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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgtcattctccttgggagtgcccataatttcttaatgtttctttaatccttccaataaatctcgatgcaagttttaaaatttcgggtctaatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACGACAAATTAGTTG

Basic information

species Glycine max
transcript GLYMA08G13810.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------------------------------------------------aatgtcattctccttgggagtgcccataatttcttaatgtttctttaatccttccaa--taaatctcgatgcaagttttaaaatttcgggtctaatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACG-ACAAATTAGTTG
                                                                                                  |  |  || |  | |    |  ||  |  |||    | | | |||  |  |||||   || |  |  | || | || |   | ||     | ||    |||||||| || ||||| ||||| ||||| |||||||| |||||||| |||||||| |||||||||||||| || ||||| |||| ||  |  ||||     | 
gtattcaaacttctatttctatgtacagtagtaatgaacactcatatcacttgaaactagtgcatagcgtttacttttgcaagttgtttccaaagcttaaatttttttgttggaatatatccccatattcggggtttctttttcctttttccattttagaaattaaagctaattctggtagtttt--cccaac---cagGCTTGCCACACAAAAGCAGAGTATGAAGAGTATGGCGCAAGCATCTGCCGGACGAATCCTGTTTTCAAAGGGATGTACTAAACCACGGCGCAAAGCTTCT-

upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------------aatgtcattctccttgggagtgcccataatttcttaatgtttctttaatccttccaataaatct-cgatgcaagttttaa---------aatttcgggtctaatgtg----------------cagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACGACAAATTAGTTG
                                                              || |  | |    |     ||   |||| |   |||| |   |    ||  | |||   || | |  ||||    | ||         ||  | |  ||||| |||                |||  ||| || ||||||| |||||| |||||| ||||||||||||| |||||||| |   | |||||||| || ||||| | |||      ||  |      
gtgccttccactttacactctttgagtcttgacacctcattctgcaaatttaataatatgacatattctgccatataactttgttaataagtcaataatatgcttcaggtcaatgcaaaccatatgcactgcacacgtgaataaagtgataagatggaatctaaagtgtttgtatgttctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGGACCAGCACCGTTTTCAAAGGGATGTACTGAATTTTTTCCACCTGTCCAA

upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 8
lower sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 9
---------------------------------------------------------------------aatgtc-attctccttgggagtgcccataatttctta---atgtttctttaatccttccaataaatct---cgatgcaa---gttttaaaatttcgggtctaatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACGACAAATTAGTTG--
                                                                     ||   |     |   ||   |||  | |   | |||    | |||  |  | | | |     || | |    | |||||    || |   | |||    ||  ||   ||||||| || ||||||||||| || |||||||| || || ||||| ||||| || |||||||| ||||| || ||||| | | |||  ||    ||   ||  
gtataccagctctcagtttatttgtgtacatacatatatagcattacaaaatttcttggaaagaaccagaacacctgaaatttctgaatgtgaacttgtctgcttggacaagttattacactaccttggtgaagtatgtgtgttgcaacttattatgggagttctttcctg-tgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCA--GAGCGGTTCCCTGTG

upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 8
aatgt-cattctccttgggagtgcccataatttcttaatgtttctttaatccttccaataaatctcgatgcaagttttaaaatttcgggtctaatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACGACA-AATTAGTTG
  | | ||  ||  ||  |||  ||  || |||   ||  |     | ||   |  |     | | ||  |||| | ||   |||  | | |    |||||  |||    || || |  || |||||||| |||||||||||||| ||||| || ||||| || |||||||||||||||| || |  |  || || || || 
-gtatgcaaactagtttagagatccgctagttt--gaagctaaacctcatggcttgatcgtgttttgaaacaagatgta---tttttgttgt----tgcagAGTTGCAGAACGAAAGAGGAGTATGAGGAATATGGAGCAAGCATATGCCGCACGAATCCGGTGTTCAAGGGAATGTATTGAAGCTGCTTCATAAATAATT-

upper sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 8
aatgtcattctccttgggagtgcccataatttctta-atgtttctttaatccttccaataa-atctcgatgcaagttttaaaatttcgggtctaatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACGACAAATTAGTTG
     |||| |  |||      |     ||| | |  || ||    || | | |      | ||     |   | | | ||||||   |||    ||  ||||||||||||||||| || || |||||||| || || |||||||| ||||| ||||||||||| |||||||| ||||||| |    | ||    || |   
--ctgcattgttgttgattccacatggtattccatgcatattatcatattacatgagtcgacattcttgtatgactatgaaaattcatggttctgtgcacagGCTTGTCATACAAAAGCTGAGTATGAGGAATACGGGGCAAGCATATGCCGAACAAATCCTGTCTTCAAGGGGATGTATTGATGTGAAGATTCTTTTGGGC

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|7285041|gb|AW597528.1|AW597528
EST:     GCATCAACACCTGAATTTTTTACG                         GCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGG
genomic: GCATCAACACCTGAATTTTTTACGgtatgcattt ... taatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGG
EST: gi|207822301|gb|GD796098.1|GD796098
EST:     CAGTTTGGTTTGGAGGATCAGTGCTTGCATCAACACCTGAATTTTTTACG                         GCTTGTCATACAAAGGCAGAATATGAGGAGTAGGGAGCAAGCATTTGCCGG
genomic: CAGTTTGGTTTGGAGGATCAGTGCTTGCATCAACACCTGAATTTTTTACGgtatgcattt ... taatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGG
EST: gi|13789657|gb|BG652248.1|BG652248
EST:     CAGTTTGGTTTGGAGGATCAGTGCTTGCATCAACACCTGAATTTTTTACG                         GCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGG
genomic: CAGTTTGGTTTGGAGGATCAGTGCTTGCATCAACACCTGAATTTTTTACGgtatgcattt ... taatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatccttccaataaatctcgatgcaagttttaaaatttcgggtctaatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACGACAAATTAGTTG
                                          gtctaat  putative branch site (score: 3)
                         aagttttaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgtcattctccttgggagtgcccataatttcttaatgtttctttaatccttccaataaatctcgatgcaagttttaaaatttcgggtctaatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACGACAAATTAGTTG

- - -cattctc
- - - - - - - -gggagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaagt