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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGATGGAACTACCTCAGTTGTTGTATTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAGgttcatttctttgtttttcatcaatggtccaactgcccttatgatgcaaattttgttgtgttttcatatcgacaaattttctactttcaactttattgat...

Basic information

species Glycine max
transcript GLYMA11G19220.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19220.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os05g48290.3 (Oryza sativa), 5'ss of exon 4
GGGGATGGAACTACCTCAGTTGTTGTATTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAGgttcatttctttgtttttcatcaatggtccaactgcccttatgatgcaaattttgttgtgttttcatatcgacaaat--tttctactttcaactttattgat------
|| ||||||||||| || |||||||| ||||||||||| ||||| ||||| || |||||| ||||       ||||| ||||| |||||||| ||  |||||  |||||   ||| | |||    | ||  ||     |  |||||| |  | | |  ||||  ||  | ||| | |  |   || |   |  || |||  |      
GGTGATGGAACTACTTCTGTTGTTGTTTTGGCTGGTGAGCTTTTGAGGGAAGCTGAAAAGTTGGTAAATATGAAGATACATCCAATGACAATCATTGCAGgtatatttca--gttctacat----gatc--accagtatactgatgccacgtatttactgttgacaattagaccactcatgcttaatcggagtttaatttgtcttctc

upper sequence: GLYMA11G19220.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 5'ss of exon 5
GGGGATGGAACTACCTCAGTTGTTGTATTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAGgttcatttctttgtttttcatcaatggtccaactgccct-tatgatgcaaattttgttgtgttttcatatcgacaaattttctactttcaactttattgat
|| |||||||||||||| |||||||| ||||| || || ||| | ||||| ||||||||||| || ||  | |||||||| |||||||| || ||| ||||| || || |     ||| |    |       |  |  | ||| | ||   | |   | ||       ||    || ||||    ||||   ||| ||   
GGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTCTAAGATTCACCCTATGACCATCATAGCAGgtacacttttggagctttaagtgttaagatgtcaactttgtatca-gcttctctcactatggcaatg-atttctaattttttcgttttctggtttcttag-

upper sequence: GLYMA11G19220.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 5'ss of exon 6
GGGGATGGAACTACCTCAGTTGTTGTATTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAGgttcatttctttgtttttcatcaatggtccaactgcccttatgatgcaaattttgttgtgttttcatatcgacaaattttctactttcaactttattgat-
|| ||||| || || ||||||||||| |||||||| || |||||||| || ||||| ||| |||| ||||| || |||||||| ||||||||||| |||||||  ||| |   |  |||        |||||     |||      |||||   |    | |   || |     | |||   | |||  | |||| |    
GGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGTGGCAGCAAAAATTCATCCCATGACAATAATTTCAGgtttgtttatagctgcttctcttgct-tccaaaatttcttccttgacaaataaggaaaggatcatatttgctgtagtttgaaattttttattttaatatga

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|207779467|gb|GD754609.1|GD754609
EST:     GGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAG                         GTTTCCGAATGGCAGCAGAGTGTGCCCGTAATGCTTTGTTGGAGAAGGTTG
genomic: GGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAGgttcatttct ... ttgtttttagGTTTCCGAATGGCAGCAGAGTGTGCTCGTAATGCTTTGTTGGAGAAGGTTG
EST: gi|254325804|gb|GR838685.1|GR838685
EST:     GGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAG                         GTTTCCGAATGGCAGCAGAGTGTGCTCGTAATGCTTTGTTGGAGAAGGTTG
genomic: GGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAGgttcatttct ... ttgtttttagGTTTCCGAATGGCAGCAGAGTGTGCTCGTAATGCTTTGTTGGAGAAGGTTG
EST: gi|298183591|gb|HO028804.1|HO028804
EST:     GGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAG                         GTTTCCGAATGGCAGCAGAGCGTGCTCGTAATGCTTTGTTGGAG
genomic: GGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAGgttcatttct ... ttgtttttagGTTTCCGAATGGCAGCAGAGTGTGCTCGTAATGCTTTGTTGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGATGGAACTACCTCAGTTGTTGTATTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAGCCAAGATTCATCCTATGACAATAATATCAGgttcatttctttgtttttcatcaatggtccaactgcccttatgatgcaaattttgttgtgttttcatatcgacaaattttctactttcaactttattgat

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