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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgtaattttttctcgagcacaaacctgattgatttgattgtcttattatgaggcttttcctgattagtgtgatgtcaacttccttcag

Basic information

species Glycine max
transcript GLYMA11G01450.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G01450.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g47180.2 (Oryza sativa), 5'ss of exon 4
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgt-aattttttctcgagcacaaacctgattgat-ttgattgtcttattatgaggcttttcctgattagtgtgatgtcaacttccttcag
 || || || ||||| ||| | ||| | ||||| ||||| || ||||| ||||||||||| |||| ||||||||||||  | || ||||||||||| ||||| | ||| |||| ||  |  |   |    |    ||  | |    | ||  |   ||| |||||     |  ||| |     || |||
CGGATTCACGCAGAACCAGCTGACATTGTGGAAGTACCCGTCGATGGTTAAGATGGCTGAACTCACTGGCCATACTTCCCGTGTCCTTTTCATGGCTCAGgtgagtttcttcttgattagtagttttgcagtcactgcctataagttaatctgttatttgctgatcgtcttactgtgattgaactacag

upper sequence: GLYMA11G01450.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os04g51110.2 (Oryza sativa), 5'ss of exon 4
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgtaatttttt--ctcgagcacaaacctgattgatttgattg-tcttattatgaggcttttcctgattagt-gtgatgtcaacttccttcag
||| ||  | ||||||||| | ||  | ||||| ||||| |||||||| ||||||||||| |||| ||||||||| ||  | || ||||||| ||| ||||| || ||||    |  | ||   || | || | ||||    | ||  | |||     || ||||||| | ||  |||     || | |||
TGGATTCGCTCAGAATCAGCTCACTTTGTGGAAGTACCCGTCAATGGTTAAGATGGCTGAACTCACTGGCCATACCTCTCGTGTCCTTTTCACGGCTCAGgttatcttttgctccttgtacctgcc-gtttaaattgacaaatattgctctgaacagattgctgattacttgtcttgtggtaatcttgcag

upper sequence: GLYMA11G01450.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G130425_T03 (Zea mays), 5'ss of exon 4
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgtaattttttctcg--agcacaaacctgattgatttgattgtcttattatgaggcttttcctgattagtgtgatgtcaacttccttcag
 || || || ||||| ||  ||||  | ||||| ||||| |||||||| ||||||||||| |||| ||||||||| ||  | || ||||||||||| ||||| |  | ||| |   | |    ||  | ||   |  ||||   || | |  |  | |  |||||   |    |||       || |||
CGGATTCACACAGAACCAACTAACCTTGTGGAAGTACCCATCAATGGTAAAGATGGCTGAACTCAGTGGCCATACCTCTCGTGTCCTTTTCATGGCTCAGgtgagctcttcgcatcaacctttacagggtttcctgcattgatataatgtttgaatatctctgatggatcctgtgtggtgaaactgcag

upper sequence: GLYMA11G01450.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G063192_T01 (Zea mays), 5'ss of exon 4
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgtaattttttctcgagcacaaacctgattgatttgattgtcttattatgaggcttttcctgattagtgtgatgtcaac-ttccttcag---------------------
||| || || ||||| ||  | ||  | ||||| ||||| || ||||||||||||||||| || ||||||||||| ||  | || || |||||||| ||||| |  || |   ||  |   | | | |    ||   ||  ||      | || |    ||  ||||||||   ||    |  |  ||                     
TGGATTCACACAGAACCAACTCACCTTGTGGAAGTACCCATCGATGGTGAAGATGGCTGAACTTAATGGCCATACCTCTCGCGTCCTCTTCATGGCTCAGgtgaaattcttcagactagttaacagtt--gcttatctgcattgagtgcatgcatgctatg-ctagtgtgagaacattgcttatatagttcttgctggttaaactgcag

upper sequence: GLYMA11G01450.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G33270.1 (Arabidopsis thaliana), 5'ss of exon 4
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgtaa-------ttttttctcgagcacaaacctgattgatttgattgtcttattatgaggctttt---cctgattagtgtgatgtca-------acttccttcag
 || ||||| ||||||||| | ||||||||||| || || || |||||||| ||||||||||||| ||| ||||| ||||||||||| |  |||||||||||||           |     |      | ||| |  |  |  |||      | |||||  |||   ||| |    |||| |||         | ||| | |||
CGGGTTTACACAGAATCAGCTCACACTTTGGAAGTATCCATCCATGGTGAAAATGGCTGAGCTCACTGGTCATACATCAAGAGTTCTATATATGGCCCAGgtaaaggaaaacaactaaatcaatttttaactgttgaaagtagttggagatgtttgaggtctttagtcctaaaacttgtgttgtttgtgttgtatttcttacag

upper sequence: GLYMA11G01450.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G33260.2 (Arabidopsis thaliana), 5'ss of exon 4
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgtaattttttctcgagcacaaacctg---attgatttgattgtctta--ttatgaggctttt---cctgattagtgtgatgtcaacttccttcag
||| ||||| ||||||||| | ||||||||||| ||||| || |||||||| ||||||||||||| ||| ||||| ||||||||||| |  |||||||||||||  |  ||     |   ||   |   | |  ||||| | | | |  | ||   |   ||   | ||  | || || |||    || || |||
TGGGTTTACACAGAATCAGCTTACACTTTGGAAGTACCCATCCATGGTGAAAATGGCTGAGCTCACTGGTCATACATCAAGAGTTCTATATATGGCCCAGgtaacgtcatcaatttctttaagtggtgaagtagtttgagtctttgaggtcattcagtccttaaacttgtgttgtttgttgt--gttttctacag

upper sequence: GLYMA11G01450.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S27_42V6.1 (Physcomitrella patens), 5'ss of exon 8
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgtaatttttt----ctcgagcacaaacctgatt---gatttgattgtcttattatgaggcttttcctgattagtgtgatgtcaacttccttcag
||| |||| ||| |||||| ||   || ||||| || || || ||||||||| |||||||||||| ||||||||| ||||||||  |     |||| |||||||  || |    ||  || | | |   |  |    |||    ||   |||        | ||  | | | |||  || |     ||   |||
TGGATTTAGCCAAAATCAGCTATGTCTGTGGAAGTATCCGTCTATGGTGAAGCTGGCTGAGCTCACTGGCCATACCTCAAGAGTCTTGCATCTGGCACAGgtaaccttctgggtctttaggagatagtggtctctcaattccgctggtgtatccaacctatgtttgtaacttgtgcaatatt---ctctggcag

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|26043786|gb|CA782170.1|CA782170
EST:     AGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAG                         AGTCCAGATGGTTGCACAGTAGCATCAGCAGCAGCAGATGAAACATTGAGG
genomic: AGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgtaatttttt ... cttccttcagAGTCCAGATGGTTGCACAGTAGCATCAGCAGCAGCAGATGAAACATTGAGG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTTACCCAGAATCAGTTAACACTTTGGAAATACCCCTCAATGGTGAAGATGGCTGAGCTCAATGGCCATACTTCAAGAGTTCTTTTCATGGCCCAGgtaattttttctcgagcacaaacctgattgatttgattgtcttattatgaggcttttcctgattagtgtgatgtcaacttccttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA