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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGCACACCAGTGCTTCTCTTACCATCAATGAGAATTATGACTCAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttctttctatcaccaatttgatgtattcattattactgttctctggtgtcacaacatgtccttatatcaagttttcgtgtgttaatgtctcgggcag

Basic information

species Glycine max
transcript GLYMA07G34680.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os06g43140.1 (Oryza sativa), 5'ss of exon 3
TGCAGCACACCAGTGCTTCTCTTACCATCAATGAGAATTATGACTCAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttctttctatcaccaatttgatgtattcattattactgttctctggtgtcacaacatgtccttatatcaagttttcgtgtgttaatgtctcgggcag
|||||||||||||||||||  | || ||||||||||| |||||||| ||||| |     || || ||||| || || | ||| || || || ||||||  |  ||  | |  |   |||   ||| |  |||      |||||    ||  |  ||   |   |   |  | || | |||  | |             
TGCAGCACACCAGTGCTTCGTTGACTATCAATGAGAACTATGACTCCGATGTCCAGTTTGACACTGAAACATTTCTTAGTCGCATTGTCCCAGAGgttaatgact--caaaaatttattatttgtttctattcaagtggttcta-attgatatgactgattgatcattttatttattgtg-atcag------------

upper sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g09460.1 (Oryza sativa), 5'ss of exon 3
TGCAGCACACCAGTGCTTCTCTTACCATCAATGAGAATTATGACTCAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttctttctatcaccaatttgatgtattcattattactgttctctggtgtcacaacatgtccttatatcaagttttcgtgtgtt-aatgtctcgggcag
|||||||||| || ||||| || |||||||||||||| |||||||| ||||| |  |  || |||||||| ||||| || || || || || |||||   |   |         |||||||   | |   | || |   |   |         | |||||        ||  |  | ||||||| | | | |   |   
TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggttg--------caatttgtcttgtctttgatcatgat---caaacaagggatcatgtaa--gagccacttcattgtgtgttcactattttcag---

upper sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 3
lower sequence: AT1G21065.1 (Arabidopsis thaliana), 5'ss of exon 3
TGCAGCACACCAGTGCTTCTCTTACCATCAATGAGAATTATGACTCAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttctttctatcaccaatttgatgtattcattattactgttctctggtgtcacaacatgtccttatatcaagttttcgtgtgttaatgtctcgggcag
| || ||||| ||||||||||| || |||||||||||||||||  |||||||||  |  ||||| || || ||| | ||  |||| ||||| ||||| | | ||| | |    |    ||  |  ||| | |  |   || ||   || | |  |  | |  |  | |  | |||  |                    
TACAACACACAAGTGCTTCTCTGACAATCAATGAGAATTATGATCCAGATGTTCAGGCTGATACTGAGACTTTCTTGAACAGGATTGTTCCTGAGgtatatctctatttg--gctggcttc-tcaatttactgatttggtgcttaagt-tgatcatttttgttgttgtggaatttcag--------------------

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|209715443|gb|BW684715.1|BW684715
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|18692788|gb|BM521636.1|BM521636
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|31456074|gb|CD398102.1|CD398102
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGCTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|9984433|gb|BE658541.1|BE658541
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|31474712|gb|CD416740.1|CD416740
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|15663182|gb|BI700553.1|BI700553
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|23733010|gb|BU764686.1|BU764686
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|16347696|gb|BI973291.1|BI973291
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|7692412|gb|AW760519.1|AW760519
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|209715444|gb|BW684716.1|BW684716
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|31472535|gb|CD414563.1|CD414563
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTNATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|298175025|gb|HO018020.1|HO018020
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|23733507|gb|BU764952.1|BU764952
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|120496558|gb|EH224725.1|EH224725
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|298172343|gb|HO019383.1|HO019383
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|6135090|gb|AW133483.1|AW133483
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|120496987|gb|EH225154.1|EH225154
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
EST: gi|27425952|gb|CA937472.1|CA937472
EST:     CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG                         GGGTCATCTGCGCCATGGAAGCATACTCTAGAGG
genomic: CAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttct ... tctcgggcagGGGTCATCTGCGCCATGGAAGCATACTCTAGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGCACACCAGTGCTTCTCTTACCATCAATGAGAATTATGACTCAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttctttctatcaccaatttgatgtattcattattactgttctctggtgtcacaacatgtccttatatcaagttttcgtgtgttaatgtctcgggcag

- - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT