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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAGgtaggttgctaattatatgacaccgattgacgaattgctttctaatgttcaataaaaaattatttatattcattggttttcttttatactatcctattatag

Basic information

species Glycine max
transcript GLYMA10G02040.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02040.1 (Glycine max), 5'ss of exon 10
lower sequence: AT5G50950.2 (Arabidopsis thaliana), 5'ss of exon 10
GCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAGgtaggttg-ctaat--tatatgacaccgattgacgaattgctt--tctaatgttcaataaaaaattatttatattcatt------ggttttcttttatactatcctattatag-------------------------------
||||| || ||||||| ||||||||| |||||| | |||||||| || ||  | || |||||||||||||| ||||||||||| ||  | |||||||| |||  |||||  | | | |      || | ||  | | |  ||| ||| | | | || |  | |||||||  | |       ||  ||    ||    || ||| |||                                
GCTGCACACGATGCTTGTGTTGAAACAAGTGGATCTCTTAACACAATCGCCACATCATTGATGAAGATTGCCAATGATATACGTTTTCTTGGAAGgtacgttatctaatattttttaatctttcttcaagatgtacatgttcttatgataatttaacatgtctttatatatactttatatagtggtccaagatgtattcttatgatattttaacatgtctttatatatactttatatag

upper sequence: GLYMA10G02040.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 11
GCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAGgtaggt-tgctaattatatgacaccgattgacgaattgctttctaatgttcaataaaaaattatttatattcattggttttcttttatactatcctattatag
||||| |||||||| |||||||||||||||||  || |||||||| ||||  ||||  ||||||||||||||||||||||||| || ||||||||||| || ||||| ||  ||  |      | ||       ||||||  |||       |   | ||| |  ||||   | | |||||    |   |        
GCTGCACATGATGCATTTGTTGAAACTAGTGGTTCAGTTAACACTGTTGCTACTTCCCTGATGAAGATTGCTAATGATATACGCTTATTAGGAAGgtatgtatgctagttggatagc-----cttacag-----tttctatcgttttgcttta---tttttgtggtcatcactctgctttt-ccttgctcag------
















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|207780421|gb|GD750774.1|GD750774
EST:     ATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAG                         TAGGTCCACGCTGCGGTCTTGGTGAACTC
genomic: ATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAGgtaggttgct ... cctattatagT-GGTCCACGCTGCGGTCTTGGTGAACTC
EST: gi|254343541|gb|GR857297.1|GR857297
EST:     TGCGGCTTCTTTGATGAAGATTGCT-ATGATATACGG-TGTTAGGAAG                         TGGTCCACGCTGCGGTCTTGGTGAACTCATTCTT-CTGAAAACGAACCAGG
genomic: TGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAGgtaggttgct ... cctattatagTGGTCCACGCTGCGGTCTTGGTGAACTCATTCTTCCTGAAAACGAACCAGG
EST: gi|254343540|gb|GR857296.1|GR857296
EST:     ATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAG                         TGGTCCACGCTGCGGTCTTGGTGAACTCATTCTTCCTGAAAACGAACCAGG
genomic: ATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAGgtaggttgct ... cctattatagTGGTCCACGCTGCGGTCTTGGTGAACTCATTCTTCCTGAAAACGAACCAGG
EST: gi|58014928|gb|CX701670.1|CX701670
EST:     TTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGG-TGTTTAGGAAG                         TGGTCCACGCTGCGGTCTTGGTGAACTCATTCTTCCTGAAAACGAACCAG
genomic: TTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTG-TTAGGAAGgtaggttgct ... cctattatagTGGTCCACGCTGCGGTCTTGGTGAACTCATTCTTCCTGAAAACGAACCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCCCATGATGCTTTTGTTGAAACTAGTGGAGCACTTAACACTATTGCGGCTTCTTTGATGAAGATTGCTAATGATATACGGTTGTTAGGAAGgtaggttgctaattatatgacaccgattgacgaattgctttctaatgttcaataaaaaattatttatattcattggttttcttttatactatcctattatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA