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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTGACATGGGTGGAGGAAGCTGGGACAGGGATACTGTTGTTCGCACCCTTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaattttaggatataactacatattctaatggctgtttttcctacagtttggctttgcttccatttgtttggaaatttggcattggattattgctttgattcttgtattatgttctcttgcactctatctaattaaaatattgttcgttcttgataattgttag

Basic information

species Glycine max
transcript GLYMA08G32090.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G32090.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ36878 (Selaginella moellendorffii), 5'ss of exon 4
CCTTGACATGGGTGGAGGAAGCTGGGACAGGGATACTGTTGTTCGCACCCTTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaattttaggatataactacatattctaatggctgtttttcctacagtttggctttgcttccatttgtttggaaatttggcattggattattgctttgattcttgtattatgttctcttgcactctatctaattaaaatattgttcgttcttgataattgttag
  | ||||||||||| |||||||||||||||||||     |  ||| | |||||||||||||| ||||| |||||||||||||| || || ||||| || ||| |       | |||| | |     ||   || |   |  | |  ||| ||                                                                                                                     
GGTAGACATGGGTGGTGGAAGCTGGGACAGGGATAGCTGCGCCCGCGCTCTTCGTGCTGCTTACAACAATCCCGAGAGAGCTGTGGAGTACTTGTACTCGgtaagctg--cctgggatttga----gtagcttactttgttctctcgctatag---------------------------------------------------------------------------------------------------------------------

upper sequence: GLYMA08G32090.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ33528 (Selaginella moellendorffii), 5'ss of exon 3
CCTTGACATGGGTGGAGGAAGCTGGGACAGGGATACTGTTGTTCGCACCCTTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaattttaggatataactacatattctaatggctgtttttcctacagtttggctttgcttccatttgtttggaaatttggcattggattattgctttgattcttgtattatgttctcttgcactctatctaattaaaatattgttcgttcttgataattgttag
  | ||||||||||| |||||||||||||||||||     || ||| | |||||||||||||| ||||| |||||||||||||| || || ||||| || ||| |       | |||| | |     ||   || |   |  | |  ||| ||                                                                                                                     
GGTAGACATGGGTGGTGGAAGCTGGGACAGGGATAGCTGCGTCCGCGCTCTTCGTGCTGCTTACAACAATCCCGAGAGAGCTGTGGAGTACTTGTACTCGgtaagctg--cctgggatttga----gtagcttactttgttctctcgctatag---------------------------------------------------------------------------------------------------------------------
















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|151411154|gb|EV280965.1|EV280965
EST:     TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCT                         GGCATACCAGAGCAAGCCGAAGCTCCAC
genomic: TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaat ... taattgttagGGCATACCAGAGCAAGCCGAAGCTCCAC
EST: gi|254335594|gb|GR847122.1|GR847122
EST:     TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCT                         GGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaat ... taattgttagGGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
EST: gi|120494681|gb|EH222848.1|EH222848
EST:     ACCCCGAGAGATCTGTTGAATATTTGTATTCT                         GGCATACCAGAGCAACCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
genomic: ACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaat ... taattgttagGGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
EST: gi|192313583|gb|FK004165.1|FK004165
EST:     TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCT                         GGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaat ... taattgttagGGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
EST: gi|16995818|gb|BM085190.1|BM085190
EST:     TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCT                         GGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaat ... taattgttagGGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
EST: gi|192313582|gb|FK004164.1|FK004164
EST:     TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCT                         GGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaat ... taattgttagGGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
EST: gi|51336342|gb|CO980208.1|CO980208
EST:     TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCT                         GGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaat ... taattgttagGGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
EST: gi|254335595|gb|GR847123.1|GR847123
EST:     TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCT                         GGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaat ... taattgttagGGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
EST: gi|120494767|gb|EH222934.1|EH222934
EST:     TGCTGCTTATAACAACGCCGAGAGATCTGTTGAATATTTGTATTCT                         GGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT
genomic: TGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaat ... taattgttagGGCATACCAGAGCAAGCCGAAGCTCCACCAGTTACCGGAGTGCCTGCAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTGACATGGGTGGAGGAAGCTGGGACAGGGATACTGTTGTTCGCACCCTTCGTGCTGCTTATAACAACCCCGAGAGAGCTGTTGAATATTTGTATTCTgtatgtgaattttaggatataactacatattctaatggctgtttttcctacagtttggctttgcttccatttgtttggaaatttggcattggattattgctttgattcttgtattatgttctcttgcactctatctaattaaaatattgttcgttcttgataattgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT