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'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatagtttctgtagttaatttaattttcagaatgctttagatttcttttggcaaccttttctcctttcctctgctgatataattaattcgagcat...

Basic information

species Glycine max
transcript GLYMA10G42250.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 5'ss of exon 8
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatagtttctgtagttaatttaattttcagaatgctttagatttcttttggcaaccttttctcctttcctctgctga--tataattaattcgagcat--
 ||||| || || ||||||||||||||||||||  |  | |||||||||||||| || || || || || || ||||||||||| |||||||| ||||||||  |  |  | | | |   | ||| || |    ||||   |   || | || ||     | |      |||  |    |||  | ||||| | || | |    
TACAATCGAACAACTTCTTCCTATTTTCCTTTCTTTGCTCAAGGATGAATTTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTAATCAGgtgatgttcatgtttttttcttattgaaat----gaatttatcttatcttttgtgatgttcatgctgtttttattagcgtgaagtctaatttactccacctcaa

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G122135_T01 (Zea mays), 5'ss of exon 8
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttat-agtttctgtagttaatttaattttcagaatgctttagatttc---ttttggcaaccttttctcctttcctctgct--gatataattaattcgag-cat----------------------------------------------------------------------
 || || || ||||||||||| ||||| || ||  |  |||||||||||||||| || || || || ||||| ||||||||||||||||| || ||||||||   ||  | ||| |||   |   ||  ||| |    | |||    |||    | || | |  ||| | | |   |   |  |  | |  ||||  ||  || ||                                                                       
TACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTAATCAGgtcagtaccattttttgttactggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgttttgatctttcag

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatagtttctgtagtta----atttaatt------ttcagaatgctttagatttcttttggcaaccttttctcctttcct--ctgctgatataattaattcgagcat---------------------------------------------------------------------------
 || ||||| |||||| |||| |||||||| ||  | ||||| || |||||||| || || || || ||||| |||||||| ||||||||||| ||||||||   ||   ||| | | ||||    ||||| ||      | |    || ||||||||| |  ||  | | |||      |  ||  |   |  |||  |  |||     |                                                                            
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 8
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgtt-gttatagtttc----tgtagttaatttaattttcagaatgctttagatttcttttggcaaccttttctcctttcctctgctgatataattaattcgagcat
||| |||||||| ||  | || ||||| |||||||||||||| ||||||||||| || |||||||| ||||| || |||||| | |||||||| || |||||| |||  |  |      |||  || |  || |  |   | |||||     ||   ||||  ||    |   ||||   | || |                   
AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatctttta-cggcag-------------------

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 8
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatagtttctgtagttaatttaattttcagaatgctttagatttct---tttggcaaccttttctcctttcctctgc--tgatataattaattcgagcat----------------------------------------------------------------------
|||||||||||| |||||||| || || ||||| || ||||| || |||||||| || || ||| |||||||||||||||| ||||| |||||||| ||||||  |    ||     ||||| |    | ||   |   | || | |||||   |||  | || | |||       || |    || | |  | || || |  |                                                                       
AACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGAACCAGgtt--tgctattgaccaagttactcatctctttgtacgacattgggtttctattttttcccacatgttcaaaggagctgtatcatgttttggtcaagtcaatgactacttgacagcaaattctttgtccatccatttttcataatgattcgattttttttccttaaaattgccag

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 5'ss of exon 7
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgtt-gttatagtttctgtagttaatttaatt--ttcagaatgcttta---------gatttcttttggcaaccttttctcctttcctctgctgatataattaattcgagcat--------------------------------
|||||||||||| || ||||| || || ||||| || ||||| ||||| || || || || ||| | |||||||||||||| ||||| ||||||||||||||| |||| |       ||   ||   |  |  | |  |  |||| |         | ||| |||     || ||  ||| |||    |||   | |     || |                                      
AACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGAATCAGgtttgttacaacagaaatacccaaaccagatcatgccaatggcttcatgataacatgttttgtttaaaagactttcactcttttaacttgcctttctcgcccatccatattcagttgatgacttctatattttatatgtggcag

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 7
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgtt-gttatagtttctgtagttaatttaattttcagaatgctttagatttcttttggcaaccttttctcctttcctctgctgatataattaattcgagcat-----
||||||||| || |||||||| ||||| ||||| |||||||||||||| ||||| || || || ||||| || || ||||||||||||||| | ||||||||| || ||| |||  | ||||   | |    ||||  |  |||  ||||  | || |      | ||  | |   | |||  | || ||  ||  |         
AACAATTGATCAACTTCTTCCAATTTTTCTTTCTCTTTTGAAGGATGACTTTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAAATCAGgtttgtcataatttaaggagtt---tca--catcagcctttttttaattttatgtg-ctctgcctacttgtctagccagctattctactttttttaaatgcaattt

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 5'ss of exon 7
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatagtttctgtagttaatttaattttcagaatg---ctttag---atttcttttggcaaccttttctcctttcctctgctgatataattaatt--cgagcat---------------------------------------------------------------------------------------
 || |||||||| ||| | || || ||||| || || ||||||||||||||||| |||||||| ||||| || ||||||||||| |||||||| || || ||  | ||   |||| |   | |   |  |||||  |     |  ||     || || |    || ||||  |    |  | |  ||      ||  ||   |  |||                                                                                       
TACTATTGAGCAACTTTTACCCATATTCCTATCACTGTTGAAGGATGAATTTCCAGACGTGCGGCTAAATATCATCAGCAAGCTAGATCAAGTCAACCAAgtaatgatcaattctattagtgaaggacatttcattacatgtccctatcttgttgctctgataaatctttgatttagttatgtattgtggcctttctttaatggacatgacattagttgggttcacatcaagacactggatgtgttccacaaagaaaagaaccaatggatctgaatttggactttttgatcacag

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 5'ss of exon 7
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgt----------tgttatagt-ttctgtagttaatttaattttcagaatgctttagatttcttttggcaaccttttctcctttcctctgctgatataattaatt-cgagcat-----------------------------------------------------------------------
 || |||||||| ||||| || || || || || || ||||||||||||||||| || ||||| ||||| |||||||||||||| |||||||||||||| ||          | ||| ||   | |  | |   | |  |  ||    |  | |   ||     | |    ||||  |  |    | |   ||| | ||   || | | | |                                                                       
TACCATTGAGCAACTTCTGCCCATATTTCTGTCACTGTTGAAGGATGAATTTCCAGATGTGCGACTAAATATTATCAGCAAGCTAGATCAAGTGAATCAAgtaagggccagttattaaagagctttacattacgtgttgtcatcttggtattctgacttaaacgtcgtcgtctttctttttactgtatatggatgtgatattttacaaacctacatgaagttactgattgtttctgactaggaggaagactaatggatctgaagttggacgtttcgttcacag

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ35758 (Selaginella moellendorffii), 5'ss of exon 7
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatagtttctgtagttaatttaattttcagaatgctttagatttcttttggcaaccttttctcctttcctctgctgatataattaattcgagcat
 ||||| || |||||| | || || ||  |  ||||||||||||||||||| || |||||  | || ||||| || |||||||| |||||||| ||  |||    |         | ||   ||| | | ||  ||||    |    || |  |  ||                                          
GACAATCGAACAGCTTTTACCAATATTTTTGGCCCTTTTGAAGGATGAATTCCCTGACGTTAGGCTCAACATCATAAGCAAGCTGGATCAAGTCAACAAGgcaagttcgcccaacgaag---attcattgttttgaat----tgatcttttcgttacag-----------------------------------------

upper sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
lower sequence: EFJ10709 (Selaginella moellendorffii), 5'ss of exon 7
-----AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatagtttctgtagttaatttaattttcagaatgctttagatttcttttggcaaccttttctcctttcctctgctgatataattaattcgagcat
      ||||| || || ||| | || || ||  |  ||||||||||||||||||| || |||||  | || ||||| || |||||||| |||||||| ||  |||    |         | ||   ||| | | ||  || |    |    || |  |  ||                                          
GACGCGACAATCGAACAACTTTTACCAATATTTTTGGCCCTTTTGAAGGATGAATTCCCTGACGTTAGGCTCAACATCATAAGCAAGCTGGATCAAgtcaacaaggcaagttcgcccaacgaag---attcattgttttgagt----tgatcttttcgttacag-----------------------------------------

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|151403929|gb|EV273739.1|EV273739
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|151407658|gb|EV277473.1|EV277473
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|17153685|gb|BM143618.1|BM143618
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|254331030|gb|GR842295.1|GR842295
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|19270079|gb|BM886335.1|BM886335
EST:     ATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: ATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|16105352|gb|BI893092.1|BI893092
EST:     CGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: CGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|7926502|gb|AW832528.1|AW832528
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|208055523|gb|GD854618.1|GD854618
EST:     CAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: CAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|26057519|gb|CA800433.1|CA800433
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAATCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
EST: gi|254343473|gb|GR857229.1|GR857229
EST:     TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAG                         GTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG
genomic: TTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatag ... atttttgcagGTTATAGGAATTGATCTGTTATCTCAGTCTTTGTTACCAGCCATTGTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatagtttctgtagttaatttaattttcagaatgctttagatttcttttggcaaccttttctcctttcctctgctgatataattaattcgagcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttcc