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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGATCAGAAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAGgtaacaactgatttgtgtcccctacatcttttccctctttccttaaatttttctagggatttatggagttagaatttggggtttcaagtgcttcagcttt...

Basic information

species Glycine max
transcript GLYMA09G38430.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38430.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os02g39300.1 (Oryza sativa), 5'ss of exon 9
ACTGATCAGAAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAGgtaacaactgatttgtgtcccctacatcttttccctctttccttaaatttttctagggatttatggagttagaatttggggtttcaagtgcttcagcttt-----------
|||||||| ||| | ||  |||| ||||| ||||||||||| ||||| || ||||||||||||      |||| |  ||  |  | |||  || ||  |   |  ||     |   ||   ||| |     | ||||||||||||||||||||||||||           
ACTGATCAAAAGTTGCGCCTGTGTGACATATGTGGAGCATTCTTGAGCGTATATGACAGgtaa------atttat--cctttttaacttcaccatcaatttctgcatgggggtcatga---atgtacgagaattttggggtttcaagtgcttcagcttttgacgaacacc

upper sequence: GLYMA09G38430.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 5'ss of exon 9
ACTGATCAGAAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAGgtaacaactgatttgtgtcccctacatcttttccctctttccttaaatttttctagggatttatggagttagaatttggggtttcaagtgcttcagcttt--------------
||||||||||||||||| || || ||||||||||||||||||||||| |||||||| ||||||      |||| | || |     ||  |||    ||||  ||  |||    ||||    |  || |||| |||||||||||||||| ||||||||||              
ACTGATCAGAAGCTACGCGTATGTGACATTTGTGGAGCATTTTTGAGCGTTTATGATAGgtaa-----aatttttatctc----gtcacttcatattttc--tagctttg---agggcgacaaagaattagtatttggggtttcaagtacttcagcttttgacctggcgatta
















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|6566492|gb|AW234137.1|AW234137
EST:     AAGCTACGTGTGTGCGACATTTGTGGAGCANTTTTGAGTGTGTATGACAG                         TGATCGCCGTTTAGCTGATCATTTTGGATGCAAACTTCATTTANGGTATAT
genomic: AAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAGgtaacaactg ... attattacagTGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATAT
EST: gi|254336538|gb|GR842717.1|GR842717
EST:     AAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAG                         TGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATAT
genomic: AAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAGgtaacaactg ... attattacagTGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATAT
EST: gi|254336539|gb|GR842718.1|GR842718
EST:     AAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAG                         TGATCGCCGTTTAGCTGATCATTTGGGAGGCAAACTTCATTTAGGGTATAT
genomic: AAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAGgtaacaactg ... attattacagTGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATAT
EST: gi|208146329|gb|GD946208.1|GD946208
EST:     AAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAG                         TGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATAT
genomic: AAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAGgtaacaactg ... attattacagTGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATAT
EST: gi|16343424|gb|BI969019.1|BI969019
EST:     AAGCTACGTGTGTGCGACATTTGTGGAGCATTNNNGAGTGTTTATGACAG                         TGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCANNNAGGGTATAT
genomic: AAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAGgtaacaactg ... attattacagTGATCGCCGTTTAGCTGATCATTTTGGAGGCAAACTTCATTTAGGGTATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGATCAGAAGCTACGTGTGTGCGACATTTGTGGAGCATTTTTGAGTGTTTATGACAGgtaacaactgatttgtgtcccctacatcttttccctctttccttaaatttttctagggatttatggagttagaatttggggtttcaagtgcttcagcttt

- - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggggt