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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctattatatccatactggattatactttattaaatcttcagcattggctactttgttattaataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA

Basic information

species Glycine max
transcript GLYMA20G33910.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 4
gtaagctattatatccatactggattatactttattaaat---cttcagcattggctact--ttgttattaa--taatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA
|      ||  | | || |    |||  |||      |||    |   | ||  |||| |  ||    ||||    |||  | |     |  ||||  |||| || || ||||||||  ||||||| ||||| |||||  | || ||||| || || || |||||||||||||||||||||||  ||||||| |||||   
gctgatgatgctttgcagagaacattg-actacgaggaatgaattatggtatatgctattggttccatttaagcagatgctgattttcacacatttttcagGGACAACATGTGCTACTGTTCTTACAAAAGCTATATTCGCTGAGGGATGCAAGTCTGTAGCAGCTGGAATGAATGCGATGGATTTGAGACGTGGTATCTC

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
-------gtaagctattatatccatactggattatactttattaaatcttcagcattggctactttgt---tattaataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA
         ||  |   ||||    | || ||| |||||||  |  |  | ||  |||  || |||||   |  |||   ||    |   ||| ||  |  |||| ||||||||||||||  |  | ||||||||||||||||| || || || || || ||||| ||||| |||||||| |||||  | || || |||||   
tatttgcacaaatt-caatatgtggattgcattgtactttaggatttgcttag--ttgcataatttgtttgttctaactgtgttattctgatccaaaatt-cagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 3
gtaagctattatatccatactggattatactttattaaatc---ttcagcat-tggctactttgtt---attaataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA
 | | |  |   |   | |||       |  || || |||    |  ||| | | | | |||| ||   | |     |||    | |  | ||     |||| ||||| ||||||||  || | || |||||||||||||| || || || ||||| ||||| |||||||||||||| |||||  | || || || ||   
-tgaccggtctaacataaactatgcctcatattgttgaattgtatgtagcttgttgatgctttcttcgaactgtacgtgatctgatatccaaaaaattcagGTACCACATGTGCTACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGTGGAATCTC

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 3
-------------gtaagctattatatccatactggattatactttattaaatcttcagcattggctactttgttattaataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA
              |||| ||   | || ||| | ||    | | |||  |   | | |   || || |||    | |     |||    |||  | ||  |  |||| ||||| ||||| ||  || | || |||||||||||||| || || || ||||| ||||| |||||||||||||| |||||  | || || || ||   
attgaatcatgtaataagttaaattttctatatttga----attgtatgtagcttgctga--tgtcttcttc-caactgtacctgatctgacatccaaaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGCGGAATCTC

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------gtaagctattatatccat--------actggattata----ctttattaaatcttcagcattggctactttgttattaataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA
                       |||    || | ||  |        | ||| || |        |||  | || |    || ||    |||||   | | ||  |   ||   | |   ||  ||||||| || ||||| ||| | ||||||| ||| || || |||||||| |||||||||||||| |||||||||||||| |||||||| ||||| ||||| ||
gtaagtgttccctttcaatggattaaaacgttttttctgtttttgctaattgggttgttagtctcctatctactcatattaatcggtgtttttgtatctgacaa--aatatatggtatgcgtta-cagGAACAACGTGTGCCACAGTCCTTACTAGAGCTATCTTCACGGAAGGTTGTAAATCAGTTGCCGCTGGAATGAATGCAATGGACCTAAGACGTGGTATCAA

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagctattatatccatactggattatactttattaaatcttcagcattggctactttgttat-taataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA
||||| ||||  ||   |  | |||||| |  |    | |  |    | |   | |     ||| ||  ||||   ||  ||  |    || |||| || |||||||||||  | || ||    || |||||| | |||||||| ||||||||||| || ||||||||||| |||||| || || |||||||   
gtaagatatttcattt-tgattgattatgcggttcatagttgtagaaact--ttgcaaaactatgtaccaatgcttgtttaacttgtcatg-cagGTACTACTTGTGCTACTGTCCTCACCCGGGCTATATTTGCCGAAGGATGCAAATCAGTTGCCGCAGGAATGAATGCAATGGACTTGCGAAGAGGTATTTC

upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------------------------------gtaagctattatatccatactggattatactttattaaatctt-cagcattggctactttgttattaataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA
                                                                                                     | |    |||| ||     | ||||       ||| |  |   || | |  |  |     || |   | |   |   | ||| |  |||| |||| || |||||||| ||  | || ||   ||| || |||   || |||||||| |||||||||||||| |||||||| |||||| |  |  | ||||| ||
gtaaagtcccggttctatctaaatttggagatatcgctcttacacgcatagttcctggacccattctttttattttgtacgaaggcttggggaattatttttgaaaatttatgtcaccttttgatttcggcgaattgatccacacaccttctgtgaaaacatt-tggctgactcgaa-agaatatgttttg-cagGGACAACTTGTGCAACGGTGCTCACCCGAGCTATTTTTGTTGAGGGATGTAAGTCAGTTGCAGCTGGCATGAATGCAATGGACTTACGTAGGGGTATCAA

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|16277971|gb|BI942659.1|BI942659
EST:     CAGTCTTGTAAAGCAGGTTGCTAATGCTACTAATGACGTGGCTGGTGATG                         GAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTA
genomic: CAGTCTTGTAAAGCAGGTTGCTAATGCTACTAATGACGTGGCTGGTGATGgtaagctatt ... aatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTA
EST: gi|209725419|gb|BW658281.1|BW658281
EST:     CAGTCTTGTAAAGCAGGTTGCTAATGCTACTAATGACGTGGCTGGTGATG                         GAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTA
genomic: CAGTCTTGTAAAGCAGGTTGCTAATGCTACTAATGACGTGGCTGGTGATGgtaagctatt ... aatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcagcattggctactttgttattaataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA
              tactttgttattaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctattatatccatactggattatactttattaaatcttcagcattggctactttgttattaataatgagggtacaatctaatttggcagGAACCACTTGTGCTACAATTCTTACTAAAGCAATATTTACGGAAGGATGTAAATCAGTTGCAGCTGGAATGAATGCGATGGACCTGAGACGAGGTATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA