AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0751270

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0751270 MtrunA17_Chr5g0394631 92.818 181 13 0 1 181 1 181 8.02e-122 350
Msa0751270 MtrunA17_Chr5g0394631 73.770 183 42 4 12 190 221 401 4.32e-86 259
Msa0751270 MtrunA17_Chr5g0394621 80.000 190 38 0 1 190 1 190 6.74e-108 306
Msa0751270 MtrunA17_Chr1g0204951 63.542 192 66 2 1 190 1 190 7.09e-84 246
Msa0751270 MtrunA17_Chr1g0204971 59.375 192 74 2 1 190 1 190 4.46e-78 231
Msa0751270 MtrunA17_Chr7g0273661 43.590 156 85 1 17 172 4 156 7.50e-43 140
Msa0751270 MtrunA17_Chr7g0223361 40.230 174 94 3 17 187 4 170 8.40e-38 128
Msa0751270 MtrunA17_Chr7g0223351 39.881 168 96 3 20 187 7 169 3.80e-35 121
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0751270 AT2G32030.1 48.634 183 79 4 6 187 17 185 4.06e-57 178
Msa0751270 AT2G32020.1 48.521 169 80 2 20 187 18 180 1.71e-53 169
Msa0751270 AT3G22560.1 42.012 169 93 2 21 187 7 172 3.94e-38 129

Find 38 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAATCAATGCTCTCTTCTT+TGG 0.193418 5_2:-4789843 None:intergenic
TCCTAAGAATTCCTTCCTTC+TGG 0.242611 5_2:-4790285 None:intergenic
CTCTTCTTTGGCACATGGTT+TGG 0.246122 5_2:-4789831 None:intergenic
GTTGATGCCTTGTTCTTTGC+TGG 0.260002 5_2:-4789969 None:intergenic
TCCTTTACCCCAGTATTTAG+AGG 0.284343 5_2:-4790134 None:intergenic
ATGTTCTAGCCTCTAAATAC+TGG 0.304005 5_2:+4790125 Msa0751270:CDS
CCTTGTTCTTTGCTGGTGTA+TGG 0.318147 5_2:-4789962 None:intergenic
TGCCTTAATGATCGTGCTAT+TGG 0.357294 5_2:+4790037 Msa0751270:CDS
ATATACCAAACAAATTTCTA+TGG 0.388477 5_2:+4790002 Msa0751270:CDS
TCCAGAAGGAAGGAATTCTT+AGG 0.397920 5_2:+4790284 Msa0751270:CDS
GGCCAATAGCACGATCATTA+AGG 0.403869 5_2:-4790039 None:intergenic
TTGCACCATAGAAATTTGTT+TGG 0.404833 5_2:-4790007 None:intergenic
TTGTTGATGTTGAAAATGTT+GGG 0.408191 5_2:+4790233 Msa0751270:CDS
TTCTGACCTTGATGATCTCC+TGG 0.414515 5_2:+4789895 Msa0751270:CDS
CCAAACAAATAAATCATAGT+TGG 0.419913 5_2:-4790372 None:intergenic
GCCTCTAAATACTGGGGTAA+AGG 0.441976 5_2:+4790133 Msa0751270:CDS
TTTGTTGATGTTGAAAATGT+TGG 0.442167 5_2:+4790232 Msa0751270:CDS
AGTGGCCAAGTTCTGCTCTT+GGG 0.462852 5_2:+4789937 Msa0751270:CDS
TGTTGTGAAACAAGCAGTTA+AGG 0.468441 5_2:+4790168 Msa0751270:CDS
AAGTGGCCAAGTTCTGCTCT+TGG 0.474319 5_2:+4789936 Msa0751270:CDS
AGGAAGTATTTGTTCATGAA+AGG 0.475944 5_2:+4790304 Msa0751270:CDS
TTTCATCAGTTCTCCATACC+AGG 0.488119 5_2:-4789913 None:intergenic
CAAAGAGTGTTGGAGAAAGC+TGG 0.497277 5_2:+4790259 Msa0751270:CDS
ATGCTCTCTTCTTTGGCACA+TGG 0.504425 5_2:-4789836 None:intergenic
GTATTTAGAGGCTAGAACAT+AGG 0.521725 5_2:-4790122 None:intergenic
TGTTCTAGCCTCTAAATACT+GGG 0.523419 5_2:+4790126 Msa0751270:CDS
ACCTTGATGATCTCCTGGTA+TGG 0.538483 5_2:+4789900 Msa0751270:CDS
ATTCAGTGAGTTGTCACACT+TGG 0.554731 5_2:+4790195 Msa0751270:CDS
GATCACCTCATGATAAAAGC+AGG 0.555612 5_2:+4790080 Msa0751270:CDS
TGTTGGGTCTCAAAGAGTGT+TGG 0.566749 5_2:+4790249 Msa0751270:CDS
TGGTTCCCAAGAGCAGAACT+TGG 0.574822 5_2:-4789942 None:intergenic
CCATACACCAGCAAAGAACA+AGG 0.601334 5_2:+4789962 Msa0751270:CDS
GGAGAAAGCTGGTTTCCAGA+AGG 0.617484 5_2:+4790270 Msa0751270:CDS
AAAGCTGGTTTCCAGAAGGA+AGG 0.623258 5_2:+4790274 Msa0751270:CDS
TCCATACCAGGAGATCATCA+AGG 0.624213 5_2:-4789901 None:intergenic
TGCTTGTTTCACAACATACG+TGG 0.636843 5_2:-4790161 None:intergenic
GTTCTAGCCTCTAAATACTG+GGG 0.689247 5_2:+4790127 Msa0751270:CDS
ATCTTGATTTCAGAGAAACA+CGG 0.706701 5_2:-4790060 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATACCAAACAAATTTCTA+TGG + chr5_2:4790002-4790021 Msa0751270:CDS 20.0%
! TTTGTTGATGTTGAAAATGT+TGG + chr5_2:4790232-4790251 Msa0751270:CDS 25.0%
! TTGTTGATGTTGAAAATGTT+GGG + chr5_2:4790233-4790252 Msa0751270:CDS 25.0%
! TTGCACCATAGAAATTTGTT+TGG - chr5_2:4790010-4790029 None:intergenic 30.0%
ATCTTGATTTCAGAGAAACA+CGG - chr5_2:4790063-4790082 None:intergenic 30.0%
!! AGGAAGTATTTGTTCATGAA+AGG + chr5_2:4790304-4790323 Msa0751270:CDS 30.0%
CAAATCAATGCTCTCTTCTT+TGG - chr5_2:4789846-4789865 None:intergenic 35.0%
GGTCAGAAAGATGAAAAAGT+CGG - chr5_2:4789883-4789902 None:intergenic 35.0%
ATGGAGAACTGATGAAAAAG+TGG + chr5_2:4789919-4789938 Msa0751270:CDS 35.0%
!! TTGTTCCTGCTTTTATCATG+AGG - chr5_2:4790088-4790107 None:intergenic 35.0%
GTATTTAGAGGCTAGAACAT+AGG - chr5_2:4790125-4790144 None:intergenic 35.0%
ATGTTCTAGCCTCTAAATAC+TGG + chr5_2:4790125-4790144 Msa0751270:CDS 35.0%
TGTTCTAGCCTCTAAATACT+GGG + chr5_2:4790126-4790145 Msa0751270:CDS 35.0%
TGTTGTGAAACAAGCAGTTA+AGG + chr5_2:4790168-4790187 Msa0751270:CDS 35.0%
GAAAAAGTCGGAGTGTGATT+TGG - chr5_2:4789871-4789890 None:intergenic 40.0%
TTTCATCAGTTCTCCATACC+AGG - chr5_2:4789916-4789935 None:intergenic 40.0%
TGCCTTAATGATCGTGCTAT+TGG + chr5_2:4790037-4790056 Msa0751270:CDS 40.0%
GATCACCTCATGATAAAAGC+AGG + chr5_2:4790080-4790099 Msa0751270:CDS 40.0%
GTTCTAGCCTCTAAATACTG+GGG + chr5_2:4790127-4790146 Msa0751270:CDS 40.0%
TCCTTTACCCCAGTATTTAG+AGG - chr5_2:4790137-4790156 None:intergenic 40.0%
TGCTTGTTTCACAACATACG+TGG - chr5_2:4790164-4790183 None:intergenic 40.0%
ATTCAGTGAGTTGTCACACT+TGG + chr5_2:4790195-4790214 Msa0751270:CDS 40.0%
TCCAGAAGGAAGGAATTCTT+AGG + chr5_2:4790284-4790303 Msa0751270:CDS 40.0%
TCCTAAGAATTCCTTCCTTC+TGG - chr5_2:4790288-4790307 None:intergenic 40.0%
CTCTTCTTTGGCACATGGTT+TGG - chr5_2:4789834-4789853 None:intergenic 45.0%
ATGCTCTCTTCTTTGGCACA+TGG - chr5_2:4789839-4789858 None:intergenic 45.0%
! TTCTGACCTTGATGATCTCC+TGG + chr5_2:4789895-4789914 Msa0751270:CDS 45.0%
! ACCTTGATGATCTCCTGGTA+TGG + chr5_2:4789900-4789919 Msa0751270:CDS 45.0%
TCCATACCAGGAGATCATCA+AGG - chr5_2:4789904-4789923 None:intergenic 45.0%
CCTTGTTCTTTGCTGGTGTA+TGG - chr5_2:4789965-4789984 None:intergenic 45.0%
CCATACACCAGCAAAGAACA+AGG + chr5_2:4789962-4789981 Msa0751270:CDS 45.0%
! GTTGATGCCTTGTTCTTTGC+TGG - chr5_2:4789972-4789991 None:intergenic 45.0%
GGCCAATAGCACGATCATTA+AGG - chr5_2:4790042-4790061 None:intergenic 45.0%
GCCTCTAAATACTGGGGTAA+AGG + chr5_2:4790133-4790152 Msa0751270:CDS 45.0%
! TGTTGGGTCTCAAAGAGTGT+TGG + chr5_2:4790249-4790268 Msa0751270:CDS 45.0%
!! CAAAGAGTGTTGGAGAAAGC+TGG + chr5_2:4790259-4790278 Msa0751270:CDS 45.0%
! AAAGCTGGTTTCCAGAAGGA+AGG + chr5_2:4790274-4790293 Msa0751270:CDS 45.0%
AAGTGGCCAAGTTCTGCTCT+TGG + chr5_2:4789936-4789955 Msa0751270:CDS 50.0%
AGTGGCCAAGTTCTGCTCTT+GGG + chr5_2:4789937-4789956 Msa0751270:CDS 50.0%
TGGTTCCCAAGAGCAGAACT+TGG - chr5_2:4789945-4789964 None:intergenic 50.0%
! GGAGAAAGCTGGTTTCCAGA+AGG + chr5_2:4790270-4790289 Msa0751270:CDS 50.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 4789809 4790381 4789809 ID=Msa0751270;Name=Msa0751270
chr5_2 mRNA 4789809 4790381 4789809 ID=Msa0751270-mRNA-1;Parent=Msa0751270;Name=Msa0751270-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|190
chr5_2 exon 4789809 4790381 4789809 ID=Msa0751270-mRNA-1:exon:1904;Parent=Msa0751270-mRNA-1
chr5_2 CDS 4789809 4790381 4789809 ID=Msa0751270-mRNA-1:cds;Parent=Msa0751270-mRNA-1
Gene Sequence

>Msa0751270

ATGGAGAAAACTTTTATTTCTTCCAAACCATGTGCCAAAGAAGAGAGCATTGATTTGAACCAAATCACACTCCGACTTTTTCATCTTTCTGACCTTGATGATCTCCTGGTATGGAGAACTGATGAAAAAGTGGCCAAGTTCTGCTCTTGGGAACCATACACCAGCAAAGAACAAGGCATCAACTTCATTGAAAATATACCAAACAAATTTCTATGGTGCAAAGCAATATGCCTTAATGATCGTGCTATTGGCCGTGTTTCTCTGAAATCAAGATCACCTCATGATAAAAGCAGGAACAAAACTGCAGAACTTGCCTATGTTCTAGCCTCTAAATACTGGGGTAAAGGAATTGCCACGTATGTTGTGAAACAAGCAGTTAAGGTTGCATTCAGTGAGTTGTCACACTTGGAAAGAGTTGAAGCTTTTGTTGATGTTGAAAATGTTGGGTCTCAAAGAGTGTTGGAGAAAGCTGGTTTCCAGAAGGAAGGAATTCTTAGGAAGTATTTGTTCATGAAAGGAAAAAGTAGAGATATGATCATATTCAGTGTTCTTTCTAATGATCTCCAACTATGA
Protein sequence

>Msa0751270

MEKTFISSKPCAKEESIDLNQITLRLFHLSDLDDLLVWRTDEKVAKFCSWEPYTSKEQGINFIENIPNKFLWCKAICLNDRAIGRVSLKSRSPHDKSRNKTAELAYVLASKYWGKGIATYVVKQAVKVAFSELSHLERVEAFVDVENVGSQRVLEKAGFQKEGILRKYLFMKGKSRDMIIFSVLSNDLQL*