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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCAAGTCCATGAAATTCAAGGATGGATATATGATTTCTTCTGGACAACCAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgattttttattcttcatagttaactgatggaatttcttttagcactaggattttcatgttgttggctcattttctttcttcatggattgatggtgctaaatgctaattgattccttactgtcttatatatag

Basic information

species Glycine max
transcript GLYMA16G33240.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 5'ss of exon 5
AGCCAAGTCCATGAAATTCAAGGATGGATATATGATTTCTTCTGGACAACCAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttg-----attttttattcttcatagttaactgatggaatttcttt-tagca-ctaggattttcatgttgttggctcattttctttcttcatggattgatggtgctaaatgctaattgattccttactgtcttatatatag
 || || |||||||| |||||||| ||||| ||||||||||||||  | || || ||    || ||||||||||| || |||||||| || || |||||||||||     |   |  || | |   | | || || ||   | || || |   | || | |||||  | ||    |||   ||  | | ||||                                                  
TGCTAAATCCATGAAGTTCAAGGACGGATACATGATTTCTTCTGGTTATCCTGTTAACTTGTATATTGACTCTGCTGTTAGACATGTTCTTCTGAGACAGgtttgtacataaaatccatccgtttgaataaaatgttgctgtctccttgtgatagcttgaatttttttcttagaagct-gcttcttgttttcag-------------------------------------------------

upper sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G093902_T02 (Zea mays), 5'ss of exon 5
AGCCAAGTCCATGAAATTCAAGGATGGATATATGATTTCTTCTGGACAACCAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgattttttattcttcatagttaactgatggaattt-cttttagcactaggattttcatgttgttggctcattttcttt-cttcatggattgatggtgctaaatgctaattgattccttactgtcttatatatag
 || ||||| ||||| ||||||||||| || |||||||||||||| || || |||||    |||||||| || || ||||||||||| ||| | ||||||||||| |  ||  |     || |||| || ||        | | || ||  |    | | | ||  |   ||  ||  |||  |||||                                                  
TGCTAAGTCTATGAAGTTCAAGGATGGGTACATGATTTCTTCTGGTCATCCTGTCAACCTATACATTGATTCAGCTGTGAGACATGTTCTATTGAGACAGgtttggtgcttggtatcagat-gttatcttattatgcaaacatataacaaaatagctgtta-gtaatactctagttgacttggcttcag-------------------------------------------------

upper sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 5
lower sequence: AT2G31610.1 (Arabidopsis thaliana), 5'ss of exon 4
AGCCAAGTCCATGAAATTCAAGGATGGATATATGATTTCTTCTGGACAACCAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgattttttattcttcatagttaactgatggaatttcttttagcactaggattttc--atgttgttggctcattttctttcttcatggattgatggtgctaaatgctaattgattccttactgtcttatatatag
 || ||||||||||| ||||||||||| || ||| |||| ||||| ||||||   ||||| ||||| ||  ||||||||||||||||  | || |||||||| || ||| | ||   ||     |     ||  | |   |      ||  |  || ||  || ||||||| ||| |   | | | ||                                                  
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGGTTTCATCTGGTCAACCAACTAAGGAATACATCGATGCTGCAGTGAGACATGTTTTGCTCAGACAGgtatgctttctaatgagtctcttatctaccatttagtgagtaagtataccggctttgtctaatcttgttggttcaatccgtatttgcag-------------------------------------------------

upper sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G53870.1 (Arabidopsis thaliana), 5'ss of exon 4
AGCCAAGTCCATGAAATTCAAGGATGGATATATGATTTCTTCTGGACAACCAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgattttttattcttcatagttaactgatggaatttcttttagcactaggattttcatgttgttggctcattttctttcttcatggattgatggtgctaaatgctaattgattccttactgtcttatatatag
||||||||| ||||| ||||| ||||| || ||| | || ||||| ||||||   ||||| ||||| ||||||||||||||||||||  | || ||||| ||  |    |||  |||   | |||   |  | || ||   |  |  |  |  |    | | |  ||      || |    |   ||   | |                                           
AGCCAAGTCTATGAAGTTCAAAGATGGCTACATGGTGTCATCTGGTCAACCAACTAAGGAATACATAGACTCTGCAGTGAGACATGTTTTGCTTAGACAAgtgag----tttcgtctgagttgttc-ttattagagttaagtaaaaaatcaacaa---cgtctaattaaagtgttgttaaaccgaatatgtag-------------------------------------------

upper sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 5
AGCCAAGTCCATGAAATTCAAGGATGGATATATGATTTCTTCTGGACAACCAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgattttttattcttcatagttaactgatggaatttctt-ttagca--ctaggattttcatgttgttggctcattttctt-tcttcatggattgatggtgctaaatgc-taattgattccttactgtcttatatatag
 ||||| |||||||| || |||||||| || ||||| |||||||| || ||||||||||| || |||||||| || |||||||||||||| |||||||||||||| ||   |   |    |  |    | |||    || || ||| ||  ||      ||   || |||    |  || |||  |||||| |       || || |     |  | |||| ||| |  ||  | |     
TGCCAAATCCATGAAGTTTAAGGATGGGTACATGATATCTTCTGGTCAGCCAGTCAAGGAATATATTGACTCAGCTGTGAGACATGTGCTTCTAAGACAGgtttgcttcactcacccagttgatctgttcatgcttctttttgttaacatcctcaaccattgcggtggttcatacggttgcttaccttcattgcaattgtgtcctgatcatgttctggattgcttgccatcaaacag----

upper sequence: GLYMA16G33240.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S136_175V6.1 (Physcomitrella patens), 5'ss of exon 5
AGCCAAGTCCATGAAATTCAAGGATGGATATATGATTTCTTCTGGACAACCAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgattttttattcttcatagttaactgatggaatttcttttagcactaggattttc-atgttgttggctcattttctttcttcatg-gattgatggtgctaa-atgctaattgattccttactgtcttatatatag
 |||||||||||||| |||||||| || ||||||||||| || |||   || ||||| |||||||||||    || || ||||| ||  |  |  ||||||| ||     |   ||||||||||    |  |||  ||   |||      | |||  |  || | ||   |   ||| || | |  |    ||  |  ||  | |  || || ||  ||  |||||||  |    |   
TGCCAAGTCCATGAAGTTCAAGGACGGCTATATGATTTCATCAGGAAGCCCTGTCAACGATTACATTGATAGCGCTGTTAGACACGTCATGTTGCGACAGgtatg-----tggatcttcatagt--gtttttggtcttcaattttctctgacgatgctagatttcgtcatcgtttttgctctatatacctaatccagtgtattgacgtgttacttttttaattactgttcttggcag--

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|12496522|gb|BG047106.1|BG047106
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAACACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|254323366|gb|GR835867.1|GR835867
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|254323365|gb|GR835866.1|GR835866
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|24135528|gb|BU926038.1|BU926038
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGGTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|7590371|gb|AW706125.1|AW706125
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|208067585|gb|GD865673.1|GD865673
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|193392562|gb|FK358721.1|FK358721
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATG
EST: gi|21995034|gb|BQ786562.1|BQ786562
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|31460672|gb|CD402700.1|CD402700
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTACCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|31459201|gb|CD401229.1|CD401229
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTACCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|5760086|gb|AI965449.1|AI965449
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|208182161|gb|GD980608.1|GD980608
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|8401719|gb|BE057353.1|BE057353
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|31460147|gb|CD402535.1|CD402535
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|254322051|gb|GR837465.1|GR837465
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|207720877|gb|GD701318.1|GD701318
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|193329772|gb|FK295722.1|FK295722
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|209709433|gb|BW668361.1|BW668361
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|7590822|gb|AW706566.1|AW706566
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|208080397|gb|GD878951.1|GD878951
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
EST: gi|4313934|gb|AI461053.1|AI461053
EST:     AGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACCAG                         G-TGTTCTTGGTATCAGGGTTAAGATCATGCT
genomic: AGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGAC-AGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCT
EST: gi|254322052|gb|GR837466.1|GR837466
EST:     CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAG                         GGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG
genomic: CAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgatttt ... ttatatatagGGTGTTCTTGGTATCAAGGTTAAGATCATGCTTGATTGGGATCCTAAAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCAAGTCCATGAAATTCAAGGATGGATATATGATTTCTTCTGGACAACCAGTCAAGGATTACATTGACTCTGCAGTGAGACATGTGCTACTAAGACAGgtttgattttttattcttcatagttaactgatggaatttcttttagcactaggattttcatgttgttggctcattttctttcttcatggattgatggtgctaaatgctaattgattccttactgtcttatatatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG