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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcgtttttggatttaattctaaattttgtttctcgtttgagacaagcctgttttttgtatggctttcaatatagg

Basic information

species Glycine max
transcript GLYMA18G08230.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 5'ss of exon 5
-TTCCTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcgttt------ttggatttaattct--aaattttgtttctcgtttg-----agacaagcctgttttttgtatggctttcaatatagg-----
 ||| || || |||||||| |||||||| || || || ||||||||||||||||||||| |    |       ||   |||   ||   ||| |  |  | | || ||     ||  ||   |    || |  |   ||||| ||| ||     
TTTCTTTCCAGCTATATGACCTCAAGCAACAAGGGTTCATTGAAAGACAAGAGgtacttctctaatcagcatgttatgtttctctcataaaagtcagcatgtagtatgtgtgaaggtaactttacaattagagtaaatttca-tattggaccat

upper sequence: GLYMA18G08230.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G173424_T02 (Zea mays), 5'ss of exon 6
-TTCCTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcgtttttggatttaattctaaattttgtttctcgtttgagacaagcctgttttttgtatggctttc---aatatagg--------------
 ||| || |  || ||||||||||||||||| || | |||||| ||||||||||||       ||   | |  ||  |  ||||  || || |  | | |     |||   | | |    ||| |  |   ||||| |               
TTTCATTCCGGCTGTATGATCTCAAGCAGCAAGGCTATATTGAGAGACAAGAGgtatggtactgtggatagtattgttgttaaaagtttttacatggtaggagttagctattatgtacagtggttgacccaaatatggtatcattaaaatctt
















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|151397479|gb|EV267352.1|EV267352
EST:     CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGG                         TGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
genomic: CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcg ... tcaatataggTGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
EST: gi|8284959|gb|BE022518.1|BE022518
EST:     CTTTCAACTATATGATCTCAAGCAGCAGGGTTNTATTGAAAGACAAGAGG                         TGAAGCAGATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
genomic: CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcg ... tcaatataggTGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
EST: gi|13791269|gb|BG653860.1|BG653860
EST:     CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGG                         TGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
genomic: CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcg ... tcaatataggTGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
EST: gi|192334402|gb|FK025551.1|FK025551
EST:     CTTTCAACTATATGATCTCAAGCAGCAGG-TTTTATTGAAAGACAAGAG-                         TGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCCATCAG
genomic: CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcg ... tcaatataggTGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
EST: gi|192320225|gb|FK014239.1|FK014239
EST:     CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAG-                         TGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
genomic: CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcg ... tcaatataggTGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
EST: gi|254324275|gb|GR840592.1|GR840592
EST:     CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGG                         TGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
genomic: CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcg ... tcaatataggTGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
EST: gi|308098080|gb|HO761251.1|HO761251
EST:     CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGG                         TGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG
genomic: CTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcg ... tcaatataggTGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGACAAGAGGtacttattcgtttttggatttaattctaaattttgtttctcgtttgagacaagcctgttttttgtatggctttcaatatagg

- - - - - - - - - - - - - - - - - - - - - - -  AAGAGG