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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctatcgtttctgctgtgaatgtttgtgcaatactgtgaatcagttttgattactaaacagtatttgacaccgatggctacatatttatcacttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG

Basic information

species Glycine max
transcript GLYMA04G08510.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g02530.3 (Oryza sativa), 3'ss of exon 5
-------------------------------attctat-cgtttctgctgtga--atgtttgtgcaatactgtgaatcagttttgattact----aaacagtatttgacaccgatggctacatatttatca----cttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
                                |  ||| | ||  ||   | |  ||| ||    |        |||  ||| || || |     ||||  || |||  |  ||   |||| |  || ||     ||||||||||||||| ||||| || ||||| || ||||| ||||||||||||||||||
gtatgcttttgtgttattttgagatataaggttaatatgcattattgaaataactatggttcaagagcttcacaaatatgttctgttttcctcccaaactttacttgg-agagaaacctacttgattctctttatcttacagGGAATTGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG

upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g36070.2 (Oryza sativa), 3'ss of exon 6
------------------------------attctatcgtttctgctgtgaatgtttgtgcaata------ctgtgaatcagttttgatt---actaaacagtatttgacaccga-tggctacatatttatcacttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
                              ||  ||   |   ||     | |  ||  |  ||         ||  ||  |||||  ||   || ||   |||    |  | || |  ||   | | | |  | | |||||||| || ||||| || ||||| || ||||| ||||||||||||||||||
gtttgatcttattgctatttttgagatataatgttaatatgcatgagtaaattaattacggtatgaaagtttcgtagatatgttttttttcccaccaacttgtagagaaacctgaatccctgattctctttgccatccagGGAATCGAGATGCTATCACTTGGATCATTCAAAACTGGTGCTATTCTCTTG

upper sequence: GLYMA04G08510.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G03120.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------attctatcgtttc--tgctgtga----atgtttgtgcaatactgtgaatc--agttttgattactaaacagtatttgacaccgatggcta-catatttatcacttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
                                 | |||   | |||  || | | |    || |||  |   ||  |||||    |||     ||  | |   || | |        |   ||      ||  || | |||||||||||| ||||| ||||| || || |||||||||||||| || || |||
gttacttcccttgcactttatgggaatacataaactctgaagcttcactgttataacataatatttaagtt-taaagtgaactggagtcactgttgttgagt-gtctctttttttactaattaatgccgttgccaat-acagGGAATTGAGATGCTCTCTCTCGGATCATTCAAGACTGGTGCCATCCTTTTG

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|207703563|gb|GD686545.1|GD686545
EST:     AGAAGCATTGGCTAGCAAATAATATATTGGGTCTTGCTTTCTGTATTCAG                         GGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
genomic: AGAAGCATTGGCTAGCAAATAATATATTGGGTCTTGCTTTCTGTATTCAGgtttgttgct ... tcacttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
EST: gi|26267892|gb|CA818955.1|CA818955
EST:     AGAAGCATTGGCTAGCAAATAATATATTGGGTCTTGCTTTCTGTATTCAG                         GGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
genomic: AGAAGCATTGGCTAGCAAATAATATATTGGGTCTTGCTTTCTGTATTCAGgtttgttgct ... tcacttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
EST: gi|6481874|gb|AW201145.1|AW201145
EST:     GAAGCATTGGCTAGCAAATAATATATTGGGGTCTGGCTTTCTGTATTCAG                         GGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
genomic: GAAGCATTGGCTAGCAAATAATATATTGGG-TCTTGCTTTCTGTATTCAGgtttgttgct ... tcacttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgattactaaacagtatttgacaccgatggctacatatttatcacttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG
                                      atatttatcactta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attctatcgtttctgctgtgaatgtttgtgcaatactgtgaatcagttttgattactaaacagtatttgacaccgatggctacatatttatcacttacagGGAATTGAAATGCTTTCTCTTGGGTCTTTCAAGACTGGTGCTATTCTCTTG

- - - - - - ctgctgt
- - - - - - - - - - - - tttgtgc
- - - - - - - - - - - - - - - - -tactgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctac