AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0116180

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0116180 MtrunA17_Chr1g0212871 96.639 238 6 1 1 238 9 244 5.19e-169 465
Msa0116180 MtrunA17_Chr1g0212861 36.441 236 104 10 43 238 123 352 8.58e-24 97.8
Msa0116180 MtrunA17_Chr1g0169511 33.014 209 108 5 43 226 39 240 1.66e-23 95.1
Msa0116180 MtrunA17_Chr1g0169291 33.493 209 107 6 43 226 39 240 1.59e-22 92.4
Msa0116180 MtrunA17_Chr4g0030681 48.571 105 47 4 110 211 178 278 1.64e-22 93.6
Msa0116180 MtrunA17_Chr7g0221601 44.262 122 62 2 116 233 267 386 2.22e-22 94.4
Msa0116180 MtrunA17_Chr4g0030731 48.571 105 47 4 110 211 177 277 2.24e-22 93.2
Msa0116180 MtrunA17_Chr1g0169281 28.287 251 145 5 4 226 3 246 5.45e-19 83.2
Msa0116180 MtrunA17_Chr4g0030671 32.500 200 105 6 43 214 61 258 1.01e-18 82.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0116180 AT1G07730.2 35.500 200 98 6 41 211 160 357 5.57e-26 104
Msa0116180 AT2G28670.1 35.644 202 97 5 41 211 205 404 5.00e-25 102
Msa0116180 AT2G28670.2 51.887 106 49 2 106 211 91 194 5.02e-25 99.0
Msa0116180 AT4G13580.1 33.333 201 104 5 47 224 39 232 8.06e-24 96.3
Msa0116180 AT3G24020.1 33.333 213 112 6 47 236 38 243 1.69e-23 95.1
Msa0116180 AT2G39430.1 32.353 238 113 9 43 236 87 320 1.20e-22 94.7
Msa0116180 AT3G55230.1 30.252 238 120 8 43 237 70 304 2.58e-20 87.8

Find 49 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATTTCAAGAGCTGGAATT+TGG 0.209367 1_3:+35057558 Msa0116180:CDS
GGTTTCTCTGTATTAATATT+AGG 0.221299 1_3:-35057390 None:intergenic
AGCTGAGGAAAATTTGTTTA+TGG 0.235026 1_3:-35057274 None:intergenic
GATGGCCATGGTAGTGATTA+GGG 0.312185 1_3:-35057317 None:intergenic
GTTTGAGTTGATTGTGGAAT+TGG 0.329326 1_3:-35057486 None:intergenic
TGATGGCCATGGTAGTGATT+AGG 0.343261 1_3:-35057318 None:intergenic
GAGTCACATGTTGCAGTTAT+TGG 0.351309 1_3:+35057783 Msa0116180:CDS
CTTCTCTTCTAGCAATTGTC+AGG 0.383847 1_3:+35057232 Msa0116180:CDS
GGAATTGGAATCCCTCCATT+TGG 0.399195 1_3:-35057471 None:intergenic
GTTAAGGTTGTGGATAAAGT+AGG 0.408640 1_3:+35057846 Msa0116180:CDS
GTAGGGTCTAGTACAGTAGA+AGG 0.416844 1_3:+35057864 Msa0116180:CDS
TCTTGAAATGCTGCTCTAGT+AGG 0.424130 1_3:-35057546 None:intergenic
GGAAAGTACTATGGTGCTAA+TGG 0.437470 1_3:+35057813 Msa0116180:CDS
TAATGGCTATGCTGTTGTTA+AGG 0.440993 1_3:+35057830 Msa0116180:CDS
GTTGCAGTTATTGGTGGTAC+TGG 0.455685 1_3:+35057792 Msa0116180:CDS
TGCTAGAAGAGAAGGGAGAT+TGG 0.464219 1_3:-35057223 None:intergenic
ACACTTGATCTTTCCACCAT+TGG 0.472073 1_3:+35057513 Msa0116180:CDS
TTGAAGGGTGAGTATGAAGA+CGG 0.482315 1_3:+35057723 Msa0116180:CDS
GTCTGTGTTTGAGTTGATTG+TGG 0.491418 1_3:-35057492 None:intergenic
CTATGCTGTTGTTAAGGTTG+TGG 0.492544 1_3:+35057836 Msa0116180:CDS
AGAGAAACCTTCCACTACTA+AGG 0.495734 1_3:+35057404 Msa0116180:CDS
GGTGGTACTGGAAAGTACTA+TGG 0.501400 1_3:+35057804 Msa0116180:CDS
CTGACAATTGCTAGAAGAGA+AGG 0.504357 1_3:-35057231 None:intergenic
TAGAGCAGCATTTCAAGAGC+TGG 0.504564 1_3:+35057551 Msa0116180:CDS
GACGAGGAACTACTAGTTGA+AGG 0.506266 1_3:+35057597 Msa0116180:CDS
TATGTAGCTAGTGAAGAGGA+TGG 0.509172 1_3:+35057666 Msa0116180:CDS
TTAAGGTTGTGGATAAAGTA+GGG 0.516469 1_3:+35057847 Msa0116180:CDS
TCACTGTCATAGCAACCATA+TGG 0.517871 1_3:-35057695 None:intergenic
GAAGATGAACTAAAGAAACT+TGG 0.528902 1_3:+35057627 Msa0116180:CDS
TCTGTATTAATATTAGGACT+AGG 0.530173 1_3:-35057384 None:intergenic
ATTGGAATCCCTCCATTTGG+AGG 0.538267 1_3:-35057468 None:intergenic
CCATGGTAGTGATTAGGGGT+TGG 0.550854 1_3:-35057312 None:intergenic
AGAGGATGGAAGTAGCCATA+TGG 0.562281 1_3:+35057680 Msa0116180:CDS
TTTGTGACCTTAGTAGTGGA+AGG 0.562764 1_3:-35057411 None:intergenic
TTGATTTGTGACCTTAGTAG+TGG 0.562901 1_3:-35057415 None:intergenic
ATGTTATTCTATGATGGCCA+TGG 0.591384 1_3:-35057329 None:intergenic
GGTGTATGTAGCTAGTGAAG+AGG 0.591556 1_3:+35057662 Msa0116180:CDS
TAAAATACACGTCATACAGA+AGG 0.595028 1_3:-35057908 None:intergenic
TCACATGTTGCAGTTATTGG+TGG 0.626055 1_3:+35057786 Msa0116180:CDS
AAGAAACTTGGAAAAGCACA+AGG 0.629760 1_3:+35057639 Msa0116180:CDS
TGACAATTGCTAGAAGAGAA+GGG 0.634492 1_3:-35057230 None:intergenic
AGGAAAAGAGAAACCAATGG+TGG 0.644162 1_3:-35057526 None:intergenic
AGTAGGAAAAGAGAAACCAA+TGG 0.647659 1_3:-35057529 None:intergenic
CCAACCCCTAATCACTACCA+TGG 0.665385 1_3:+35057312 Msa0116180:CDS
GAAACTTGGAAAAGCACAAG+GGG 0.665476 1_3:+35057641 Msa0116180:CDS
ATGGCCATGGTAGTGATTAG+GGG 0.679512 1_3:-35057316 None:intergenic
AGAAACTTGGAAAAGCACAA+GGG 0.691717 1_3:+35057640 Msa0116180:CDS
ATTACCAAGAGTTCTAGCTG+AGG 0.711799 1_3:-35057289 None:intergenic
ATCAGTAACATCGATCGACG+AGG 0.719628 1_3:+35057581 Msa0116180:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAAATGTTATTCTATGA+TGG - chr1_3:35057338-35057357 None:intergenic 15.0%
! TCTGTATTAATATTAGGACT+AGG - chr1_3:35057387-35057406 None:intergenic 25.0%
! GGTTTCTCTGTATTAATATT+AGG - chr1_3:35057393-35057412 None:intergenic 25.0%
! AGCTGAGGAAAATTTGTTTA+TGG - chr1_3:35057277-35057296 None:intergenic 30.0%
GAAGATGAACTAAAGAAACT+TGG + chr1_3:35057627-35057646 Msa0116180:CDS 30.0%
!!! TATGACAGTGAGTTTTTTGA+AGG + chr1_3:35057707-35057726 Msa0116180:CDS 30.0%
!!! ATGACAGTGAGTTTTTTGAA+GGG + chr1_3:35057708-35057727 Msa0116180:CDS 30.0%
TTAAGGTTGTGGATAAAGTA+GGG + chr1_3:35057847-35057866 Msa0116180:CDS 30.0%
TAAAATACACGTCATACAGA+AGG - chr1_3:35057911-35057930 None:intergenic 30.0%
TGACAATTGCTAGAAGAGAA+GGG - chr1_3:35057233-35057252 None:intergenic 35.0%
ATGTTATTCTATGATGGCCA+TGG - chr1_3:35057332-35057351 None:intergenic 35.0%
!! TTGATTTGTGACCTTAGTAG+TGG - chr1_3:35057418-35057437 None:intergenic 35.0%
! TTACCTTTTCCAAAACCTCT+AGG + chr1_3:35057438-35057457 Msa0116180:CDS 35.0%
!!! AATCCTAGAGGTTTTGGAAA+AGG - chr1_3:35057444-35057463 None:intergenic 35.0%
! GGAAAAAATCCTAGAGGTTT+TGG - chr1_3:35057450-35057469 None:intergenic 35.0%
TTTGGAGGAAAAAATCCTAG+AGG - chr1_3:35057456-35057475 None:intergenic 35.0%
!!! CTAGGATTTTTTCCTCCAAA+TGG + chr1_3:35057456-35057475 Msa0116180:CDS 35.0%
!!! GATTTTTTCCTCCAAATGGA+GGG + chr1_3:35057460-35057479 Msa0116180:CDS 35.0%
!! GTTTGAGTTGATTGTGGAAT+TGG - chr1_3:35057489-35057508 None:intergenic 35.0%
AGTAGGAAAAGAGAAACCAA+TGG - chr1_3:35057532-35057551 None:intergenic 35.0%
! AAGAAACTTGGAAAAGCACA+AGG + chr1_3:35057639-35057658 Msa0116180:CDS 35.0%
! AGAAACTTGGAAAAGCACAA+GGG + chr1_3:35057640-35057659 Msa0116180:CDS 35.0%
!!! TGAGACTTTTTGGAGTTCAT+AGG + chr1_3:35057748-35057767 Msa0116180:CDS 35.0%
TAATGGCTATGCTGTTGTTA+AGG + chr1_3:35057830-35057849 Msa0116180:CDS 35.0%
GTTAAGGTTGTGGATAAAGT+AGG + chr1_3:35057846-35057865 Msa0116180:CDS 35.0%
CTGACAATTGCTAGAAGAGA+AGG - chr1_3:35057234-35057253 None:intergenic 40.0%
CTTCTCTTCTAGCAATTGTC+AGG + chr1_3:35057232-35057251 Msa0116180:CDS 40.0%
! TTTTCCTCAGCTAGAACTCT+TGG + chr1_3:35057285-35057304 Msa0116180:CDS 40.0%
! ATTACCAAGAGTTCTAGCTG+AGG - chr1_3:35057292-35057311 None:intergenic 40.0%
AGAGAAACCTTCCACTACTA+AGG + chr1_3:35057404-35057423 Msa0116180:CDS 40.0%
! TTTGTGACCTTAGTAGTGGA+AGG - chr1_3:35057414-35057433 None:intergenic 40.0%
!!! GGATTTTTTCCTCCAAATGG+AGG + chr1_3:35057459-35057478 Msa0116180:CDS 40.0%
!! GTCTGTGTTTGAGTTGATTG+TGG - chr1_3:35057495-35057514 None:intergenic 40.0%
ACACTTGATCTTTCCACCAT+TGG + chr1_3:35057513-35057532 Msa0116180:CDS 40.0%
AGGAAAAGAGAAACCAATGG+TGG - chr1_3:35057529-35057548 None:intergenic 40.0%
TCTTGAAATGCTGCTCTAGT+AGG - chr1_3:35057549-35057568 None:intergenic 40.0%
GCATTTCAAGAGCTGGAATT+TGG + chr1_3:35057558-35057577 Msa0116180:CDS 40.0%
! GAAACTTGGAAAAGCACAAG+GGG + chr1_3:35057641-35057660 Msa0116180:CDS 40.0%
TATGTAGCTAGTGAAGAGGA+TGG + chr1_3:35057666-35057685 Msa0116180:CDS 40.0%
TCACTGTCATAGCAACCATA+TGG - chr1_3:35057698-35057717 None:intergenic 40.0%
TTGAAGGGTGAGTATGAAGA+CGG + chr1_3:35057723-35057742 Msa0116180:CDS 40.0%
!!! GAAGACGGATTGAGACTTTT+TGG + chr1_3:35057738-35057757 Msa0116180:CDS 40.0%
GAGTCACATGTTGCAGTTAT+TGG + chr1_3:35057783-35057802 Msa0116180:CDS 40.0%
TCACATGTTGCAGTTATTGG+TGG + chr1_3:35057786-35057805 Msa0116180:CDS 40.0%
!! GGAAAGTACTATGGTGCTAA+TGG + chr1_3:35057813-35057832 Msa0116180:CDS 40.0%
CTATGCTGTTGTTAAGGTTG+TGG + chr1_3:35057836-35057855 Msa0116180:CDS 40.0%
TGCTAGAAGAGAAGGGAGAT+TGG - chr1_3:35057226-35057245 None:intergenic 45.0%
! ATGGCCATGGTAGTGATTAG+GGG - chr1_3:35057319-35057338 None:intergenic 45.0%
! GATGGCCATGGTAGTGATTA+GGG - chr1_3:35057320-35057339 None:intergenic 45.0%
! TGATGGCCATGGTAGTGATT+AGG - chr1_3:35057321-35057340 None:intergenic 45.0%
ATTGGAATCCCTCCATTTGG+AGG - chr1_3:35057471-35057490 None:intergenic 45.0%
GGAATTGGAATCCCTCCATT+TGG - chr1_3:35057474-35057493 None:intergenic 45.0%
TAGAGCAGCATTTCAAGAGC+TGG + chr1_3:35057551-35057570 Msa0116180:CDS 45.0%
ATCAGTAACATCGATCGACG+AGG + chr1_3:35057581-35057600 Msa0116180:CDS 45.0%
GACGAGGAACTACTAGTTGA+AGG + chr1_3:35057597-35057616 Msa0116180:CDS 45.0%
GGTGTATGTAGCTAGTGAAG+AGG + chr1_3:35057662-35057681 Msa0116180:CDS 45.0%
AGAGGATGGAAGTAGCCATA+TGG + chr1_3:35057680-35057699 Msa0116180:CDS 45.0%
! GTTGCAGTTATTGGTGGTAC+TGG + chr1_3:35057792-35057811 Msa0116180:CDS 45.0%
!! GGTGGTACTGGAAAGTACTA+TGG + chr1_3:35057804-35057823 Msa0116180:CDS 45.0%
GTAGGGTCTAGTACAGTAGA+AGG + chr1_3:35057864-35057883 Msa0116180:CDS 45.0%
! CCATGGTAGTGATTAGGGGT+TGG - chr1_3:35057315-35057334 None:intergenic 50.0%
CCAACCCCTAATCACTACCA+TGG + chr1_3:35057312-35057331 Msa0116180:CDS 50.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 35057219 35057935 35057219 ID=Msa0116180;Name=Msa0116180
chr1_3 mRNA 35057219 35057935 35057219 ID=Msa0116180-mRNA-1;Parent=Msa0116180;Name=Msa0116180-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|238
chr1_3 exon 35057219 35057935 35057219 ID=Msa0116180-mRNA-1:exon:11182;Parent=Msa0116180-mRNA-1
chr1_3 CDS 35057219 35057935 35057219 ID=Msa0116180-mRNA-1:cds;Parent=Msa0116180-mRNA-1
Gene Sequence

>Msa0116180

ATGGCCAATCTCCCTTCTCTTCTAGCAATTGTCAGGTTACTTTTGCTAATGACTACCATAAACAAATTTTCCTCAGCTAGAACTCTTGGTAATCCAACCCCTAATCACTACCATGGCCATCATAGAATAACATTTTTAATGAAGCATATGCTCAATGATACACATCCTAGTCCTAATATTAATACAGAGAAACCTTCCACTACTAAGGTCACAAATCAATTACCTTTTCCAAAACCTCTAGGATTTTTTCCTCCAAATGGAGGGATTCCAATTCCACAATCAACTCAAACACAGACACTTGATCTTTCCACCATTGGTTTCTCTTTTCCTACTAGAGCAGCATTTCAAGAGCTGGAATTTGGATCAGTAACATCGATCGACGAGGAACTACTAGTTGAAGGTGATCATGAAGATGAACTAAAGAAACTTGGAAAAGCACAAGGGGTGTATGTAGCTAGTGAAGAGGATGGAAGTAGCCATATGGTTGCTATGACAGTGAGTTTTTTGAAGGGTGAGTATGAAGACGGATTGAGACTTTTTGGAGTTCATAGGAGTGATGTTTTTGAGTCACATGTTGCAGTTATTGGTGGTACTGGAAAGTACTATGGTGCTAATGGCTATGCTGTTGTTAAGGTTGTGGATAAAGTAGGGTCTAGTACAGTAGAAGGAAAAGTTACAAGTTCTAAGTTCCTTCTGTATGACGTGTATTTTAGTTAG
Protein sequence

>Msa0116180

MANLPSLLAIVRLLLLMTTINKFSSARTLGNPTPNHYHGHHRITFLMKHMLNDTHPSPNINTEKPSTTKVTNQLPFPKPLGFFPPNGGIPIPQSTQTQTLDLSTIGFSFPTRAAFQELEFGSVTSIDEELLVEGDHEDELKKLGKAQGVYVASEEDGSSHMVAMTVSFLKGEYEDGLRLFGVHRSDVFESHVAVIGGTGKYYGANGYAVVKVVDKVGSSTVEGKVTSSKFLLYDVYFS*