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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatcttatcagtatcaattttatgcactattattttattttattcaatactattatattatatattgtacctcaccacttgatgtgaggaccaat...

Basic information

species Glycine max
transcript GLYMA13G43050.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43050.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g53880.4 (Oryza sativa), 5'ss of exon 5
AGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatcttatcagtatcaattttatgca-ctattattttattttattcaatactattatattatatattgtacctcaccacttgatgtgaggaccaat------------------------------------------------------
| ||| | || || |||||||| ||| || | |||||| |||||||| || | |||||||||||||||||| |||||||| ||||||||| |||||| | | | | | || | ||| | |||| |||| | || ||| | | | |||| | | | ||
ACAAAATATTTTATCAATTGTTGGATGGGTCTGGTGAATATACTCTAGTTTATGAAGACAGTGAAGGAGACAGGATGCTGGTTGGGGACGTGCCATGGAAgtaagtttgctggtcccccttgtcatttacagtttttactggcatttacaaaataatcaaatcttaaaaacaacaaaaggacact-gccaccataatttatattaggcaccaccaaaccatctaaattatttttcctgttctccaattcctgcag

upper sequence: GLYMA13G43050.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G51950.1 (Arabidopsis thaliana), 5'ss of exon 3
AGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatcttatcagtatcaattttatgcactattattttattttattcaatactattatattatatattgtacctcaccacttgatgtgaggaccaat-------
| ||| |||| || || ||||| ||||| | |||||| | ||||||| ||||| || ||||||||||||| ||||||||| || ||||| ||||||||||||| ||||| || | | || | | | || | | | | | | | || | ||| || | | | | | ||| | | ||
AAAAACCAATCACTGGATTATTAGATGGGAATGGAGAATATACTCTTACATATGAAGACAATGAAGGAGACAAGATGCTTGTAGGAGATGTTCCATGGCAgtaagaatcttttcttt-----tctttttcgtttttttctgaatctgagtcagctttttgttctatctaaaggaga--agtattagattcctagtcacatatttatt

upper sequence: GLYMA13G43050.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G16500.1 (Arabidopsis thaliana), 5'ss of exon 3
AGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatcttatcagtatcaattttatgca-ctattattttattttattcaatactattatattatatattgtacctcaccacttgatgtgaggaccaat
||||| | || | || ||||| ||||| | ||||| |||||| | ||||| || |||||||| |||| |||||||||||||||||| ||||||||||||| ||||| || | || | || | || | | |||| ||| ||| | |||| | | | | | | | |||
AGAAACCTATCATTGGATTATTAGATGGGAAAGGAGAATTTACTTTAACCTATGAAGACAATGAAGGGGACAAGATGCTTGTTGGGGATGTTCCATGGCAgtaagaatcttttccccttttgttctctgaatctgattcagtgttttgcagaattagattcttgatcatataacaacaaaagttctcagcttttaatcaa-

upper sequence: GLYMA13G43050.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv09s0002g03410.t01 (Vitis vinifera), 5'ss of exon 5
AGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatcttatcagtatcaattttatgcactattattttattttattcaatactattatattatatattgtacctcaccactt--gatgtgaggaccaat--
||||| | ||||| || || | ||||| ||||| || | ||| |||||||| |||||||| ||||||||||| | |||||||||||||| |||||||||||||||||| | || | | || | ||||| | || |||| | || || ||| | |||| ||||||| || | || || |
AGAAAACTATTACTGGTTTGCTCGATGGGAGTGGCGAATATACGCTTGTTTACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatctaaccactgtggatctgatgcatttcaat--tattcaaatcccatttagtatgcaa-atat-gtacctcttttgttctgtagttagagtttgtcc

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|207697981|gb|GD681046.1|GD681046
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|208234357|gb|GE034506.1|GE034506
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|208329805|gb|GE128838.1|GE128838
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTTGTATCAACAGTGAAAGAAGGCTACGAGTGTTGAAGAGTTCTGA
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTT-GTATCAACAGTGAA-GA-GGCTACGAGTGTTGAAGAGTTCTGA
EST: gi|22928435|gb|BU545574.1|BU545574
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|193355500|gb|FK322157.1|FK322157
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|192297031|gb|FG990317.1|FG990317
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|302141315|gb|HO212191.1|HO212191
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|208103627|gb|GD904038.1|GD904038
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|193677010|gb|FK618762.1|FK618762
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|207787661|gb|GD762033.1|GD762033
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAAGC
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGA-GC
EST: gi|193571278|gb|FK532257.1|FK532257
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|192308530|gb|FK002426.1|FK002426
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|7692407|gb|AW760514.1|AW760514
EST:     TATGACGATAATGAACGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCATCAGTGAAGACGCTACTAGTG
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTG
EST: gi|5058123|gb|AI736599.1|AI736599
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|207818234|gb|GD792323.1|GD792323
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTT
EST: gi|193510942|gb|FK468882.1|FK468882
EST:     CTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: CTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|193464135|gb|FK427919.1|FK427919
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|208170090|gb|GD966525.1|GD966525
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGNGCT
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAGTTCTGAGCT
EST: gi|13312662|gb|BG406313.1|BG406313
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCA                         CATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGAAGTTCTGAGC
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAGTGAAGAGGCTACGAGTGTTGAAGA-GTTCTGAGC
EST: gi|193387770|gb|FK350975.1|FK350975
EST:     TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGG-ATGTGCCATGGCA                         CATGTTTGTATCAACAG
genomic: TATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatct ... tgcttggcagCATGTTTGTATCAACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatcttatcagtatcaattttatgcactattattttattttattcaatactattatattatatattgtacctcaccacttgatgtgaggaccaat

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG