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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGTGGGAACTTTTAAATGATGTGAAAGCTATATGGCTGAGGAATCCAAAAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgccaatttgccatgcttgttccttatacatcaagggaatttattgtgaaattcacttcactgagtttgttaatattcataaagttgtggatttatgttttgtgcag

Basic information

species Glycine max
transcript GLYMA14G40320.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40320.2 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 9
TGAGTGGGAACTTTTAAATGATGTGAAAGCTATATGGCTGAGGAATCCAAAAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgccaatttgccatgcttgttccttatacatcaagggaatttattgtgaaattcacttcactgagtttgttaatattcataaagttgtggatttatgttttgtgcag
||||||||| ||| | ||||||||||| |||||||||||  | |  || || |||||||| |||||||||||||| || || |||||||| ||||| |||||| ||    ||   |||  || |   |  ||| |     |    ||||  ||| |   |  |   |   ||   || |    ||||  | |     |||    ||||||    
TGAGTGGGAGCTTCTGAATGATGTGAAGGCTATATGGCTTCGTAGCCCTAAGGAGGTTACTGAAGAAGAATACACAAAGTTTTACCACTCACTTGCTAAGgta-ca----cagactgcagtgatgaat--ttacaggagcataacattttatgtaagccttgcagaagaaagcaagtaacc--tcatttaatatcaaatt---attttgtag--

upper sequence: GLYMA14G40320.2 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G141931_T01 (Zea mays), 5'ss of exon 9
TGAGTGGGAACTTTTAAATGATGTGAAAGCTATATGGCTGAGGAATCCAAAAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaa-cattgccaatttgccatgcttgttccttatacatcaagggaatttattgtgaaa---ttcactt---cactgagtttgttaa-tattcataaagttgtggatttatgttttgtgcag
||||||||||||| | ||||||||||| ||| |||||||  | |  ||||| |||||||| || ||||||||| | || || ||||| || || ||||||||||  | ||      ||   |  ||  |  | |  || ||   |  |||       ||   ||  |||   |||   ||||| ||| ||||  || | |     |   ||  ||| | |||
TGAGTGGGAACTTCTGAATGATGTGAAGGCTGTATGGCTTCGCAGCCCAAAGGAGGTTACCGATGAAGAATACTCGAAGTTTTACCATTCACTAGCCAAGgtaaatactgtagcaatggattagttagtagt-actcaacatttgtttttgccaaagaaagctttgcttgtacaccttgtttgataaatatttgtata-taacttaacaattcttttttcag

upper sequence: GLYMA14G40320.2 (Glycine max), 5'ss of exon 9
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 9
TGAGTGGGAACTTTTAAATGATGTGAAAGCTATATGGCTGAGGAATCCAAAAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaa----cat-tgccaatttg-ccatgcttgttccttatacatcaagggaatttattgtgaaattcacttcactgagtttgttaatattcataaagttgtggatttatgttttgtgcag
||| ||||| ||| | |||||||| || |||||||||||||| | |||||| ||||| ||||| ||||| ||||| |||||||||||||||||  | ||||| |    |||  |  || |    ||| |||||| | ||           | |||  |||| | ||| ||   |  ||||  |  | |                                
TGAATGGGAGCTTCTGAATGATGTTAAGGCTATATGGCTGAGAAGTCCAAAGGAGGTGACAGAGGAAGAGTACACTAAATTCTACCACTCTCTCTCAAAGgtgaaaaccatgcgttaactaaatcatacttgttacatactaggtgtaaaattttcgtgtggatttccctgaccccagttgttatacag-------------------------------

upper sequence: GLYMA14G40320.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 9
TGAGTGGGAACTTTTAAATGATGTGAAAGCTATATGGCTGAGGAATCCAAAAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgccaatttgccatgcttgttccttatacatcaagggaattt-attgtgaaattcacttcactgagtttgttaatattcataaagttgtggatttatgtt---ttgtgcag---
||||||||| ||||| ||||||||||| ||||||||| |  |||||||||| ||||| || || ||||| ||||| ||||||||||| ||||| || |||| || ||| ||||||  || || |  ||| ||| |  ||||   | | | |||||    ||    |  |  ||| |     | | ||| |  | |   |  ||| ||   |||| ||    
TGAGTGGGAGCTTTTGAATGATGTGAAGGCTATATGGTTACGGAATCCAAAGGAGGTGACGGAGGAAGAGTACACAAAATTCTACCAGTCTCTAGCTAAGgcaa-att-ccaattc-ccttggt--ttcattacatttcaaaatactctgattgttttttttggcttcccaagtatcactctttccatcagttggataacatattttatcttgttcaacag

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|298169805|gb|HO018429.1|HO018429
EST:     AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATCTCACTGCTGAGGGT
genomic: AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|57574607|gb|CX547582.1|CX547582
EST:     AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|8283891|gb|BE021450.1|BE021450
EST:     AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|192301679|gb|FG997621.1|FG997621
EST:     AGAATACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: AGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|193583665|gb|FK539323.1|FK539323
EST:     AATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: AATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|58019806|gb|CX706548.1|CX706548
EST:     AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|208331878|gb|GE130701.1|GE130701
EST:     CACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGC
genomic: CACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|208227053|gb|GE024154.1|GE024154
EST:     TACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCAT
genomic: TACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCAT
EST: gi|192309871|gb|FK001415.1|FK001415
EST:     AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|193429754|gb|FK392798.1|FK392798
EST:     AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|193476836|gb|FK442637.1|FK442637
EST:     AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|23059035|gb|BU578351.1|BU578351
EST:     CACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: CACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|7233546|gb|AW568951.1|AW568951
EST:     CACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: CACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|213592217|gb|DB965980.1|DB965980
EST:     AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
EST: gi|254328195|gb|GR835160.1|GR835160
EST:     AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAG                         GATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT
genomic: AAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgc ... ttttgtgcagGATTTCAGTGATGAGAAACCTTTAGCATGGAGTCATTTCACTGCTGAGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGTGGGAACTTTTAAATGATGTGAAAGCTATATGGCTGAGGAATCCAAAAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaacattgccaatttgccatgcttgttccttatacatcaagggaatttattgtgaaattcacttcactgagtttgttaatattcataaagttgtggatttatgttttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG