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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCTTTGGATCTGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttcattccttactcttccaatttattgctttttattttatttctattctattgcattttctgttcattatgctatgactttgtagtgtcctcaa...

Basic information

species Glycine max
transcript GLYMA15G04730.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04730.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ36167 (Selaginella moellendorffii), 5'ss of exon 3
GGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCTTTGGATCTGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttcattccttactcttccaatttattgctttttattttatttctattctattgcattttctgttcattatgctatgactttgtagtgtcctcaa
||| | |||| || || |||||||| ||||| ||| | ||| ||||||| ||||||||||||||| |||| ||||| | ||||| || || || |||||| |||| | | | ||||| | || || | |
GGCCAAGCTGAGAGAGGCCTACAAGAACAAGAAGTACATGCCTCTGGATCTTCGTCCCAAGAAGACCCGAGCGATCAGGCGACGCTTGACAAAACATCAGgtaaacaattttccattgtagaggtggtggcagctttaaaactttctttcttcgcag-------------------------------------------

upper sequence: GLYMA15G04730.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ18648 (Selaginella moellendorffii), 5'ss of exon 3
GGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCTTTGGATCTGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttcattccttactcttccaatttattgcttt----ttattttatttctattctattgcattttctgttcattatgctatgactttgtagtgtcctcaa
||| | |||| || || |||||||| ||||| ||| | ||| ||||||| ||||||||||||||| |||| ||||| | ||||| || || || |||||| |||| | | | ||| | | | | ||| | || | | |||
GGCCAAGCTGAGAGAGGCGTACAAGAACAAGAAGTACATGCCTCTGGATCTTCGTCCCAAGAAGACCCGAGCGATCAGGCGACGCTTGACAAAACATCAGgtaagcaattttccattgtagaggtggtggcagctctgaaactttctcgtttgtgttttttcgcag--------------------------------------
















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|14258928|gb|BG881827.1|BG881827
EST:     TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAAGAATTGTATTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|26269460|gb|CA820523.1|CA820523
EST:     TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|298199272|gb|HO042635.1|HO042635
EST:     TGCGTCCCAAGAAGACTAGAGCCATCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTACTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|22539768|gb|BU089611.1|BU089611
EST:     TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|14259744|gb|BG882652.1|BG882652
EST:     TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|7028584|gb|AW458367.1|AW458367
EST:     TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|7233279|gb|AW568627.1|AW568627
EST:     TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|207796380|gb|GD769730.1|GD769730
EST:     GTCCCAAGAAGACCAGTAGTCCATTCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
genomic: GTCCCAAGAAGACCAG-AG-CCA-TCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|298185885|gb|HO031046.1|HO031046
EST:     TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACTAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|298173583|gb|HO016919.1|HO016919
EST:     TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|207840821|gb|GD811014.1|GD811014
EST:     TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
EST: gi|6341759|gb|AW164645.1|AW164645
EST:     TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAG                         GCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG
genomic: TGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttca ... ttccttacagGCTTCATTGAAGACACAGCGTGAGAAGAAGAAGGAATTGTATTTTCCAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAGCGTTGAGGGAAGCTTACAAGAAGAAGAAATACCTTCCTTTGGATCTGCGTCCCAAGAAGACCAGAGCCATCAGAAGGCGCTTAACTAAGCACCAGgtacctttcattccttactcttccaatttattgctttttattttatttctattctattgcattttctgttcattatgctatgactttgtagtgtcctcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttcc