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

...tcaacttttaggggctaagttttattaaattggtcaaatataatttgaaatggccttttcttagaggactgaatttgtgcaactgctgtttgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATAT

Basic information

species Glycine max
transcript GLYMA19G35370.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 11
-tcaacttttaggggctaagttttattaaattggtcaaatataatttgaaatggccttttcttagaggactgaatttgtgcaactgctgtttgata---tgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATAT
 | | | ||| || |   | || | |     || |||  || | |||| | ||    | |  ||    |     | ||    |      ||| ||    ||||||| ||||||||||| |||||||||||||| || |||||||| || |||   || ||||| |   | ||| |||| |||||  | || ||| | ||| | |
ctaacccttttggtggacaattctgtagttctgatcattta-attttggactga---tgtgatatgaaatctgttctgcatgatgatatttttattcgctgcagTTTTCACCTACATCAGAGCACATACTACTGGCATATGGTCGTCGTCATAACTCACTTCTGAGGGGCATTTTCATGGATGGCAAGACCACAATCCCTGTGT

upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 10
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 10
-----tcaacttttaggggc---taagttttattaaattggtcaaatataatttgaaatggccttttcttagaggactgaatttgtgcaactgct-----gtttgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATAT
     ||  |||||  |       |  ||  |||    |||||   | |  ||||| |        |  ||      ||||  |     | |  |      ||     ||||||||||||| || || ||||| ||||||||||| ||||| ||||| |||||||||||| | |  || || || | |||||| |||||||||| || | | |
gttagtcgccttttgagaataatcagattgaatttttatggtctc-tttgttttgagaacataacatggtaagttgttgaaaatacttgaatatttgagaattctgggtgcagTTCTCACCCACTTCGGAGCATATACTACTTGCATATGGGCGGCGTCATGGTTCTCTTTTGAGGAGCATCGTTAGTGATGGTGAAACAACATCACATTTTT

upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 10
lower sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
------------------------------------------------------------------------------------tcaacttttaggggctaagttttattaaattgg---tcaaata-taatttgaaatggcctttt---cttagaggactgaat-ttgtgcaactgctgtttgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATAT
                                                                                      |  |  ||   || |||||   | | |||      | |||| ||| | ||  ||  |  ||    ||    ||   |||  | |  || |     ||    ||||||||||||| || || |||||||| || ||||| |||||||| || |||||||||||| | || || ||||| | ||||||||||||||||| || | | |
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT

upper sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 10
tcaacttttaggggctaagttttattaaattggtcaaatataa---tttgaaatggccttttcttagaggactgaatttgtgcaactgctgtttgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATAT
  ||||| ||         |      |||      |   |||    ||| |  |||    |   | | |||  || ||  |        | | | | |||||||| || || |||||||| |||||| ||||||| || |||||||| ||| ||||||| ||||||||  |||| || ||||| ||||| ||||||||||| |
-aaacttataataaactgttcaggcaaaagccaatattcatatcacttttatttggtaactatattgtgga--gacttcttattttgattttcttacatgcagTTTTCTCCGACATCTGAACACATATTACTTGCCTACGGTCGGCGTCATAGTTCTCTCCTTAAAAGCCTTGTTATCGATGGGGAAACGACATTACCTATTT

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|10847791|gb|BF071604.1|BF071604
EST:     TGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAG                         TTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGT
genomic: TGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAGgtcagttaat ... tgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGT
EST: gi|21889859|gb|BQ743072.1|BQ743072
EST:     TGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAG                         TTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGT
genomic: TGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAGgtcagttaat ... tgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGT
EST: gi|193686900|gb|FK632523.1|FK632523
EST:     TGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAG                         TTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGT
genomic: TGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAGgtcagttaat ... tgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGT
EST: gi|12690329|gb|BG156665.1|BG156665
EST:     TGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAG                         TTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGT
genomic: TGCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTCAGgtcagttaat ... tgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGT
EST: gi|26047106|gb|CA783997.1|CA783997
EST:     GCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATTTCAG                         T-CTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGG
genomic: GCTTGCTTCACGAGCAATTAGAGCAGCTCATTGTCTGACTTCAATT-CAGgtcagttaat ... tgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatggccttttcttagaggactgaatttgtgcaactgctgtttgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATAT
                                          gtttgat  putative branch site (score: 5)
          ttttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaacttttaggggctaagttttattaaattggtcaaatataatttgaaatggccttttcttagaggactgaatttgtgcaactgctgtttgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA