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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTCTACTGTGTGAGTGGGAAGGATGTAGAGGGCCCAGGTGCTGATTTCGAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaattagttgactgaaattccaactactatttctggtggctactttctactttactagtcacacaataagaacattgatgcattaataatgtcaatatattttaatttttctttgccttttgtttatag

Basic information

species Glycine max
transcript GLYMA03G39530.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39530.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0060g02220.t01 (Vitis vinifera), 5'ss of exon 5
CTGTCTACTGTGTGAGTGGGAAGGATGTAGAGGGCCCAGGTGCTGATTTCGAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaattagttgactgaaattccaactactatttctggtggctactttctactttactagtcacacaataagaacattgatgcattaataatgtcaatatattttaatttttctttgccttttgtttatag
|||| |||||| | | ||| || |||| ||| || || |||   ||||| ||| |||| ||||||||||| || ||||| |||||||||||||||||||||||||| ||||| ||  | | | |||     |    |  ||| |   | | || |||||   |             |    ||  |   ||    |||    |                                 
CTGTTTACTGTATAAATGGAAAAGATGCAGAAGGACCTGGTTGCGATTTTGAGTTTGCAGTGGTGATTTCAGCGGCTAGACATAGCCCACAGAATTTCTGgtgtgtgaaattggtcaagttacattt----tgtagtaactgttatttgccttttacttgtttttatgtttttcttggttttttttttttttgggatgcgtgtg--------------------------------
















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|192308192|gb|FK001290.1|FK001290
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|151403727|gb|EV273537.1|EV273537
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|7692294|gb|AW760404.1|AW760404
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCATAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|207740500|gb|GD713766.1|GD713766
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|192295129|gb|FG986848.1|FG986848
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|192303311|gb|FG995619.1|FG995619
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGGATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|298184842|gb|HO030055.1|HO030055
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|193654550|gb|FK597860.1|FK597860
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTG
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTG
EST: gi|9903152|gb|BE612120.1|BE612120
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATANCCCACAGAATGTCTG                         CAACGGAAAGTTG-TGTTCAATATGGAATATTGAGTTCAAAGATGAGCAAC
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAA-GTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAAC
EST: gi|18040959|gb|BM309253.1|BM309253
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|24135512|gb|BU926022.1|BU926022
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|9987385|gb|BE661493.1|BE661493
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|151397822|gb|EV267695.1|EV267695
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|58019780|gb|CX706522.1|CX706522
EST:     CTGCTGCTAGGCATAGCCCACAGATTTTCTG                         CAACGGAAGTGGGTGTTCAATATGGAATATTGAGTTCAAAGATGACCAACA
genomic: CTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|192313101|gb|FK004691.1|FK004691
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|10231910|gb|BE800798.1|BE800798
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|151399910|gb|EV269781.1|EV269781
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|192313102|gb|FK004692.1|FK004692
EST:     GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAATATTGAGTTCAAAGATGAACAACA
EST: gi|9203900|gb|BE330124.1|BE330124
EST:     GAGCTGGCTGTGGTGATGTCTGCTGCTAGGCATAGCCCACAGAATTTCTG                         CAACGGAAGTTGGTGTTCAATATGGAATTAT-GAGTTCAA-GATGAACCAA
genomic: GAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaa ... ttgtttatagCAACGGAAGTTGGTGTTCAATATGGAAT-ATTGAGTTCAAAGATGAAC-AA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTCTACTGTGTGAGTGGGAAGGATGTAGAGGGCCCAGGTGCTGATTTCGAGCTTGCTGTGGTGATTTCTGCTGCTAGGCATAGCCCACAGAATTTCTGgtgtgtaaaattagttgactgaaattccaactactatttctggtggctactttctactttactagtcacacaataagaacattgatgcattaataatgtcaatatattttaatttttctttgccttttgtttatag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT