Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatatatgtttatttgtttcattcccttgctggtaatcagtctgtagcatattcgttaagtataaaaaaagattacttttgtcttctgtgtatgc...

Basic information

species Glycine max
transcript GLYMA04G41530.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41530.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os03g50850.1 (Oryza sativa), 5'ss of exon 11
GGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatatatgtttatttgtttcattcccttgctggtaatcagtctgtagcatattcgttaagtataaaaaaagattacttt-tgtcttctgtgtatgc--------------------------------------------------------------------------------------------------
|||||  || || ||||| || || ||||||||||| || |||||||| |||||||| || || ||||||||||| ||||| ||||||||||| ||  |||||     ||   |||||        | |     |||   | |    | |    | |  |  |  |   | ||| || ||||||   |  |||    ||                                                                                                    
GGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTCTTGGAATTCCTAATACTAAGAACTTCAATGAAATCACATCCATCCAGgtaaat-catcactttatgctacctgtacatccactgaatagcttaatttgttctctcagaaatttgagagaaatgagtactttgcttaatcttcccatattggctgtttttatacatgttctcagaaattactgttgctgcgaatgtggtaaattggtaatggaaggggcaattgacacctcttatttctgttttcag

upper sequence: GLYMA04G41530.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G178227_T01 (Zea mays), 5'ss of exon 11
GGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatg-catatat--gtttatttgtttcattcccttg--ctggtaatcagtctgtagcatattcgttaagtataaaaaaagattacttttgtcttctgtgtatgc
|||||  || || ||||| || |||||||| ||||| ||||||||||| || ||||| || || ||||||||||||||||| ||||| ||||| || |||||||  ||| | |   ||||||  | | |||   ||    |||||  |    ||  |||||   | | | || ||       ||||||||  ||  | |  ||  
GGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCCTTGGCATTCCCAATACTAAGAATTTCAATGAAATTACATCCATCGAGgtatatcatctcttgttttattgatattattttatttacttggtatacttattggtgcata---gcttactacaatgtttatttactttttactagtata-ata-

upper sequence: GLYMA04G41530.1 (Glycine max), 5'ss of exon 11
lower sequence: AT5G06160.1 (Arabidopsis thaliana), 5'ss of exon 10
GGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatatatgtttatttgtttcattcccttgctggtaatcagtctgtagcatattcgttaagtataaaaaaagattacttttgtcttctgtgtatgc
|||||| ||  ||||||||||||||||||| || ||||| || ||||| || || || || ||||| || ||||| |||||||||||||| || |||||||||   |||||   | ||      | ||     |||   ||  |||   |||  |  |  ||   | |       | ||  |||    ||| |       
GGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCCTAGGAATCCCAAACACAAAGAACTTCAACGAAATCACTTCGATTGAGgtaataatataatatgatcaaagactttgtacagctta-aagtagtaaatagtttggtaatttgatcttgttgttgtttggtttg--tttcag-------

upper sequence: GLYMA04G41530.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv16s0098g00320.t01 (Vitis vinifera), 5'ss of exon 11
GGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatatatgt----ttatttgtttcattcccttgctggtaatcagtctgtagcatattcgttaagtataaaaaaagattacttttgtcttctgtgtatgc
|||||| || || |||||||| |||||||||||||| ||||| ||||| || || || || || ||||| || || ||||| ||||||||||||||| ||||||||   ||| |    |  ||||  | || |    | | ||||   | ||    || || |    |   |       |  |     ||       | ||   
GGCTTTTGAGCGGCATTTTAAGGAATGGCGCCATCAGCATGGTATGCGTTGCCTCGGCATTCCCAATACCAAAAACTTCAATGAAATCACATCAATTAAGgtatgctcttatctgatatcctttgcctaatacttaggtttgtaagttggctagtcca-atgcacccaacttggggtttggattggcgtgaggatgttata---

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|193379139|gb|FK343913.1|FK343913
EST:     CAAATACTAAGAATTTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: CAAATACTAAGAA-TTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
EST: gi|193413714|gb|FK378229.1|FK378229
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAAC
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAAC
EST: gi|193410766|gb|FK378909.1|FK378909
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
EST: gi|193386672|gb|FK352047.1|FK352047
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAAGCAAAGACAAGGAGTGAACAA
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATAC-AGCAAAGACAAGGAGTGAACAA
EST: gi|208266814|gb|GE061929.1|GE061929
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
EST: gi|193378398|gb|FK345089.1|FK345089
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGG
EST: gi|193340200|gb|FK307821.1|FK307821
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGC-AAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
EST: gi|193407740|gb|FK372332.1|FK372332
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
EST: gi|193386667|gb|FK352042.1|FK352042
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
EST: gi|193378207|gb|FK343652.1|FK343652
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
EST: gi|193418574|gb|FK383988.1|FK383988
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
EST: gi|193340254|gb|FK307875.1|FK307875
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
EST: gi|193347970|gb|FK309822.1|FK309822
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAA
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAA-
EST: gi|192328855|gb|FK023257.1|FK023257
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
EST: gi|193331501|gb|FK294207.1|FK294207
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGC
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGC
EST: gi|193451880|gb|FK419392.1|FK419392
EST:     GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAG                         GAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG
genomic: GTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatat ... tctgttgcagGAAGCAAAGGAACTTTGGAAGAAGATACAGCAAAGACAAGGAGTGAACAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTCTTGGTATACCAAATACTAAGAATTTCAACGAAATCACATCAATTGAGgtatgcatatatgtttatttgtttcattcccttgctggtaatcagtctgtagcatattcgttaagtataaaaaaagattacttttgtcttctgtgtatgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaaaa