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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttcatttgtcttggttcagtttttcttgcattattcggttacatcctcatcagtttatgtattgcag

Basic information

species Glycine max
transcript GLYMA05G26240.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G26240.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os08g10600.1 (Oryza sativa), 5'ss of exon 5
ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGA-GAgtaagtttcatttgtct----tggttcagtttttcttgcattattcggttacatcctcatca-gtttatgtattgcag------
  || || |||||||||||||| |||||||| ||||||||||||||  | ||||||||   |||||  || ||||||||  | ||  |||   | | |||      || |     |||||   ||  |||| | |||     | ||||  ||| || ||| |  |  ||||       
GCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATGgtaatttagtcaagcatgccattaatggtttctttactctttc-ttaaaaaatcacatgttcaacatgttaactttgtgcaaccccag

upper sequence: GLYMA05G26240.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 5
ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttcatttgtcttggttc-agtttttcttgcattattcggttacatcctcatc----agttt---atgtattgcag
 ||| |||||||| |||||||| || ||||| ||||| ||||||||  ||||||||||||  || |  || ||||||||| |   || ||| |||||  |   ||   |    ||  | | | | ||  | | |    | ||||| | | |    | |||   ||   ||||||
GTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATC---AAgtgatagtaatgtcttttaaccacaattttactctcttttttaatttcgtttcacatctttaccctgaaatttgaaataacttgcag

upper sequence: GLYMA05G26240.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G019986_T04 (Zea mays), 5'ss of exon 5
ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttca-tttgtcttggttcagttttt--------cttgcattattcgg-tta-catcctcatca---gtttatgtattgcag
|||||||||||||||||||||| |||||||| ||||| ||||||||  |||| ||||| |  ||||  || ||||||||| | |   |    | ||  ||  |   |||| |  |  |||| ||        |||    | ||| | ||| ||  ||||  |   ||| ||   ||||||
ATATTGGACTTCCATCTGGAAAGTCACTTTTCCAACTCCAAGCTGAACGGATCTTGTGCGTTCAGAAGCTGGCTGCTCAATCCAGTGAAAgtaatagtttcaaacctgtcatcttctagttatttattacctcttcttctcttcagattatcacactcaaaaaatgttaataacttgcag

upper sequence: GLYMA05G26240.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G044629_T01 (Zea mays), 5'ss of exon 5
ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtt-tcatttgtcttg----gttcagtttttcttgcattattcggttacatcctcatcagtttatgtattgcag
|||| ||||||||||| ||||| |||||||| || || |||||||| |||||| |||| |  || |  || ||||||||| |||     || ||||| || |||  | ||| |     ||  |||||  | || | |     | ||   |  ||   |  ||   ||||||
ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTA---GCGAAAgtaatttctcacctttctagcaattttatgttttcttggcttcagattatcaccctcagattcata-ataacttgcag

upper sequence: GLYMA05G26240.1 (Glycine max), 5'ss of exon 5
lower sequence: AT2G35020.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttcatttgtcttggttcagtttttcttgcattattcggttacatcct---catcagtttatgtattgcag---------
|||| ||||| |||||||| ||||||||||||||  |||||||||||||||| || ||||  || || || ||| |||| || |  | |||| |||   |||     |||   |||  ||| ||| | |  | ||    |  || |   | |   || |  || |             
ATATCGGACTGCCATCTGGGAAATCACTTTTTCAGATTCAAGCTGAGAGGATCTTATGTGTCCAAAGGCTTGCTTCTCAGGCAATGAGTGAGGgtatagttctcaactctgtattctatttatct-gtacaactctaccatttcttataccttgtttcacataatattttgcctgcag

upper sequence: GLYMA05G26240.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 5'ss of exon 5
ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttcatttgtcttggttcagtttttcttgcattattcggttacatcctcatcagtttatgtattgcag
|||||||||||||||| ||||| ||||| |||||||||||||||||  | ||||||||||  || ||||| ||||||||| ||||||||||| ||||| ||  | ||  ||   |  |||| | || |||| |    |     ||| || | |||||   ||||||
ATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGGgtaaggttattctgcattctgtttgtttgtatttcatt-tgacatgctgcccttattattttattacttgcag

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|7924327|gb|AW830353.1|AW830353
EST:     TGAGAGGATTTTGCGTGCACATAGACTAGCTGCTCAAGCTACAAATGAGA                         ATTCTGCTTCTTCAGTGCAAATACACTGGTACATCATGACCAGTCCATTCA
genomic: TGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttca ... tgtattgcagATTCTGCTTCTTCAGTGCAAATACACTGGTACATCATGACCAGTCCATTCA
EST: gi|151393104|gb|EV262979.1|EV262979
EST:     TGAGAGGATTT-GTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA                         ATTCTGCTTCTTCAGTGCAAATACACTGGTACATCATGACCAGTCCATTCA
genomic: TGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttca ... tgtattgcagATTCTGCTTCTTCAGTGCAAATACACTGGTACATCATGACCAGTCCATTCA
EST: gi|13480594|gb|BG509937.1|BG509937
EST:     GAGAGGATTNTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA                         ATTCTGCTTCTTCAGTGCA
genomic: GAGAGGATT-TTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttca ... tgtattgcagATTCTGCTTCTTCAGTGCA
EST: gi|254340891|gb|GR854619.1|GR854619
EST:     TGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA                         ATTCTGCTTCTTCAGTGCAAATACACTGGTACATCATGACCAGTCCATTCA
genomic: TGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttca ... tgtattgcagATTCTGCTTCTTCAGTGCAAATACACTGGTACATCATGACCAGTCCATTCA
EST: gi|254346278|gb|GR859891.1|GR859891
EST:     TGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA                         ATTCTGCTTCTTCAGTGCAAATACACTGGTACATCATGACCAGTCCATTCA
genomic: TGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttca ... tgtattgcagATTCTGCTTCTTCAGTGCAAATACACTGGTACATCATGACCAGTCCATTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtttcatttgtcttggttcagtttttcttgcattattcggttacatcctcatcagtttatgtattgcag

- - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT