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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGGAAGCGCCTTGTGCCAGTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATGgtattgaaataattaattaagttggcatgaatatattggagcaggaatctattttttatgctttatttccctccttccctaactatgtctgctattgcag

Basic information

species Glycine max
transcript GLYMA17G07050.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07050.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 5'ss of exon 6
GGGGGAAGCGCCTTGTGCCAGTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATGgtattgaaataattaattaagttggcatgaatata-ttggagcaggaatctattttttatgctttatttccctccttccctaactatgtctgctattgcag
| || || || ||||| || || ||||| || ||||||||||||||||||||||||||||| |  ||||||||  | | ||  |   |   |     | | | || ||     ||| || |      | ||  ||| || | | | |  || |   | |         |||
GTGGAAAACGTCTTGTTCCGGTTGGTCTTGGAGATGATGATCAATGCATTGAGGATGACTTCAACGCATGgtac-gcattatcttgctctttcaagcttattttagttattttaggcatttccgcact-tgtgttacttacattcctttctgaacttttacatatcaccag

upper sequence: GLYMA17G07050.2 (Glycine max), 5'ss of exon 7
lower sequence: AC217947.4_FGT002 (Zea mays), 5'ss of exon 6
GGGGGAAGCGCCTTGTGCCAGTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATGgtattgaaataattaattaagttggcatgaatatattggagcaggaatctattttttatgctttatttccct--ccttccctaactatg-tctgctattgcag
| || ||||||||||| ||||| ||||| || || ||||| |||||||||||||||||||| | |||||||||   | ||  |   ||   |||   |   | | || ||     | |  | |  ||  |  |||||| | |  | || |  |||| || | || | ||    
GTGGAAAGCGCCTTGTTCCAGTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATGgtac--atattctggtttcttttgagctctttttttttgac----atttgactgcttcagtgttatttacgttgcttttctgaactctgatgtgttcttag--

upper sequence: GLYMA17G07050.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G144407_T01 (Zea mays), 5'ss of exon 7
GGGGGAAGCGCCTTGTGCCAGTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATGgtat-tgaaataattaatt--aagttggca---tgaatatattggagcaggaatct-attttttatgctttatttccctccttccctaactatgtctgctattgcag----------------------
| || ||||||||||| ||||| ||||| || ||||||||  ||||||||||||||||||| |   |||||||  |    |  ||  ||   || |  |    |   | | ||      || || | | |  ||  |  ||||||   | || |  |   |     ||   ||| |                       
GCGGAAAGCGCCTTGTTCCAGTTGGTCTTGGAGATGATGACAAATGCATTGAGGATGACTTCAACACATGgtacatattctggtttcttttgagctctctctctctctgttttttttttggcatttgactgcttcagtgttattta--tgctgcattgtttgaacttgaagttgaactctgttgtgttcttatatttag

upper sequence: GLYMA17G07050.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 7
GGGGGAAGCGCCTTGTGCCAGTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATGgtattgaaat-aattaattaagttggcatgaatatattggagcaggaatctattttttatgctttatttccctccttccctaact--atgtctgctattgcag
| || |||||| |||| ||||||||||| || |||||||| ||||||||||||||||||||  ||||||||||   ||||  | | | ||    || ||  | |   ||  |  |     |   ||||||  |  | |   ||  |  | ||  |  |    |||||||  ||
GTGGAAAGCGCATTGTCCCAGTGGGTCTTGGGGATGATGACCAATGCATTGAGGATGACTTCGCTGCATGgtacaaaaattgaatcactac-ccggaatatacaatgtgttgatgtgcattcccttttatattaaaataatcttatatcttatgtcaactgttgctattctag

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|6134738|gb|AW133131.1|AW133131
EST:     GTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATG                         GAAAGAAGAACTGTGGCCAGCATTGGATGAATTGCCTTAGAGATGAGGACG
genomic: GTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATGgtattgaaat ... gctattgcagGAAAGAAGAACTGTGGCCAGCATTGGATGAATTG-CTTAGAGATGAGGACG
EST: gi|192316747|gb|FK006450.1|FK006450
EST:     GTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATG                         GAAAGAAGAACTGTGGCCAGCATTGGATGAATTGCTTAGAGATGAGGACGA
genomic: GTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATGgtattgaaat ... gctattgcagGAAAGAAGAACTGTGGCCAGCATTGGATGAATTGCTTAGAGATGAGGACGA
EST: gi|193439204|gb|FK406331.1|FK406331
EST:     TGATCAATGCATTGAGGATGACTTTACTGCATG                         GAAAGAAGAACTGTGGCCAGCATTGGATGAATTGCTTAGAGATGAGGACGA
genomic: TGATCAATGCATTGAGGATGACTTTACTGCATGgtattgaaat ... gctattgcagGAAAGAAGAACTGTGGCCAGCATTGGATGAATTGCTTAGAGATGAGGACGA
EST: gi|192316746|gb|FK006449.1|FK006449
EST:     GTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATG                         GAAAGAAGAACTGTGGCCAGCATTGGATGAATTGCTTAGAGATGAGGACGA
genomic: GTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATGgtattgaaat ... gctattgcagGAAAGAAGAACTGTGGCCAGCATTGGATGAATTGCTTAGAGATGAGGACGA
EST: gi|21887259|gb|BQ740472.1|BQ740472
EST:     ATGATCAATGCATTGAGGATGACTTTACTGCATG                         GAAAGAAGAACTGTGGCCAGCATTGGATGAATTGCTTAGAGATGAGGACGA
genomic: ATGATCAATGCATTGAGGATGACTTTACTGCATGgtattgaaat ... gctattgcagGAAAGAAGAACTGTGGCCAGCATTGGATGAATTGCTTAGAGATGAGGACGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGGAAGCGCCTTGTGCCAGTGGGTCTAGGTGATGATGATCAATGCATTGAGGATGACTTTACTGCATGgtattgaaataattaattaagttggcatgaatatattggagcaggaatctattttttatgctttatttccctccttccctaactatgtctgctattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG