Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgcgagattttcaattgggtgcaataatatattgctttacagactgtgtttgcttcctttccatttata...

Basic information

species Glycine max
transcript GLYMA12G31040.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
lower sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 3
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgcgagattttcaattgg-gtgcaataatatattgctttacagactgtgtttgcttcctttccatttata
 || ||||||||| | ||||| || ||||| || ||||||||| ||||| | || |||||||||||||| |||||||| |||||||| ||||| ||||||||          | |  |   |     ||| ||  |   ||   ||| |     | || |||| | |  || |   || | ||| ||   ||         
TCAAAAGGACAAGAGATTTAGCGGTTCTGTGAAATTGCCTCACGTTCCTAGGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgt------tcacttttttccgccttttcttttgaaaatgttatgattagtacttagtagtatagtac--tataacttgcggttggtttacttag-------

upper sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
lower sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgcgagattttcaattgggtgcaataatatattgctttacagactgtgtttgcttcctttccatttata-
 || ||||| |||||||| ||||| ||||| ||| | || || ||||||||||| || |||||||| ||||||||||||||||| || || ||||| |||||        |||  || | || |  | || || |    | |   |||| |  |||    |  || || ||| |  ||||||| |   |||   || ||| 
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgt--------gattgaaatctctatactttttgtgta--tcttgtttggtttgaat----tggtgattgacacaaagtgtttgat--gtttgttttgatag

upper sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
lower sequence: AT1G08360.1 (Arabidopsis thaliana), 5'ss of exon 3
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaata-agctgatctaattatcaaacccttgtgcgagattttcaattgggtgcaataatatattgct--ttacagactgtgtttgcttcctttccatttata
 || |||||||||||||| ||||| ||||| ||||| || || || || || || || |||||||| || ||||| ||||||||||| || ||||||||||| ||| | ||  ||     |    | | || || |   | ||   |   ||  |||  | |  ||||  || ||    |||  |   |   || |||||   
TCAAAAGGACAAGCGTTTCAGTGGATCTGTCAAGTTACCACATATCCCCCGTCCTAAAATGAAGATCTGCATGCTCGGAGATGCCCAGCATGTTGAAGAGgtgatatatcttttcatggaaattgatcattttgtgctctgtttctt---gtataatggttttgtgctcatttcatttggtggctctattagtttcatttgat

upper sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 5
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgcgagattttcaattgggtgcaataatatattgct--ttacagactgtgttt--gcttcctttccatttata
|||||||||||||||||| ||||| ||||| |||||||| ||||| |||||||||||||||||| | || |||||||| ||||| |||||||| |||||||||||    || || | ||  |          || | |     | |      |||   |  ||||||  ||  ||| | | |||   ||   |||   ||||  
CCAGAAGGACAAGCGTTTCAGTGGTTCTGTGAAGTTGCCCCACATCCCTCGCCCCAAGATGAAGGTCTGCATGCTTGGTGATGCTCAACACGTGGAAGAGgtaattg--tgctccacttggctgcattaatggcaataaaagaagtgaaagacaagtgt-cattgctaattgaagaatatttttcaactatttttttgtttaa-

upper sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 5'ss of exon 2
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgcgagattttcaattgggtgcaataatatattgctttacagactgtgttt--gcttcctttccatttata----
|||||| ||||| ||||| || |||||||| ||| |||| ||||||||||| || |||||||   | || |||||||||||||| || ||||| || ||||| |||  |  |  |    ||  ||   |||  |   || ||   ||   |   | | ||| ||| || |       | | |   |   | |||   | | |    
CCAGAAAGACAAACGTTTCAGCGGCTCTGTGAAGCTGCCACACATTCCTCGTCCTAAGATGAGAGTGTGCATGCTTGGAGATGCTCAGCACGTCGAGGAGgtcatattcgcacattggaat--aatttttgc-cttcatatttgtttcatttttagattatcttgattaatgtctcatttcttaaccaacgttcatctgacaatag

upper sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 5'ss of exon 2
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaaccct-----tgtgcgagattttc--aattgggtgcaataatatattgctttacagactgtgttt-gcttcctttccatttata-------------------------------------------------------------------------------------
|||||| ||||||||||| |||||||| || ||| | || ||||||||||| || ||||||| |||||||||||||||||||||||||||  |||||||||||      |  || |||| | |  |  |     |||    | |      |||||  |  || | | ||    |||     ||| || |    ||  |  | ||| ||                                                                                     
CCAGAAAGACAAGCGTTTCAGTGGCTCCGTGAAGCTTCCCCACATTCCTCGTCCTAAGATGAGGATTTGTATGCTTGGAGATGCCCAACATATTGAAGAGgtatgcttattctcaaattttgattctttctatttgttgatggtgccagaaattgaataaaacattgtagaattttctgctctgggtctcatctcactggcctttgtatattaaaactagaaattatcaccctttacttgataatggataattgctgatgtcgtgagtttcttttggtcgtaactcgtcacag

upper sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 5'ss of exon 2
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataag-ctgatctaattatcaa-acccttgt-gcgagattttcaattgg-gtgcaataatatattgctttacagactgtgtttgcttcctttccatttata--------
|||||| ||||||||||| ||||| || || ||| |||| |||||||||||||| ||||||    | || ||||| ||||||||||| |||||||| |||||| |    || |   || ||     |||| ||| | ||    ||   |  |  ||| | | ||    | || |    || |  ||  |||    |||||  |         
CCAGAAAGACAAGCGTTTCAGTGGTTCCGTGAAGCTGCCACACATTCCTCGCCCTAAGATGCGCGTGTGCATGCTCGGAGATGCCCAGCACGTTGAGGAGgtatttcctctaactcaactaatgccacccatgttgagaagcattttgtcagcatgccacattacgcaggttgattacctcttatttattcgcc-ccattattgcgtaacag

upper sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
lower sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgcgagattttcaattgggtgcaataatatattgctttacag-actgtgtttgcttcctttccatttata
 ||||||||||||||||| || ||||| || ||| ||||||||||| | || ||||||||||   | || ||||| || ||||| || || || |  |||||||      |||  |     |   | | | |   || |     ||||  | || |  |  ||||||||   | || |                       
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaa------gattgagcgccctctctccttt---agttgccggattgaat-cactggtccattgcttttttgcacag-----------------------

upper sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 2
lower sequence: EFJ34353 (Selaginella moellendorffii), 5'ss of exon 2
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgcgagattttcaattgggtgcaataatatattgctttacagactgtgtttgcttcctttccatttata
 ||||||||||||||||| || ||||| || ||| ||||||||||| | || ||||||||||   | || ||||| || ||||| || || || |  ||||||| |   ||| |    | ||    |||| ||     |     ||||  | || |  |   |||||||     |   |                     
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCCCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGGGAGgtaaga--ttgagcgccctgtc---tccttttgt----tgccggattgaat-cactggtccgttgctttttttgcacag---------------------

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|31309902|gb|CD395105.1|CD395105
EST:     TGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTTGAGGCCTTGAAGAAGCTT
genomic: TGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|298169144|gb|HO020504.1|HO020504
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACATGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTTGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|207709585|gb|GD691599.1|GD691599
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAG
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAG
EST: gi|151413165|gb|EV282973.1|EV282973
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|207745327|gb|GD716311.1|GD716311
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|192315372|gb|FK009636.1|FK009636
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|192315373|gb|FK009637.1|FK009637
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|207715980|gb|GD699372.1|GD699372
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|207751720|gb|GD722621.1|GD722621
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGG
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGG
EST: gi|254329947|gb|GR839500.1|GR839500
EST:     GAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|19934524|gb|BQ079554.1|BQ079554
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|120495150|gb|EH223317.1|EH223317
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGAAGGACAAGCGTTTTAGTGGCTCTGTTAAGTTGCCTCACATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagctgatctaattatcaaacccttgtgcgagattttcaattgggtgcaataatatattgctttacagactgtgtttgcttcctttccatttata

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctttcc