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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtcttcgttgttttatattttgattttggtgtcattattcatttacttgatcttaatagttctagtggatttcag

Basic information

species Glycine max
transcript GLYMA09G33480.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os03g52840.3 (Oryza sativa), 5'ss of exon 10
TCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtcttcgt---tgttttatattttgattttggtgtcattattcatttacttgatcttaat---agttctagtggatttcag
|| |||||  ||||||| || |||   || ||||||||||| ||||| ||||||||||| || ||||| || |||||||| || || || ||||| ||||||| |   |   | |   || ||| | |||| ||||     | |  ||  |||| |   |||| |||   || || |      | |||
TCAAGAGTGGAGAAGGTTTTAGAAAACGTGCACATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTACCAGGAGGCATCAGGATGGgtaaaatctgcccctatgtggttttttttttaatttac---ttaaaatagatttgcaaaatctcaatatcagctccatgatcatgcag

upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G135283_T02 (Zea mays), 5'ss of exon 12
TCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtcttcgttgttttatattttgattttggtgtcattattcatttacttgatcttaatagttctagtggatttcag
|| || ||  ||||||| || |||   || || |||||||| ||||| ||||||||||| || ||||| || |||||||| || || || ||||| |||||||     | || ||  |   || |||  ||  |    || | |||     | ||  |  || ||| |||   |   | |||
TCAAGGGTGGAGAAGGTTTTAGAAAGTGTGCATATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTGCCAGGAGGCATCAGGATGGgtacgatatttt-gtcatagaatgtttgtatactttattcttaattttgcaaattcttaatattagctctcccgtcatgcag

upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 13
TCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtcttcgttgttttatattttgattttggtgtcattattca---tttacttgatcttaatagttctagtggatttcag
||||||||| | |||||||||||||| ||||| |||||||||||||| ||||| ||||| ||||||||||| || |||||||||||||| ||||| ||||||  || || || |||| |  | ||  || || ||   |  ||||| |   ||||||||||||     | |||  ||   |||||
TCCAGAGTTGAAAAGGTGTTGGAATCTGTTCATATTGCAGCTAACAAGAACACCGTTCCTGGAGATGTGTCGGCCATGGTTCCTGGTGGCATCAGGATGGgt--agagtttttgttgatc-acatggtgcttgtgtgatttttatttaagttttacttgatct-----gctctcttg--cttcag

upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 5'ss of exon 13
TCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtcttcgttgttttatattttgattttggtgtcattattcatttacttgatcttaatagttctagtggatttcag
||||||||| | |||||||| ||||| ||||| |||| ||||||||||||||| ||||| ||||||||||| || ||||||||| |||| ||||| ||||||  || || || |||| |  | ||  || || ||   |  |||||  |    || || | |   | |||  ||   |||||
TCCAGAGTTGAAAAGGTGTTAGAATCTGTTCATATTGTAGCTAACAAAAACACTGTTCCTGGAGATGTGTCGGCCATGGTTCCTAGTGGCATCAGGATGGgt--agagtttttgttgatc-acatggtgcttgtgtgatttttattt-taagttttatttgatccgctctcttg--cttcag

upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 5'ss of exon 5
TCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtcttcgttgttttatattttgattttggtgtcattattcatttacttgatcttaatagttctagtggatttcag
||||||||| | |||||||||||||| ||||| |||| ||||||||||||||| ||||| ||||||||||| || ||||||||| |||| ||||| ||||||  || || || |||| |  | ||  || || ||   |  |||||  |    || |  | |   | |||  ||  ||||||
TCCAGAGTTGAAAAGGTGTTGGAATCTGTTCATATTGTAGCTAACAAAAACACCGTTCCTGGAGATGTGTCGGCCATGGTTCCTAGTGGCATCAGGATGGgt--agagtttttgttgatc-acatggtgcttgtgtgatttttattt-taagttttacttgatccgctctcttg--tttcag

upper sequence: GLYMA09G33480.1 (Glycine max), 5'ss of exon 13
lower sequence: PP1S21_270V6.1 (Physcomitrella patens), 5'ss of exon 12
TCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtcttcgttgttttatattttgattttggtgtcattattcatttacttgatcttaatagttctagtggatt---tcag--------------------
|| || ||  ||   ||| ||||    |  ||||||||||| ||||| ||||| ||||||||||||||||| ||  |||| ||||| |||||| | ||||||| || ||   ||  | | |  | |  |    | || |  |||||     ||    |    |||   | |||| | |   | |                     
TCAAGGGTGGAGCGAGTGATGGAGCTTGCCCACATTGCAGCAAACAAGAACACTGTTCCAGGAGATGTGTCTGCATTGGTACCTGGAGGTATCCGTATGGgta-agtgtaaacgaagctctcgaatcag----tagtcttcttatttgaaaacgatctagagataaaaccagtgaaatgacttaatgcattaatgtaatcttgta

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|193392884|gb|FK359660.1|FK359660
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|207828088|gb|GD797979.1|GD797979
EST:     CACGGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGACTACTTACTTCTAGGGGATTT
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTG-CT-CTTACTTCTAGGGGATTT
EST: gi|208197654|gb|GD998875.1|GD998875
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGC
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGC
EST: gi|208217259|gb|GE008655.1|GE008655
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|207753907|gb|GD724303.1|GD724303
EST:     GTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: GTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|208201733|gb|GE000507.1|GE000507
EST:     CACGGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTACTTACTTCTAGGGGATTT
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCT-CTTACTTCTAGGGGATTT
EST: gi|193305610|gb|FK270967.1|FK270967
EST:     GTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: GTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|208165351|gb|GD964459.1|GD964459
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|193427342|gb|FK396168.1|FK396168
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTTGTTATG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTT-GTTATG
EST: gi|208062781|gb|GD861069.1|GD861069
EST:     TGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: TGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|208298055|gb|GE091030.1|GE091030
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATAG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|193316691|gb|FK281931.1|FK281931
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|193364197|gb|FK331767.1|FK331767
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|207827493|gb|GD800730.1|GD800730
EST:     GGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: GGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|208293963|gb|GE092564.1|GE092564
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|193668912|gb|FK611148.1|FK611148
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|193403630|gb|FK369884.1|FK369884
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|193396652|gb|FK364562.1|FK364562
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|208290230|gb|GE084492.1|GE084492
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCT
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCT
EST: gi|22931030|gb|BU548169.1|BU548169
EST:     CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|16346437|gb|BI972032.1|BI972032
EST:     CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|193667155|gb|FK610947.1|FK610947
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTTCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|208091250|gb|GD890961.1|GD890961
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|193385890|gb|FK351112.1|FK351112
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTTGTTATG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTT-GTTATG
EST: gi|193381576|gb|FK348903.1|FK348903
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|208134534|gb|GD930927.1|GD930927
EST:     CACAGTTCCAGGAGATGTGTCAGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGATTTGCTGAGGAGGATTTTGTTATGG
EST: gi|16348582|gb|BI974177.1|BI974177
EST:     CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGG                         GAACTCCTGCTCTTACTTCTAGGGGA
genomic: CACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtc ... tggatttcagGAACTCCTGCTCTTACTTCTAGGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTGGTATCAGAATGGgtatagggtcttcgttgttttatattttgattttggtgtcattattcatttacttgatcttaatagttctagtggatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG