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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatcttgtatagtatagtctacaattctacatttcatctttagtatattacaaatgaagatagcatgcacatatatctacataattaactctacac...

Basic information

species Glycine max
transcript GLYMA17G10640.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G10640.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 5'ss of exon 5
TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtat----tatcttgtatagtatagtctacaattctacatttcatctttagtatattacaaatgaagatagcatgcacatatatctacataattaactctacac
||||||| ||||| || || || || |||||| |||||||||||||||| || |||||||||||||||||||||||||| || |||||||||     |  ||| | | |     |   ||  ||   || || | |   || | || |||       || ||||   ||| ||         | | | |    
TTTATGCTGATGGGAGCATATGCTTAGATATACTACAAAACCAGTGGAGCCCCATATATGATGTAGCTGCTATACTCACATCCATCCAGgtagatgatgccttttttgggggtattagcatgtcatgatgtcctgtcatgtttgttgcaatattttgtatcatgtttata-attcgtgcttctgattttg---

upper sequence: GLYMA17G10640.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G110983_T03 (Zea mays), 5'ss of exon 3
TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatcttgtatagtatagtctacaatt--ctacatttcatctttagtatattacaaatgaagatagcatgcacatatatctacataattaactctacac-
||||||| |||||||| || || || |||||  | || || ||||||||||| ||||||||||||||||| |||||||| || |||||||||  | | |  |    ||  | ||    |  | | |  | ||  ||  |  |  |    | |   | || ||   ||| |   ||||  | |||| | ||  
TTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccatacaagaaatcttttatttcttacaagagattattgtttttccaacatttgtaacttttgcttgt-tatacagtaacat--tcaactttgcagt

upper sequence: GLYMA17G10640.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G110983_T02 (Zea mays), 5'ss of exon 4
TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatcttgtatagtatagtctacaatt--ctacatttcatctttagtatattacaaatgaagatagcatgcacatatatctacataattaactctacac-
                           ||||  | || || ||||||||||| ||||||||||||||||| |||||||| || |||||||||  | | |  |    ||  | ||    |  | | |  | ||  ||  |  |  |    | |   | || ||   ||| |   ||||  | |||| | ||  
---------------------------ATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAGgtacaaccatacaagaaatcttttatttcttacaagagattattgtttttccaacatttgtaacttttgcttgt-tatacagtaacat--tcaactttgcagt

upper sequence: GLYMA17G10640.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 5'ss of exon 5
TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatct-tgtatagtatagtctacaattctacatttcatctttagtatattacaaatgaagatagcatgcacatatatctacataattaactctacac--
| ||||| ||||||||||||||| | |||||  ||||||| |||||||||||||||||||||||||| |||||||| || ||||| |||||||| ||  | || | | || | |     |     |  |||  ||  ||  | |||| || |    | |   |  || |   | ||   | ||  | ||   
TCTATGCAGATGGAAGTATTTGTCTCGATATTCTACAAAATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAGgtattgtcaatatacaat-tattatgtggataatgttgccattgtttttagttaacaattgtatgagggacttaactacaagaaaatg--tgaccattcatat

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|6846800|gb|AW349090.1|AW349090
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|254335070|gb|GR844855.1|GR844855
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|16106211|gb|BI893951.1|BI893951
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAAT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAAT
EST: gi|254335069|gb|GR844854.1|GR844854
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|15001308|gb|BI322122.1|BI322122
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|10235145|gb|BE804033.1|BE804033
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|192331367|gb|FK021035.1|FK021035
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|21888252|gb|BQ741465.1|BQ741465
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|192330437|gb|FK021196.1|FK021196
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|254331190|gb|GR843309.1|GR843309
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|192330438|gb|FK021197.1|FK021197
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|151412180|gb|EV281992.1|EV281992
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|16996966|gb|BM086338.1|BM086338
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|254317222|gb|GR826167.1|GR826167
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|192331366|gb|FK021034.1|FK021034
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|8284603|gb|BE022162.1|BE022162
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|14259666|gb|BG882574.1|BG882574
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCT
EST: gi|254317221|gb|GR826166.1|GR826166
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatcttgtatagtatagtctacaattctacatttcatctttagtatattacaaatgaagatagcatgcacatatatctacataattaactctacac

- - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT