTCAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGGCTGAAGTGCGAATAGCAGCAGCGGGAAAAGTGACCAAGTTCTGTCGGCTTTTGAATCCAGAGCTTGCGATTCAGCACATCCTTCCTTGTGTGAAGgtaagactccttaaattctatataaacgagttgtttgatgtcccctgtctcgtaatattctgatacatactgatgtctggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT