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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTGACATGGGTGGAGGAAGCTGGGACAGGGATACTGTTGTTCGTGCTCTTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttgtaggatataactactttatattttaatggctgttttttctacagtttggctttgcttccatttgtttggaaatttagcgttggattattgctttggttcttttattatgttctcttgcactctatttaattaaaatattgtttgttgttgataattgttag

Basic information

species Glycine max
transcript GLYMA01G20670.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G20670.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ36878 (Selaginella moellendorffii), 5'ss of exon 4
CCTTGACATGGGTGGAGGAAGCTGGGACAGGGATACTGTTGTTCGTGCTCTTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttg--taggatataactactttatattttaatggctgttttttctacagtttggctttgcttccatttgtttggaaatttagcgttggattattgctttggttcttttattatgttctcttgcactctatttaattaaaatattgtttgttgttgataattgttag
  | ||||||||||| |||||||||||||||||||     |  || ||||||||||||||||| ||||| || ||||||||||| || || ||||| || ||| | ||  | |||| | | ||  |||  || |         | |  ||| ||                                                                                                                     
GGTAGACATGGGTGGTGGAAGCTGGGACAGGGATAGCTGCGCCCGCGCTCTTCGTGCTGCTTACAACAATCCCGAGAGAGCTGTGGAGTACTTGTACTCGgtaagctgcctgggatttgagtagcttactttgtt-------ctctcgctatag---------------------------------------------------------------------------------------------------------------------

upper sequence: GLYMA01G20670.1 (Glycine max), 5'ss of exon 6
lower sequence: EFJ33528 (Selaginella moellendorffii), 5'ss of exon 3
CCTTGACATGGGTGGAGGAAGCTGGGACAGGGATACTGTTGTTCGTGCTCTTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttg--taggatataactactttatattttaatggctgttttttctacagtttggctttgcttccatttgtttggaaatttagcgttggattattgctttggttcttttattatgttctcttgcactctatttaattaaaatattgtttgttgttgataattgttag
  | ||||||||||| |||||||||||||||||||     || || ||||||||||||||||| ||||| || ||||||||||| || || ||||| || ||| | ||  | |||| | | ||  |||  || |         | |  ||| ||                                                                                                                     
GGTAGACATGGGTGGTGGAAGCTGGGACAGGGATAGCTGCGTCCGCGCTCTTCGTGCTGCTTACAACAATCCCGAGAGAGCTGTGGAGTACTTGTACTCGgtaagctgcctgggatttgagtagcttactttgtt-------ctctcgctatag---------------------------------------------------------------------------------------------------------------------
















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|31560965|gb|CD486803.1|CD486803
EST:     TGCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCC                         GGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
genomic: T-CGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttgta ... taattgttagGGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
EST: gi|5508981|gb|AI855539.1|AI855539
EST:     TTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCC                         GGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttgta ... taattgttagGGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
EST: gi|254337503|gb|GR845180.1|GR845180
EST:     TTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCC                         GGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttgta ... taattgttagGGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
EST: gi|57575208|gb|CX548183.1|CX548183
EST:     TTCGTGCTGCTTATAACAACCNTGAGAGAGCTGTTGAATATTTGTATTCC                         GGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttgta ... taattgttagGGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
EST: gi|254343685|gb|GR857441.1|GR857441
EST:     GAATATTTGTATTCC                         GGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
genomic: GAATATTTGTATTCCgtatgttgta ... taattgttagGGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
EST: gi|254341730|gb|GR852867.1|GR852867
EST:     GAGAGAGCTGTTGAATATTTGTATTCC                         GGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
genomic: GAGAGAGCTGTTGAATATTTGTATTCCgtatgttgta ... taattgttagGGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
EST: gi|21888703|gb|BQ741916.1|BQ741916
EST:     TTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCC                         GGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttgta ... taattgttagGGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
EST: gi|151395622|gb|EV265499.1|EV265499
EST:     TTCGTGCTGCCTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCC                         GGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttgta ... taattgttagGGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
EST: gi|7146671|gb|AW508593.1|AW508593
EST:     TTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCC                         GGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT
genomic: TTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttgta ... taattgttagGGCATACCAGAGCAAGCTGAAGCTCCACCTGTTACCCGAGAGCCTGCAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTGACATGGGTGGAGGAAGCTGGGACAGGGATACTGTTGTTCGTGCTCTTCGTGCTGCTTATAACAACCCTGAGAGAGCTGTTGAATATTTGTATTCCgtatgttgtaggatataactactttatattttaatggctgttttttctacagtttggctttgcttccatttgtttggaaatttagcgttggattattgctttggttcttttattatgttctcttgcactctatttaattaaaatattgtttgttgttgataattgttag

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