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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttgtgattaaataaaaacgacacacttctgatgctacttttgtctgattttcggggatataatactcactttaggtatttattattttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTCATTGACAGGGAGTATCTAGAGAGGGACAAGAGCAATCCTCAAATATACA

Basic information

species Glycine max
transcript GLYMA05G27240.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 16
----tctgttgtgattaaataaaaacgacacacttctgatgctacttttgtctgattttcggggatataatactcactttaggtatttattattttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTCATTGACAGGGAGTATCTAGAGAGGGACAAGAGCAATCCTCAAATATACA
    |   |  |||     | |    || |    |  |     | ||     | ||    |  ||| | ||    |    | || ||| || ||  |    ||||| ||||| |||||||| |||||||||||||| |||||||||||||||||||| ||||||||||| |||||| ||||||| | ||| || || |||||||
tagatagctaatgacccggttaggtggagattgctgggggagaatttgaacttcata---gaagatttgattgaaaaaccatgtttttgtt-ttgatgaaacagCTAAAATTTCCAATAAAGCCAGCTGATTTGAAGAAAAGGATTGAAAGCCTCATCGACAGGGAGTACCTAGAGCGGGACAAAAACAACCCCCAGATATACA

upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S204_102V6.1 (Physcomitrella patens), 3'ss of exon 15
----------------------------------------------------------------------------------tctgttgtgattaaataaaaacgacacactt-ctgatgctacttttgtctgatt-ttcggggatataatactcactttaggtatttattattttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTCATTGACAGGGAGTATCTAGAGAGGGACAAGAGCAATCCTCAAATATACA
                                                                                    | || |            |   | ||||| || ||   | || |  || ||  |||   | |||  |    |||  |   | |  ||   |||||  ||||||||||| ||||| |||||||||||| |||| || || ||||| ||||| || ||  |||||||||| || ||||||||   ||| |||||||||||||
gtaatacgttcattctcggaaattgtgccttcatgttttgggtgtggacacgcaagttttttattttattttattttattttatttttttagccctccgtggatatctcacttgcttatttgatttcttgcttataattctttgttatttttgcgactccaatgactcgttgaattttg--cagCTGAAATTTCCAATTAAACCAGCTGATCTGAAGAAGAGAATTGAGAGCCTGATCGATCGGGAGTATCTGGAAAGGGACAAAGCCAACCCTCAAATATACA

upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 16
lower sequence: PP1S70_181V6.1 (Physcomitrella patens), 3'ss of exon 15
------------------------------------tctgttgtgattaaataaa--aacgacacacttctgatgctacttttg----tctgattttcggggatataatactcactttaggtatttattattttttgtc-cagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTCATTGACAGGGAGTATCTAGAGAGGGACAAGAGCAATCCTCAAATATACA
                                    || | |    ||    ||   | |||   |  | |  ||||  | |||    ||||  ||||  |  | |  |  |    |||      | | || ||   |  ||||||||||| ||||| ||||||||||| ||||| ||||| || || ||| | |||||| ||||||| || || ||||||||   ||||||||| || ||||
gtgaatatttcatacctcgaattattatccagaatttcggattcacttctgcaagtcatcgatg-atgtgtagtgctgttattgaaattctgtatttcaagtgtttt-ttttgttgttaaacgcatgtgatgttaaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTGATTGACCGGGAGTACCTTGAAAGGGACAAAGCCAATCCTCAGATCTACA

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|16344341|gb|BI969936.1|BI969936
EST:     CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG                         CTGAAATTCCCAATAAAACCAGCTGATTTGNNNNNNNGGATTGAAAGCCTC
genomic: CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAGgtgaactcag ... ttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTC
EST: gi|23733442|gb|BU764920.1|BU764920
EST:     CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG                         CTGAAATTCCCAATAAAACCAGCTGATTTGNNNNNNNGGATTGAAAGCCTC
genomic: CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAGgtgaactcag ... ttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTC
EST: gi|12773136|gb|BG238063.1|BG238063
EST:     CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG                         CTGAAATTCCCAATAAAACCAGCTGATTTGNNNNNNNGGATTGAAAGCCTC
genomic: CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAGgtgaactcag ... ttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTC
EST: gi|31471408|gb|CD413436.1|CD413436
EST:     CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG                         CTGAAATTCCCAATAAAACCAGCTGATTTGNNNNNNNGGATTGAAAGCCTC
genomic: CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAGgtgaactcag ... ttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTC
EST: gi|27809423|gb|CB063845.1|CB063845
EST:     CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG                         CTGAAATTCCCAATAAAACCAGCTGATTTGNNNNNNNGGATTGAAAGCCTC
genomic: CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAGgtgaactcag ... ttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTC
EST: gi|209698239|gb|BW667542.1|BW667542
EST:     CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG                         CTGAAATTCCCAATAAAACCAGCTGATTTGNNNNNNNGGATTGAAAGCCTC
genomic: CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAGgtgaactcag ... ttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTC
EST: gi|7690871|gb|AW759008.1|AW759008
EST:     CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG                         CTGAAATTCCCAATAAAACCAGCTGATTTGNNNNNNNGGATTGAAAGCCTC
genomic: CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAGgtgaactcag ... ttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTC
EST: gi|31305219|gb|CD390422.1|CD390422
EST:     CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG                         CTGAAATTCCCAATAAAACCAGCTGATTTGNNNNNNNGGATTGAAAGCCTC
genomic: CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAGgtgaactcag ... ttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTC
EST: gi|209705497|gb|BW668075.1|BW668075
EST:     CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAG                         CTGAAATTCCCAATAAAACCAGCTGATTTGNNNNNNNGGATTGAAAGCCTC
genomic: CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAGgtgaactcag ... ttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTC
EST: gi|7686211|gb|AW756922.1|AW756922
EST:     CTAGAAAAGTGCTTACTCACACCCTTCTTATTACTGAACTCTTCCAACAG                         CTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAGATGATTGAAAGCCTC
genomic: CTAGAAAAGTGCTTAGTCACACCCTTCTTATTACTGAACTCTTCCAACAGgtgaactcag ... ttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgattttcggggatataatactcactttaggtatttattattttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTCATTGACAGGGAGTATCTAGAGAGGGACAAGAGCAATCCTCAAATATACA
                     tactcac  putative branch site (score: 1)
                                           ttttttgtcc  putative PPT
               atataatactcacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttgtgattaaataaaaacgacacacttctgatgctacttttgtctgattttcggggatataatactcactttaggtatttattattttttgtccagCTGAAATTCCCAATAAAACCAGCTGATTTGAAAAAAAGGATTGAAAGCCTCATTGACAGGGAGTATCTAGAGAGGGACAAGAGCAATCCTCAAATATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
tctgttg
- - - - - - aaataaa
- - - - - - - - - - - gacacac
- - - - - - - - - - - - - - - -ctgatgc