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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGCATGTAATGACTTGATGGCATATTCTTTAATTTTGTCTTGTTGTTGCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttccttccttttctgcataaatatgatatctcatctcctcttttttggcacttagtgtttgtggtttttttatatatcattagcttttaagat...

Basic information

species Glycine max
transcript GLYMA01G36860.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G36860.1 (Glycine max), 5'ss of exon 7
lower sequence: AT2G17780.3 (Arabidopsis thaliana), 5'ss of exon 7
AGAAGCATGTAATGACTTGATGGCATATTCTTTAATTTTGTCTTGTTGTTGCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgta-atgcttccttccttttctgcataaatatgatatctcatctcctcttttttggcacttagtgtttgtggtttttttatatatcattagcttttaagat
 ||||  |||||  || | || |  |||||||| ||  | || || |||||||||||||||||| |||||| ||||||||| ||||   ||||||| || ||| ||   |    ||| | ||   | ||  |  |    | |    | |||   |     | |  ||||  |                             
TGAAGTGTGTAAGAACCTAATCGTGTATTCTTTGATACTCTCATGCTGTTGCTATACTTGCTGCATAAGGAAGAAGCTTCGAAAGACACTGAACATAACGgtacatcaattaaacctctactttcttaaggtcgtgatgc-taaggtttttacggatgtcttgaatttgcag-----------------------------

upper sequence: GLYMA01G36860.1 (Glycine max), 5'ss of exon 7
lower sequence: AT4G35920.3 (Arabidopsis thaliana), 5'ss of exon 7
AGAAGCATGTAATGACTTGATGGCATATTCTTTAATTTTGTCTTGTTGTTGCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttccttccttttctgcataaatatgatatctcatctcc--tcttttttggcacttagtgtttgtg-gtttttttatatatcattagcttttaagat
 ||||||||||||||  | ||||| |||||||| ||  | |||||||| ||||||||||| ||||| |||||||| || |||||||   |||||||||| ||| | | | ||   | |  | ||      |||   || | |     ||   ||||   |  |   | | |  | ||      | ||   || | |||     
TGAAGCATGTAATGAGCTAATGGCGTATTCTTTGATACTTTCTTGTTGCTGCTATACTTGTTGCGTGAGGAGGAAACTCCGGAAGACACTGAACATCACGgtattacattctcattctcttccactcgcttgaatccttaccattaatcccatttgatcccaaaaatctatatgcttccgagaaaatttctatcatttgc---

upper sequence: GLYMA01G36860.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv00s0349g00020.t01 (Vitis vinifera), 5'ss of exon 5
AGAAGCATGTAATGACTTGATGGCATATTCTTTAATTTTGTCTTGTTGTTGCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttccttccttttctgcataaatatgatatctcatctcctcttttttggc--acttagtgtttgtggtttttttatatatcattagcttttaagat-
|||||| |||||||| ||||||||||||||  | || || || ||||||||||||||||||||  | || ||||||||||| || |||||||||||||| ||||  || |  ||   | |||||| |  |   | |   ||    | | || ||    |   ||        |  || | || |  ||   || | |      
AGAAGCCTGTAATGAATTGATGGCATATTCAATGATATTATCATGTTGTTGCTATACTTGCTGTATCAGAAGGAAGCTTCGCAACATGTTGAACATCACGgtaa--ctcctctctgctgctgcattatcagattcttatatgggatatattgtgattgagacaggaacccctgaattatgat-ttccacctgcatgtgctcct

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|208052065|gb|GD853000.1|GD853000
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTAT
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTAT
EST: gi|193611170|gb|FK563038.1|FK563038
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTATTGATGATTT
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTT
EST: gi|193706751|gb|FK644900.1|FK644900
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTTATTTGTATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGT
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTT-ATT-G-ATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGT
EST: gi|193467641|gb|FK433538.1|FK433538
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
EST: gi|193404515|gb|FK368196.1|FK368196
EST:     GGAAGATGTTGAACTATCACA                         -GGGGATTTATTGATGATTTCCTCTCTCATTTGATATGTTGCTGCTGTGC
genomic: GGAAGATGTTGAAC-ATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGC
EST: gi|193418897|gb|FK382239.1|FK382239
EST:     GGAAGATGTTGAACATCACA                         GGGGGATTTATTGATGATTTCCTCTCTCATTTGATATGTTGCTGCTGTGCC
genomic: GGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
EST: gi|193427696|gb|FK394380.1|FK394380
EST:     GGAAGATGTTGAACATCACA                         GGGGGATTTATTGATGATTTCCTCTCTCATTTGATATGTTGCTGCTGTGCC
genomic: GGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
EST: gi|193545650|gb|FK501245.1|FK501245
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
EST: gi|58017076|gb|CX703818.1|CX703818
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
EST: gi|58015866|gb|CX702608.1|CX702608
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
EST: gi|58016776|gb|CX703518.1|CX703518
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
EST: gi|193377090|gb|FK342727.1|FK342727
EST:     GGAAGATGTTGGACATCACA                         GGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTTGTTGCTGCTGTGC
genomic: GGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATG-TGTTGCTGCTGTGC
EST: gi|193511931|gb|FK471383.1|FK471383
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTATTGATGATTTCCTC
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTC
EST: gi|57574765|gb|CX547740.1|CX547740
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC
EST: gi|207697583|gb|GD679528.1|GD679528
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGGGGATTTATTGA
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGA
EST: gi|6134694|gb|AW133087.1|AW133087
EST:     GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACA                         GGCGGATGTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCN
genomic: GCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttc ... tctatgccagGGGGGATTTATTGATGATTTCCTCTCTCATTTGATGTGTTGCTGCTGTGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGCATGTAATGACTTGATGGCATATTCTTTAATTTTGTCTTGTTGTTGCTATACTTGCTGCGTAAGGAGGAAGCTTCGGAAGATGTTGAACATCACAgtaatgcttccttccttttctgcataaatatgatatctcatctcctcttttttggcacttagtgtttgtggtttttttatatatcattagcttttaagat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttcct