AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1163240

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1163240 MtrunA17_Chr7g0259971 96.923 65 2 0 1 65 1 65 1.52e-41 129
Msa1163240 MtrunA17_Chr5g0394401 72.131 61 16 1 1 61 1 60 1.14e-26 91.7
Msa1163240 MtrunA17_Chr1g0205521 72.581 62 16 1 1 62 1 61 2.51e-26 90.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAAGTATTATATTCTTTC+TGG 0.087702 7_4:-54321104 None:intergenic
GGATTTGAATTATCTATCTT+TGG 0.233172 7_4:+54320836 Msa1163240:three_prime_UTR
TGGTGAAGTGCTACTACTTT+TGG 0.272794 7_4:-54320363 None:intergenic
GGATTGAAGCCACCCCATTT+TGG 0.303345 7_4:-54320383 None:intergenic
CCATCAAAATATACACGTTA+AGG 0.316896 7_4:+54320814 Msa1163240:CDS
GTAGTAGCACTTCACCAAAA+TGG 0.326072 7_4:+54320369 Msa1163240:exon
TCTACCCATTGAAGAAGCTT+TGG 0.346676 7_4:+54320410 Msa1163240:CDS
TAGTAGCACTTCACCAAAAT+GGG 0.356184 7_4:+54320370 Msa1163240:exon
GATTTGAATTATCTATCTTT+GGG 0.371999 7_4:+54320837 Msa1163240:three_prime_UTR
CTACCCATTGAAGAAGCTTT+GGG 0.376258 7_4:+54320411 Msa1163240:CDS
TGGGTGAGTTTCGACAAATA+TGG 0.383460 7_4:+54320856 Msa1163240:three_prime_UTR
ACAAGTATTATATTCTTTCT+GGG 0.397148 7_4:-54321103 None:intergenic
GGGTGAGTTTCGACAAATAT+GGG 0.397445 7_4:+54320857 Msa1163240:three_prime_UTR
CATCAAAATATACACGTTAA+GGG 0.412552 7_4:+54320815 Msa1163240:CDS
TGGTCAATCCTGGTCGAGTC+GGG 0.436022 7_4:+54320775 Msa1163240:CDS
CATTGAAGAAGCTTTGGGTT+CGG 0.445914 7_4:+54320416 Msa1163240:CDS
AGAGAGATAGAAAGAAAGAA+AGG 0.457527 7_4:+54320918 Msa1163240:three_prime_UTR
CTGGTCAATCCTGGTCGAGT+CGG 0.460174 7_4:+54320774 Msa1163240:CDS
AAACTTTACAAGTATTTGAA+AGG 0.476738 7_4:-54321018 None:intergenic
GCTTCTTCAATGGGTAGAGT+AGG 0.487680 7_4:-54320405 None:intergenic
GCAAGTTCTCTGGTCAATCC+TGG 0.497290 7_4:+54320765 Msa1163240:CDS
CGAACCCAAAGCTTCTTCAA+TGG 0.503333 7_4:-54320415 None:intergenic
GTGAAGATGTGCAAGTTCTC+TGG 0.505261 7_4:+54320755 Msa1163240:CDS
GAACCCAAAGCTTCTTCAAT+GGG 0.506226 7_4:-54320414 None:intergenic
CTTCTTCAATGGGTAGAGTA+GGG 0.513099 7_4:-54320404 None:intergenic
AACTTTACAAGTATTTGAAA+GGG 0.516791 7_4:-54321017 None:intergenic
TGTATATACTAGTCTTGATG+TGG 0.538227 7_4:-54320965 None:intergenic
GTATATACTAGTCTTGATGT+GGG 0.554173 7_4:-54320964 None:intergenic
AGGCGGCACCCGACTCGACC+AGG 0.560698 7_4:-54320783 None:intergenic
ATATACTAGTCTTGATGTGG+GGG 0.612239 7_4:-54320962 None:intergenic
TATATACTAGTCTTGATGTG+GGG 0.621823 7_4:-54320963 None:intergenic
AGGATTATACATCTTATACA+AGG 0.638133 7_4:+54320714 Msa1163240:CDS
AGAACTTGCACATCTTCACA+CGG 0.663889 7_4:-54320751 None:intergenic
AGCACTTCACCAAAATGGGG+TGG 0.674042 7_4:+54320374 Msa1163240:exon
GAACTTGCACATCTTCACAC+GGG 0.699833 7_4:-54320750 None:intergenic
AGTAGCACTTCACCAAAATG+GGG 0.708319 7_4:+54320371 Msa1163240:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AACTTTACAATTATTTTTTT+AGG - chr7_4:54321045-54321064 None:intergenic 10.0%
!!! AACTTTACAATTATTTTTTT+AGG - chr7_4:54321045-54321064 None:intergenic 10.0%
!! ATATATGAACATGAATTATA+TGG - chr7_4:54320611-54320630 None:intergenic 15.0%
!! CATAAGAAACAAAAATTAAT+CGG - chr7_4:54320682-54320701 None:intergenic 15.0%
!!! TTTTGTTTCTTATGTAAAAT+AGG + chr7_4:54320688-54320707 Msa1163240:intron 15.0%
!! ATTTGAAAAAAAAAATATGG+AGG + chr7_4:54320887-54320906 Msa1163240:three_prime_UTR 15.0%
!! ATATATGAACATGAATTATA+TGG - chr7_4:54320611-54320630 None:intergenic 15.0%
!! CATAAGAAACAAAAATTAAT+CGG - chr7_4:54320682-54320701 None:intergenic 15.0%
!!! TTTTGTTTCTTATGTAAAAT+AGG + chr7_4:54320688-54320707 Msa1163240:intron 15.0%
!! ATTTGAAAAAAAAAATATGG+AGG + chr7_4:54320887-54320906 Msa1163240:three_prime_UTR 15.0%
!!! ATCATTGTTTTGTATAAAGT+AGG - chr7_4:54320643-54320662 None:intergenic 20.0%
!! GATTTGAATTATCTATCTTT+GGG + chr7_4:54320837-54320856 Msa1163240:three_prime_UTR 20.0%
!! AACTTTACAAGTATTTGAAA+GGG - chr7_4:54321020-54321039 None:intergenic 20.0%
!! AAACTTTACAAGTATTTGAA+AGG - chr7_4:54321021-54321040 None:intergenic 20.0%
!! ACAAGTATTATATTCTTTCT+GGG - chr7_4:54321106-54321125 None:intergenic 20.0%
!! TACAAGTATTATATTCTTTC+TGG - chr7_4:54321107-54321126 None:intergenic 20.0%
!!! ATCATTGTTTTGTATAAAGT+AGG - chr7_4:54320643-54320662 None:intergenic 20.0%
!! GATTTGAATTATCTATCTTT+GGG + chr7_4:54320837-54320856 Msa1163240:three_prime_UTR 20.0%
!! AACTTTACAAGTATTTGAAA+GGG - chr7_4:54321020-54321039 None:intergenic 20.0%
!! AAACTTTACAAGTATTTGAA+AGG - chr7_4:54321021-54321040 None:intergenic 20.0%
!! ACAAGTATTATATTCTTTCT+GGG - chr7_4:54321106-54321125 None:intergenic 20.0%
!! TACAAGTATTATATTCTTTC+TGG - chr7_4:54321107-54321126 None:intergenic 20.0%
! AAAGATGGAATCATATTGTA+TGG - chr7_4:54320504-54320523 None:intergenic 25.0%
! TACAATTGCATAATCAAAGA+TGG - chr7_4:54320519-54320538 None:intergenic 25.0%
!! TTATATGGATTGTACAAGAA+TGG - chr7_4:54320596-54320615 None:intergenic 25.0%
! TTCTTATGTAAAATAGGTAG+AGG + chr7_4:54320694-54320713 Msa1163240:intron 25.0%
! AGGATTATACATCTTATACA+AGG + chr7_4:54320714-54320733 Msa1163240:CDS 25.0%
! CATCAAAATATACACGTTAA+GGG + chr7_4:54320815-54320834 Msa1163240:CDS 25.0%
! GGATTTGAATTATCTATCTT+TGG + chr7_4:54320836-54320855 Msa1163240:three_prime_UTR 25.0%
! AAAGATGGAATCATATTGTA+TGG - chr7_4:54320504-54320523 None:intergenic 25.0%
! TACAATTGCATAATCAAAGA+TGG - chr7_4:54320519-54320538 None:intergenic 25.0%
!! TTATATGGATTGTACAAGAA+TGG - chr7_4:54320596-54320615 None:intergenic 25.0%
! TTCTTATGTAAAATAGGTAG+AGG + chr7_4:54320694-54320713 Msa1163240:intron 25.0%
! AGGATTATACATCTTATACA+AGG + chr7_4:54320714-54320733 Msa1163240:CDS 25.0%
! CATCAAAATATACACGTTAA+GGG + chr7_4:54320815-54320834 Msa1163240:CDS 25.0%
! GGATTTGAATTATCTATCTT+TGG + chr7_4:54320836-54320855 Msa1163240:three_prime_UTR 25.0%
!! TACGTCTTTTATTGGTTGAA+TGG - chr7_4:54320444-54320463 None:intergenic 30.0%
! TGCTAACTTACGTCTTTTAT+TGG - chr7_4:54320452-54320471 None:intergenic 30.0%
TACAAGAATGGTCTAAGAAA+AGG - chr7_4:54320584-54320603 None:intergenic 30.0%
!!! ATATTTTGATGGCAAAGTAG+AGG - chr7_4:54320806-54320825 None:intergenic 30.0%
!! CCTTAACGTGTATATTTTGA+TGG - chr7_4:54320817-54320836 None:intergenic 30.0%
CCATCAAAATATACACGTTA+AGG + chr7_4:54320814-54320833 Msa1163240:CDS 30.0%
AGAGAGATAGAAAGAAAGAA+AGG + chr7_4:54320918-54320937 Msa1163240:three_prime_UTR 30.0%
!! TATATACTAGTCTTGATGTG+GGG - chr7_4:54320966-54320985 None:intergenic 30.0%
!! GTATATACTAGTCTTGATGT+GGG - chr7_4:54320967-54320986 None:intergenic 30.0%
!! TGTATATACTAGTCTTGATG+TGG - chr7_4:54320968-54320987 None:intergenic 30.0%
!!! CATTTTTATGTGCTGATTTC+TGG + chr7_4:54321140-54321159 Msa1163240:three_prime_UTR 30.0%
!! TACGTCTTTTATTGGTTGAA+TGG - chr7_4:54320444-54320463 None:intergenic 30.0%
! TGCTAACTTACGTCTTTTAT+TGG - chr7_4:54320452-54320471 None:intergenic 30.0%
TACAAGAATGGTCTAAGAAA+AGG - chr7_4:54320584-54320603 None:intergenic 30.0%
!!! ATATTTTGATGGCAAAGTAG+AGG - chr7_4:54320806-54320825 None:intergenic 30.0%
!! CCTTAACGTGTATATTTTGA+TGG - chr7_4:54320817-54320836 None:intergenic 30.0%
CCATCAAAATATACACGTTA+AGG + chr7_4:54320814-54320833 Msa1163240:CDS 30.0%
AGAGAGATAGAAAGAAAGAA+AGG + chr7_4:54320918-54320937 Msa1163240:three_prime_UTR 30.0%
!! TATATACTAGTCTTGATGTG+GGG - chr7_4:54320966-54320985 None:intergenic 30.0%
!! GTATATACTAGTCTTGATGT+GGG - chr7_4:54320967-54320986 None:intergenic 30.0%
!! TGTATATACTAGTCTTGATG+TGG - chr7_4:54320968-54320987 None:intergenic 30.0%
!!! CATTTTTATGTGCTGATTTC+TGG + chr7_4:54321140-54321159 Msa1163240:three_prime_UTR 30.0%
TAGTAGCACTTCACCAAAAT+GGG + chr7_4:54320370-54320389 Msa1163240:exon 35.0%
!! ATATACTAGTCTTGATGTGG+GGG - chr7_4:54320965-54320984 None:intergenic 35.0%
!!! TTTTATGTGCTGATTTCTGG+TGG + chr7_4:54321143-54321162 Msa1163240:three_prime_UTR 35.0%
TAGTAGCACTTCACCAAAAT+GGG + chr7_4:54320370-54320389 Msa1163240:exon 35.0%
!! ATATACTAGTCTTGATGTGG+GGG - chr7_4:54320965-54320984 None:intergenic 35.0%
!!! TTTTATGTGCTGATTTCTGG+TGG + chr7_4:54321143-54321162 Msa1163240:three_prime_UTR 35.0%
!! TGGTGAAGTGCTACTACTTT+TGG - chr7_4:54320366-54320385 None:intergenic 40.0%
GTAGTAGCACTTCACCAAAA+TGG + chr7_4:54320369-54320388 Msa1163240:exon 40.0%
AGTAGCACTTCACCAAAATG+GGG + chr7_4:54320371-54320390 Msa1163240:exon 40.0%
CTTCTTCAATGGGTAGAGTA+GGG - chr7_4:54320407-54320426 None:intergenic 40.0%
TCTACCCATTGAAGAAGCTT+TGG + chr7_4:54320410-54320429 Msa1163240:CDS 40.0%
CTACCCATTGAAGAAGCTTT+GGG + chr7_4:54320411-54320430 Msa1163240:CDS 40.0%
GAACCCAAAGCTTCTTCAAT+GGG - chr7_4:54320417-54320436 None:intergenic 40.0%
!! CATTGAAGAAGCTTTGGGTT+CGG + chr7_4:54320416-54320435 Msa1163240:CDS 40.0%
AGAACTTGCACATCTTCACA+CGG - chr7_4:54320754-54320773 None:intergenic 40.0%
!! TTTTGATGGCAAAGTAGAGG+CGG - chr7_4:54320803-54320822 None:intergenic 40.0%
TGGGTGAGTTTCGACAAATA+TGG + chr7_4:54320856-54320875 Msa1163240:three_prime_UTR 40.0%
GGGTGAGTTTCGACAAATAT+GGG + chr7_4:54320857-54320876 Msa1163240:three_prime_UTR 40.0%
!! TGGTGAAGTGCTACTACTTT+TGG - chr7_4:54320366-54320385 None:intergenic 40.0%
GTAGTAGCACTTCACCAAAA+TGG + chr7_4:54320369-54320388 Msa1163240:exon 40.0%
AGTAGCACTTCACCAAAATG+GGG + chr7_4:54320371-54320390 Msa1163240:exon 40.0%
CTTCTTCAATGGGTAGAGTA+GGG - chr7_4:54320407-54320426 None:intergenic 40.0%
TCTACCCATTGAAGAAGCTT+TGG + chr7_4:54320410-54320429 Msa1163240:CDS 40.0%
CTACCCATTGAAGAAGCTTT+GGG + chr7_4:54320411-54320430 Msa1163240:CDS 40.0%
GAACCCAAAGCTTCTTCAAT+GGG - chr7_4:54320417-54320436 None:intergenic 40.0%
!! CATTGAAGAAGCTTTGGGTT+CGG + chr7_4:54320416-54320435 Msa1163240:CDS 40.0%
AGAACTTGCACATCTTCACA+CGG - chr7_4:54320754-54320773 None:intergenic 40.0%
!! TTTTGATGGCAAAGTAGAGG+CGG - chr7_4:54320803-54320822 None:intergenic 40.0%
TGGGTGAGTTTCGACAAATA+TGG + chr7_4:54320856-54320875 Msa1163240:three_prime_UTR 40.0%
GGGTGAGTTTCGACAAATAT+GGG + chr7_4:54320857-54320876 Msa1163240:three_prime_UTR 40.0%
GCTTCTTCAATGGGTAGAGT+AGG - chr7_4:54320408-54320427 None:intergenic 45.0%
CGAACCCAAAGCTTCTTCAA+TGG - chr7_4:54320418-54320437 None:intergenic 45.0%
GAACTTGCACATCTTCACAC+GGG - chr7_4:54320753-54320772 None:intergenic 45.0%
GTGAAGATGTGCAAGTTCTC+TGG + chr7_4:54320755-54320774 Msa1163240:CDS 45.0%
GCTTCTTCAATGGGTAGAGT+AGG - chr7_4:54320408-54320427 None:intergenic 45.0%
CGAACCCAAAGCTTCTTCAA+TGG - chr7_4:54320418-54320437 None:intergenic 45.0%
GAACTTGCACATCTTCACAC+GGG - chr7_4:54320753-54320772 None:intergenic 45.0%
GTGAAGATGTGCAAGTTCTC+TGG + chr7_4:54320755-54320774 Msa1163240:CDS 45.0%
!! AAAATTTGAAAAAAAAAATA+TGG + chr7_4:54320884-54320903 Msa1163240:three_prime_UTR 5.0%
!! AAAATTTGAAAAAAAAAATA+TGG + chr7_4:54320884-54320903 Msa1163240:three_prime_UTR 5.0%
AGCACTTCACCAAAATGGGG+TGG + chr7_4:54320374-54320393 Msa1163240:exon 50.0%
! GGATTGAAGCCACCCCATTT+TGG - chr7_4:54320386-54320405 None:intergenic 50.0%
GCAAGTTCTCTGGTCAATCC+TGG + chr7_4:54320765-54320784 Msa1163240:CDS 50.0%
AGCACTTCACCAAAATGGGG+TGG + chr7_4:54320374-54320393 Msa1163240:exon 50.0%
! GGATTGAAGCCACCCCATTT+TGG - chr7_4:54320386-54320405 None:intergenic 50.0%
GCAAGTTCTCTGGTCAATCC+TGG + chr7_4:54320765-54320784 Msa1163240:CDS 50.0%
CTGGTCAATCCTGGTCGAGT+CGG + chr7_4:54320774-54320793 Msa1163240:CDS 55.0%
TGGTCAATCCTGGTCGAGTC+GGG + chr7_4:54320775-54320794 Msa1163240:CDS 55.0%
CTGGTCAATCCTGGTCGAGT+CGG + chr7_4:54320774-54320793 Msa1163240:CDS 55.0%
TGGTCAATCCTGGTCGAGTC+GGG + chr7_4:54320775-54320794 Msa1163240:CDS 55.0%
! AGGCGGCACCCGACTCGACC+AGG - chr7_4:54320786-54320805 None:intergenic 75.0%
! AGGCGGCACCCGACTCGACC+AGG - chr7_4:54320786-54320805 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 54320362 54321172 54320362 ID=Msa1163240;Name=Msa1163240
chr7_4 mRNA 54320362 54321172 54320362 ID=Msa1163240-mRNA-1;Parent=Msa1163240;Name=Msa1163240-mRNA-1;_AED=0.01;_eAED=0.01;_QI=26|1|1|1|1|1|2|338|65
chr7_4 exon 54320362 54320460 54320362 ID=Msa1163240-mRNA-1:exon:15792;Parent=Msa1163240-mRNA-1
chr7_4 exon 54320710 54321172 54320710 ID=Msa1163240-mRNA-1:exon:15793;Parent=Msa1163240-mRNA-1
chr7_4 five_prime_UTR 54320362 54320387 54320362 ID=Msa1163240-mRNA-1:five_prime_utr;Parent=Msa1163240-mRNA-1
chr7_4 CDS 54320388 54320460 54320388 ID=Msa1163240-mRNA-1:cds;Parent=Msa1163240-mRNA-1
chr7_4 CDS 54320710 54320834 54320710 ID=Msa1163240-mRNA-1:cds;Parent=Msa1163240-mRNA-1
chr7_4 three_prime_UTR 54320835 54321172 54320835 ID=Msa1163240-mRNA-1:three_prime_utr;Parent=Msa1163240-mRNA-1
Gene Sequence

>Msa1163240

ATGGGGTGGCTTCAATCCCTACTCTACCCATTGAAGAAGCTTTGGGTTCGGATCCATTCAACCAATAAAAGACGTAGAGGATTATACATCTTATACAAGGATGTTAAGTCATGCCCGTGTGAAGATGTGCAAGTTCTCTGGTCAATCCTGGTCGAGTCGGGTGCCGCCTCTACTTTGCCATCAAAATATACACGTTAA
Protein sequence

>Msa1163240

MGWLQSLLYPLKKLWVRIHSTNKRRRGLYILYKDVKSCPCEDVQVLWSILVESGAASTLPSKYTR*