Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttaccgaaaaacactcattttaacatttgacttgtgattgttcctcaaactaccaatttcaatttcatggtaacagaagatgtgttttgtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTACCGCAAATCATCAAGAAGAACATATGTGCTACTTGGGAGCATGTTGCTTA

Basic information

species Glycine max
transcript GLYMA02G12980.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G12980.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G03530.1 (Arabidopsis thaliana), 3'ss of exon 6
gcttaccgaaaaacactcattttaacatttgacttgtgattgttcctcaaactaccaatttcaat-ttcatggtaacagaagatgtgttttgtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTACCGCAAATCATCAAGAAGAACATATGTGCTACTTGGGAGCATGTTGCTTA
               |  || || ||||||   |    ||  ||   |||| | | |   ||||| || |||||         | | || ||| | || |||| |||||||| |||||||| ||||||||  | |||||||||||||| ||| | | ||| ||| | | ||| ||| | || ||     | |||||| |||
------------gttcatatattcacatttctttcaaaatattttggcaaaattcaagaatcaatctttatggttttga---gtattttgtgtct-tatagGCTCTTCCACTTGTGAGTACATTTTGGGGAGTGGTTTTGTTTGGAGAATACAGAAGATCGTCACGGAAAACTTATCTACTTCTCTTCTGTATGTTGTTTA

upper sequence: GLYMA02G12980.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G03590.1 (Arabidopsis thaliana), 3'ss of exon 5
gcttaccgaaaaacactcattttaacatttgacttgtgat-tgttcctcaaactaccaatttca-atttcatggtaacagaagatgtgttttgtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTACCGCAAATCATCAAGAAGAACATATGTGCTACTTGGGAGCATGTTGCTTA
                   |||  ||| |  ||   |  | ||||||   |  ||  | |   | || |  |  | |       |    | |||||   |||||||||||||| |||||||| |||||||| ||  | ||||||||||| ||  | | ||||||||||| |||||||   || ||    || ||| | ||||
------------------gtttagacaataaacaaatcctctgttccatgatttaagagtgaaatatgttttacttattatgatttgaatatgttt---cagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATATAGAAGATCATCAAGAAAAACATATACACTTCTCATCAGTATGCTTCTTA

upper sequence: GLYMA02G12980.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g00530.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------gcttaccgaaaaacactcattttaacatttgacttgtgattgttcctcaaactaccaatttcaatttcatggtaacagaagatgtgttttgtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTACCGCAAATCATCAAGAAGAACATATGTGCTACTTGGGAGCATGTTGCTTA
                                       ||  | |  || ||||   | |       |||||  ||||   |      |||||   ||| |  || | |    |  | |   | ||     |||||||| ||||| ||||| || || ||||| || ||| |||||||||| ||||| ||||| ||||||||||||||| |  | |||||||||||| || | |
gtgagtttaagcacagcatacatattgacaaacacatacacatagaggcaatcataa-atcggggtgtttgtgtgtgttttcctgcaatccaatcagaatgtgctgatcatttgaacttttcatggtaacatcagGCACTCCCACTTGTGAGCACTTTCTGGGGAATAGTTCTGTTTGGAGAATACCGAAAATCGTCAAGAAGAACATATATATTGCTTGGGAGCATGCTGTTCA

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|22933806|gb|BU550945.1|BU550945
EST:     AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAA                         GCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
genomic: AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAAgtgagttttt ... gtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
EST: gi|254322156|gb|GR837570.1|GR837570
EST:     AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAA                         GCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
genomic: AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAAgtgagttttt ... gtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
EST: gi|214005293|gb|DB985135.1|DB985135
EST:     AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAA                         GCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
genomic: AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAAgtgagttttt ... gtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
EST: gi|13563518|gb|BG551738.1|BG551738
EST:     AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAA                         GCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
genomic: AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAAgtgagttttt ... gtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
EST: gi|254337751|gb|GR845321.1|GR845321
EST:     AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAA                         GCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
genomic: AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAAgtgagttttt ... gtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
EST: gi|254322157|gb|GR837571.1|GR837571
EST:     AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAA                         GCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
genomic: AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAAgtgagttttt ... gtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
EST: gi|254337752|gb|GR845322.1|GR845322
EST:     AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAA                         GCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
genomic: AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAAgtgagttttt ... gtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
EST: gi|254348162|gb|GR851841.1|GR851841
EST:     AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAA                         GCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC
genomic: AATTTATGGGAGGTCAAGCTGCAGGATATGCAGCAGCAGATGCTGTTCAAgtgagttttt ... gtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaaactaccaatttcaatttcatggtaacagaagatgtgttttgtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTACCGCAAATCATCAAGAAGAACATATGTGCTACTTGGGAGCATGTTGCTTA
                        tggtaac  putative branch site (score: 2)
                                         ttttgttt  putative PPT
           aatttcaatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttaccgaaaaacactcattttaacatttgacttgtgattgttcctcaaactaccaatttcaatttcatggtaacagaagatgtgttttgtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTACCGCAAATCATCAAGAAGAACATATGTGCTACTTGGGAGCATGTTGCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
gcttacc
- - - - - - -cactcat
- - - - - - - - - - - - - - - -acttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - -ctaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatgg