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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGAAAAGGCCAAGTATATTTATATTGCCGGCTTTTTCCTCACTGTATCACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatgattagaaaattgcttctttctattaaatggctgtttctgatgctttattttattcctgtatgcag

Basic information

species Glycine max
transcript GLYMA19G36630.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36630.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 5'ss of exon 8
TTGAAAAGGCCAAGTATATTTATATTGCCGGCTTTTTCCTCACTGTATCACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaata-tgattagaaaattgcttctttctattaaatggctgtttctg-atgctttattttattcctgtatgcag
|||| ||||| || |||||||| ||||| |||||||||||||| ||||| || |||||||| ||  | |||||||||||| ||||||||| ||||||||| ||||| | ||||  |||  |    | | |  ||      |||| | | ||   | |||  |   || | |||||
TTGAGAAGGCAAAATATATTTACATTGCTGGCTTTTTCCTCACGGTATCCCCGGATTCCATTCAACTTGTTGCTGAGCATGCTGCTGCAACTAACAAGgtaaaatactaattactaaaaggagaatattttctagc--attgttacagtataaatgattaaa---ctatttgcag

upper sequence: GLYMA19G36630.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 8
TTGAAAAGGCCAAGTATATTTATATTGCCGGCTTTTTCCTCACTGTATCACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatgattagaaaattgcttctttctattaaatggctgtttctgatgctttattt-tattcctgtatgcag
| || || || || || || || ||||| ||||||||||| || || || |||||||| || ||| | |||||||||||| |||| || || |||||||| ||||   || |  |||  | | | ||   | || |||   ||| |   | || | |     |  ||| | |||
TGGAGAAAGCAAAATACATCTACATTGCTGGCTTTTTCCTTACGGTCTCCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgt-aaattctatcactaaagagttccctt---tgaagtgg---tttttagagtttgactaaccgtgttgttttcag

upper sequence: GLYMA19G36630.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 8
TTGAAAAGGCCAAGTATATTTATATTGCCGGCTTTTTCCTCACTGTATCACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaa---atatgattagaaaattgcttctttctattaaatggctgtttctgatgctttattttattcctgtatgcag
|||| ||||| || || || || ||||| || ||||||||||| || ||||| ||||| ||||||||||||||||||||| |||| |||||||||||||| ||   |||  | ||  ||| |||   ||    ||   ||  |   | ||||     ||| ||||           
TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcataataatatgaaaatgccagttgaagttgt-tgttttagtttgattgaccattctattttcag------

upper sequence: GLYMA19G36630.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G540538_T02 (Zea mays), 5'ss of exon 8
TTGAAAAGGCCAAGTATATTTATATTGCCGGCTTTTTCCTCACTGTATCACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatgattagaaaattgcttctttctattaaatggctgtttctgatgctttattttattcctgtatgcag
|||||||||| || || || || ||||| || |||||||| || || || || ||||| |||||| |||| ||||||||| |||| |||||||||||||| || |   |||| ||      | |  | |   |  |   |   | ||||   | ||  ||||           
TTGAAAAGGCAAAATACATCTACATTGCTGGATTTTTCCTTACAGTGTCGCCTGATTCTATCCAGCTAGTCGCTGAGCATGCTGCAGCAAATAACAAGgtaaattcatattataatgaaagtaccctttga-agttcttttagtttgattggtcatgctattttcag------

upper sequence: GLYMA19G36630.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G089767_T01 (Zea mays), 5'ss of exon 6
TTGAAAAGGCCAAGTATATTTATATTGCCGGCTTTTTCCTCACTGTATCACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaata-tgat--tagaaaattgcttctttctattaaatggctgtttctgatgctttattttattcctgtatgcag
|||| ||||| || |||||||| ||||| || |||||||| || ||||| || ||||| || ||  | |||||||||||| | ||||||| ||||||||| ||| | ||||  |||  ||  |   |  |||    | ||    | ||||||     |         | | || ||
TTGAGAAGGCAAAATATATTTACATTGCTGGATTTTTCCTTACGGTATCCCCGGATTCTATTCAACTTGTTGCTGAGCATGCCGCTGCAACTAACAAGgtaaaaaaatgatgctagtgaaaggaaaccatcttgctagtgt---tgtctgatttccaacggctgcaatatttgtag

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|10254148|gb|BE821914.1|BE821914
EST:     CNNCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATNNNAAG                         ATCTTCTCAATGNNNNNTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
genomic: CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatg ... ctgtatgcagATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
EST: gi|192295218|gb|FG986937.1|FG986937
EST:     CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAG                         ATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
genomic: CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatg ... ctgtatgcagATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
EST: gi|151393153|gb|EV263028.1|EV263028
EST:     CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAG                         ATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
genomic: CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatg ... ctgtatgcagATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
EST: gi|26045675|gb|CA783183.1|CA783183
EST:     CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAG                         ATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
genomic: CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatg ... ctgtatgcagATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
EST: gi|6455199|gb|AW185882.1|AW185882
EST:     CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAG                         ATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
genomic: CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatg ... ctgtatgcagATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
EST: gi|192304064|gb|FG993894.1|FG993894
EST:     CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAG                         ATCTTCTCAATGAA
genomic: CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatg ... ctgtatgcagATCTTCTCAATGAA
EST: gi|26045783|gb|CA783264.1|CA783264
EST:     CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAG                         ATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
genomic: CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatg ... ctgtatgcagATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
EST: gi|37996713|gb|CF808302.1|CF808302
EST:     CAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAG                         ATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
genomic: CAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatg ... ctgtatgcagATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
EST: gi|192329140|gb|FK021127.1|FK021127
EST:     CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAACTAACAAG                         ATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT
genomic: CACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatg ... ctgtatgcagATCTTCTCAATGAACCTTTCTGCTCCTTTTATCTGTGAGTTTTTCAGGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGAAAAGGCCAAGTATATTTATATTGCCGGCTTTTTCCTCACTGTATCACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaaatatgattagaaaattgcttctttctattaaatggctgtttctgatgctttattttattcctgtatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC