AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1456830


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1456830 MtrunA17_Chr7g0274161 93.878 147 4 2 5 150 2 144 4.35e-92 263
Msa1456830 MtrunA17_Chr1g0190751 67.647 102 28 1 49 150 43 139 6.94e-42 136
Msa1456830 MtrunA17_Chr1g0194691 77.778 45 9 1 106 150 11 54 3.66e-14 63.2
Msa1456830 MtrunA17_Chr1g0202801 47.541 61 25 1 65 118 86 146 2.90e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1456830 AT5G28750.1 65.347 101 35 0 50 150 47 147 9.43e-39 129
Msa1456830 AT5G52440.1 35.833 120 58 3 6 118 38 145 8.05e-13 64.3

Find 24 sgRNAs with CRISPR-Local

Find 144 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACTGAGGTTTCTAGTTCTA+AGG 0.292945 tig0037821:+5172 Msa1456830:CDS
GTTTGAGTCTGAGCTTAAAA+AGG 0.305627 tig0037821:+5082 Msa1456830:CDS
CCTGAACTCGTTGTTATTGC+TGG 0.366575 tig0037821:+3095 Msa1456830:CDS
GGTGTTGTGTTGATGCAATT+GGG 0.379796 tig0037821:-2941 None:intergenic
AACTGTCAAAAGCTTTCAAC+AGG 0.389906 tig0037821:+3178 Msa1456830:CDS
CCGATACTGCGACCAACTTC+AGG 0.394518 tig0037821:-3152 None:intergenic
AGAAGAAGAATAAACAATAA+TGG 0.400103 tig0037821:+3038 Msa1456830:CDS
GGCTCCCCTCCTGAGGAATC+TGG 0.401880 tig0037821:-5107 None:intergenic
AGGTGTTGTGTTGATGCAAT+TGG 0.404660 tig0037821:-2942 None:intergenic
ATTGATAGAAACCCTTGAAA+TGG 0.413952 tig0037821:-2994 None:intergenic
TGTGTTGATGCAATTGGGGT+TGG 0.431544 tig0037821:-2936 None:intergenic
CCAGCAATAACAACGAGTTC+AGG 0.481286 tig0037821:-3095 None:intergenic
CCTGAAGTTGGTCGCAGTAT+CGG 0.502726 tig0037821:+3152 Msa1456830:CDS
GTAAATCATGTAGGCAGCAA+AGG 0.522582 tig0037821:+5058 Msa1456830:intron
ACAGCAATTGATTTCTCAGA+TGG 0.525895 tig0037821:-5128 None:intergenic
ATGAAGAAGAAGAGAAAGCG+AGG 0.549986 tig0037821:-2962 None:intergenic
CTCAGATGGCTCCCCTCCTG+AGG 0.577964 tig0037821:-5114 None:intergenic
GTGTTGTGTTGATGCAATTG+GGG 0.599012 tig0037821:-2940 None:intergenic
GGAACCAGATTCCTCAGGAG+GGG 0.609899 tig0037821:+5103 Msa1456830:CDS
AAGGAACCAGATTCCTCAGG+AGG 0.613287 tig0037821:+5101 Msa1456830:CDS
AGGAACCAGATTCCTCAGGA+GGG 0.620434 tig0037821:+5102 Msa1456830:CDS
ATAGATGTGATATGATGAGT+AGG 0.635858 tig0037821:+5214 Msa1456830:three_prime_UTR
AGAGAAGAAGCAAGATACTG+AGG 0.643616 tig0037821:+5157 Msa1456830:CDS
AAAGTAAAATCTAAACGCAG+TGG 0.668233 tig0037821:+2838 Msa1456830:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTAAGTTGTTTATCTAAAT+AGG + tig0037821:3434-3453 Msa1456830:intron 15.0%
!!! TTAAGTTGTTTATCTAAATA+GGG + tig0037821:3435-3454 Msa1456830:intron 15.0%
!!! CCATAAACTTTATTTTAATT+AGG - tig0037821:4028-4047 None:intergenic 15.0%
!! CCTAATTAAAATAAAGTTTA+TGG + tig0037821:4025-4044 Msa1456830:intron 15.0%
!!! TTTATTTTACTTTTACAACA+CGG - tig0037821:4486-4505 None:intergenic 15.0%
!!! ATTCTCTTCTTTTTATATAA+AGG - tig0037821:4580-4599 None:intergenic 15.0%
!! TATATAAAAAGAAGAGAATT+TGG + tig0037821:4581-4600 Msa1456830:intron 15.0%
!!! ATATATTTTGTAAATCATGT+AGG + tig0037821:5049-5068 Msa1456830:intron 15.0%
!!! TTTTTGAATATATATTGTCA+TGG - tig0037821:5253-5272 None:intergenic 15.0%
!! AGAAGAAGAATAAACAATAA+TGG + tig0037821:3038-3057 Msa1456830:CDS 20.0%
!! AATGAGAAGAAATAAAGAAA+GGG - tig0037821:3210-3229 None:intergenic 20.0%
!! AAAAGATAAATGTTTCTCTT+AGG - tig0037821:3772-3791 None:intergenic 20.0%
!! AACTTTATTGAGAAATACTA+GGG + tig0037821:3956-3975 Msa1456830:intron 20.0%
!! TAACTTGAAAAGCTTATATT+AGG + tig0037821:4247-4266 Msa1456830:intron 20.0%
!! ATCAAAATGTCAATCTTATT+TGG + tig0037821:4299-4318 Msa1456830:intron 20.0%
!!! GAAAATAGTTTTCAATCAAA+TGG + tig0037821:4374-4393 Msa1456830:intron 20.0%
!!! TTATTTTACTTTTACAACAC+GGG - tig0037821:4485-4504 None:intergenic 20.0%
!! TAAAATAAACAAGCAAAGAA+GGG + tig0037821:4497-4516 Msa1456830:intron 20.0%
!! ATCTTTTTGTTCCATTTCAA+GGG + tig0037821:2983-3002 Msa1456830:CDS 25.0%
! GAATGAGAAGAAATAAAGAA+AGG - tig0037821:3211-3230 None:intergenic 25.0%
!!! AACTCGTAACTTTAATTTGA+AGG - tig0037821:3233-3252 None:intergenic 25.0%
! AGTTTCAAATGTGTTTATGT+CGG - tig0037821:3262-3281 None:intergenic 25.0%
!!! GTATAAGATGTTTTAAGAGT+AGG + tig0037821:3660-3679 Msa1456830:intron 25.0%
!! TGAAAAATGTGTTTTCTTTG+CGG + tig0037821:3717-3736 Msa1456830:intron 25.0%
!! GAAACATTTATCTTTTTGCT+TGG + tig0037821:3776-3795 Msa1456830:intron 25.0%
! GAACTTTATTGAGAAATACT+AGG + tig0037821:3955-3974 Msa1456830:intron 25.0%
! TGAAAAGCTTATATTAGGTT+TGG + tig0037821:4252-4271 Msa1456830:intron 25.0%
! GAAAAGCTTATATTAGGTTT+GGG + tig0037821:4253-4272 Msa1456830:intron 25.0%
!!! CTAAAACGTCACTTTTATTT+TGG - tig0037821:4333-4352 None:intergenic 25.0%
!!! TATTTTACTTTTACAACACG+GGG - tig0037821:4484-4503 None:intergenic 25.0%
! GTAAAATAAACAAGCAAAGA+AGG + tig0037821:4496-4515 Msa1456830:intron 25.0%
! CACACAAATATTCTTTCAAA+TGG - tig0037821:4766-4785 None:intergenic 25.0%
! AAATAACCATATAAGCAATG+AGG - tig0037821:5028-5047 None:intergenic 25.0%
AAAGTAAAATCTAAACGCAG+TGG + tig0037821:2838-2857 Msa1456830:five_prime_UTR 30.0%
! CATCTTTTTGTTCCATTTCA+AGG + tig0037821:2982-3001 Msa1456830:CDS 30.0%
ATTGATAGAAACCCTTGAAA+TGG - tig0037821:2997-3016 None:intergenic 30.0%
!! GCTGTTTTCATAAGTTATCT+TGG - tig0037821:3308-3327 None:intergenic 30.0%
CACTAATCATATAAGTGCTT+AGG - tig0037821:3395-3414 None:intergenic 30.0%
AATGACAATGTGATATTGCT+TGG - tig0037821:3602-3621 None:intergenic 30.0%
GTCATTTGAATTATGCCTTA+CGG + tig0037821:3616-3635 Msa1456830:intron 30.0%
ATAAAGTTCATGTGAAACAG+AGG - tig0037821:3944-3963 None:intergenic 30.0%
GAAATACTAGGGAAAAACAA+AGG + tig0037821:3967-3986 Msa1456830:intron 30.0%
ACTAGAAGCTAATCTACATT+AGG - tig0037821:3993-4012 None:intergenic 30.0%
TTAAATTTGAACGACTGGAT+CGG - tig0037821:4230-4249 None:intergenic 30.0%
TCAAGTTAAATTTGAACGAC+TGG - tig0037821:4235-4254 None:intergenic 30.0%
!! ATTTTACTTTTACAACACGG+GGG - tig0037821:4483-4502 None:intergenic 30.0%
ATGCAATACTTTCTTGCATT+TGG + tig0037821:4666-4685 Msa1456830:intron 30.0%
CAAAGTAATATGCTGTAATG+TGG - tig0037821:4872-4891 None:intergenic 30.0%
CACATTACAGCATATTACTT+TGG + tig0037821:4870-4889 Msa1456830:intron 30.0%
TACTTTCCTCATTGCTTATA+TGG + tig0037821:5019-5038 Msa1456830:intron 30.0%
ATAGATGTGATATGATGAGT+AGG + tig0037821:5214-5233 Msa1456830:three_prime_UTR 30.0%
!!! TTTTTTGGGACCAAAAACGA+TGG - tig0037821:3129-3148 None:intergenic 35.0%
!!! CCAACTTCAGGCAATTTTTT+GGG - tig0037821:3143-3162 None:intergenic 35.0%
!!! ACCAACTTCAGGCAATTTTT+TGG - tig0037821:3144-3163 None:intergenic 35.0%
AACTGTCAAAAGCTTTCAAC+AGG + tig0037821:3178-3197 Msa1456830:CDS 35.0%
AATTGTGTGTGAGTTTCAAG+TGG - tig0037821:3541-3560 None:intergenic 35.0%
ACTTGAAACTCACACACAAT+TGG + tig0037821:3540-3559 Msa1456830:intron 35.0%
CTTGAAACTCACACACAATT+GGG + tig0037821:3541-3560 Msa1456830:intron 35.0%
CTAATGCCAATACGTTTGTT+TGG - tig0037821:3687-3706 None:intergenic 35.0%
AGACTCAGATATTTGTGTAG+TGG + tig0037821:3741-3760 Msa1456830:intron 35.0%
CATGCTTGAATTTCTCTATC+AGG - tig0037821:3815-3834 None:intergenic 35.0%
CTGATAGAGAAATTCAAGCA+TGG + tig0037821:3813-3832 Msa1456830:intron 35.0%
!! TGTTTTCGAGGGAGATTATA+CGG - tig0037821:3885-3904 None:intergenic 35.0%
! AATCCTGAGATGCTACTTAA+GGG - tig0037821:4204-4223 None:intergenic 35.0%
AATGGCCCCATAAACTATAT+TGG + tig0037821:4392-4411 Msa1456830:intron 35.0%
TGCCTCCAATATAGTTTATG+GGG - tig0037821:4400-4419 None:intergenic 35.0%
CTGCCTCCAATATAGTTTAT+GGG - tig0037821:4401-4420 None:intergenic 35.0%
TCTGCCTCCAATATAGTTTA+TGG - tig0037821:4402-4421 None:intergenic 35.0%
ATAAACTATATTGGAGGCAG+AGG + tig0037821:4401-4420 Msa1456830:intron 35.0%
! GTTTGGCTCATATAACTCAT+TGG + tig0037821:4429-4448 Msa1456830:intron 35.0%
ATAACTCATTGGATTGTTCC+AGG + tig0037821:4440-4459 Msa1456830:intron 35.0%
AATAAACAAGCAAAGAAGGG+AGG + tig0037821:4500-4519 Msa1456830:intron 35.0%
!! AACTAATAGCTTCTAAAGCG+TGG + tig0037821:4548-4567 Msa1456830:intron 35.0%
TATTGCATGCCATAGACTAA+CGG - tig0037821:4654-4673 None:intergenic 35.0%
TACTTTCTTGCATTTGGAAG+AGG + tig0037821:4672-4691 Msa1456830:intron 35.0%
CAACATCAGACATTGCTTTA+AGG + tig0037821:4736-4755 Msa1456830:intron 35.0%
TGTGTGAGAAAAATGCCATA+TGG + tig0037821:4780-4799 Msa1456830:intron 35.0%
ATTACAACAGTAGCACCATA+TGG - tig0037821:4798-4817 None:intergenic 35.0%
TATATCATCCCCTAATGTTC+AGG + tig0037821:4838-4857 Msa1456830:intron 35.0%
ACTCAAGCAGCCAAATAATT+TGG + tig0037821:4926-4945 Msa1456830:intron 35.0%
CAGCCAAATAATTTGGATTC+TGG + tig0037821:4933-4952 Msa1456830:intron 35.0%
ACGCCAGAATCCAAATTATT+TGG - tig0037821:4939-4958 None:intergenic 35.0%
GTTTGAGTCTGAGCTTAAAA+AGG + tig0037821:5082-5101 Msa1456830:CDS 35.0%
! ACAGCAATTGATTTCTCAGA+TGG - tig0037821:5131-5150 None:intergenic 35.0%
!! TACTGAGGTTTCTAGTTCTA+AGG + tig0037821:5172-5191 Msa1456830:CDS 35.0%
! GTGTTGTGTTGATGCAATTG+GGG - tig0037821:2943-2962 None:intergenic 40.0%
! GGTGTTGTGTTGATGCAATT+GGG - tig0037821:2944-2963 None:intergenic 40.0%
! AGGTGTTGTGTTGATGCAAT+TGG - tig0037821:2945-2964 None:intergenic 40.0%
ATGAAGAAGAAGAGAAAGCG+AGG - tig0037821:2965-2984 None:intergenic 40.0%
CTTCTTCTTCTTCTTCTTCG+TGG - tig0037821:3023-3042 None:intergenic 40.0%
! TTCACTTGCAACGCACTTTT+CGG + tig0037821:3062-3081 Msa1456830:CDS 40.0%
CCCAAAAAATTGCCTGAAGT+TGG + tig0037821:3140-3159 Msa1456830:CDS 40.0%
ACAATGTGATATTGCTTGGC+TGG - tig0037821:3598-3617 None:intergenic 40.0%
TGTAGTCATCTTTGTCCGTA+AGG - tig0037821:3634-3653 None:intergenic 40.0%
GTAGGACCAAACAAACGTAT+TGG + tig0037821:3678-3697 Msa1456830:intron 40.0%
GCTAAAGAAGTAGGCAGAAA+AGG - tig0037821:3908-3927 None:intergenic 40.0%
AGGAAGCTAGCTAAAGAAGT+AGG - tig0037821:3917-3936 None:intergenic 40.0%
TTTCCCTTAAGTAGCATCTC+AGG + tig0037821:4198-4217 Msa1456830:intron 40.0%
! GAATCCTGAGATGCTACTTA+AGG - tig0037821:4205-4224 None:intergenic 40.0%
GAATAGTAAAACAGCATGCC+TGG - tig0037821:4461-4480 None:intergenic 40.0%
!! ATAGCTTCTAAAGCGTGGAA+AGG + tig0037821:4553-4572 Msa1456830:intron 40.0%
GTTACGTGACTCGAAAATCA+TGG - tig0037821:4717-4736 None:intergenic 40.0%
ATGCCAATCCTGAACATTAG+GGG - tig0037821:4849-4868 None:intergenic 40.0%
GATGCCAATCCTGAACATTA+GGG - tig0037821:4850-4869 None:intergenic 40.0%
GTAAATCATGTAGGCAGCAA+AGG + tig0037821:5058-5077 Msa1456830:intron 40.0%
AAAAAGGAACCAGATTCCTC+AGG + tig0037821:5098-5117 Msa1456830:CDS 40.0%
AGAGAAGAAGCAAGATACTG+AGG + tig0037821:5157-5176 Msa1456830:CDS 40.0%
! TGTGTTGATGCAATTGGGGT+TGG - tig0037821:2939-2958 None:intergenic 45.0%
CTTCTTCTTCTTCTTCGTGG+AGG - tig0037821:3020-3039 None:intergenic 45.0%
! TGCAACGCACTTTTCGGATT+AGG + tig0037821:3068-3087 Msa1456830:CDS 45.0%
CCAGCAATAACAACGAGTTC+AGG - tig0037821:3098-3117 None:intergenic 45.0%
! CCTGAACTCGTTGTTATTGC+TGG + tig0037821:3095-3114 Msa1456830:CDS 45.0%
TCTGTTCTCTGTAGACGAAG+TGG + tig0037821:3509-3528 Msa1456830:intron 45.0%
ACACACAATTGGGAAGTCCT+GGG + tig0037821:3551-3570 Msa1456830:intron 45.0%
!!! GGCAGAAAAGGTGTTTTCGA+GGG - tig0037821:3896-3915 None:intergenic 45.0%
!!! AGGCAGAAAAGGTGTTTTCG+AGG - tig0037821:3897-3916 None:intergenic 45.0%
AGTTCATGTGAAACAGAGGC+AGG - tig0037821:3940-3959 None:intergenic 45.0%
AATTTGAACGACTGGATCGG+TGG - tig0037821:4227-4246 None:intergenic 45.0%
GGCCCCATAAACTATATTGG+AGG + tig0037821:4395-4414 Msa1456830:intron 45.0%
GTTTCAACGCTCTTGACTCA+TGG + tig0037821:4605-4624 Msa1456830:intron 45.0%
TCATGGCAAGATCCAGGAAA+GGG + tig0037821:4622-4641 Msa1456830:intron 45.0%
CATCCCCTAATGTTCAGGAT+TGG + tig0037821:4843-4862 Msa1456830:intron 45.0%
GGATGCCAATCCTGAACATT+AGG - tig0037821:4851-4870 None:intergenic 45.0%
TATTTGGCTGCTTGAGTGCA+TGG - tig0037821:4923-4942 None:intergenic 45.0%
!!! GGTGTTGCTGCCATCGTTTT+TGG + tig0037821:3116-3135 Msa1456830:CDS 50.0%
! CCTGAAGTTGGTCGCAGTAT+CGG + tig0037821:3152-3171 Msa1456830:CDS 50.0%
CACACACAATTGGGAAGTCC+TGG + tig0037821:3550-3569 Msa1456830:intron 50.0%
TTTCACTCGGGTTCAAACCC+AGG - tig0037821:3571-3590 None:intergenic 50.0%
TTGGCTGGACACTTTCACTC+GGG - tig0037821:3583-3602 None:intergenic 50.0%
CTTGGCTGGACACTTTCACT+CGG - tig0037821:3584-3603 None:intergenic 50.0%
TCATGTGAAACAGAGGCAGG+AGG - tig0037821:3937-3956 None:intergenic 50.0%
CTTGACTCATGGCAAGATCC+AGG + tig0037821:4616-4635 Msa1456830:intron 50.0%
CTCATGGCAAGATCCAGGAA+AGG + tig0037821:4621-4640 Msa1456830:intron 50.0%
AAGGAACCAGATTCCTCAGG+AGG + tig0037821:5101-5120 Msa1456830:CDS 50.0%
AGGAACCAGATTCCTCAGGA+GGG + tig0037821:5102-5121 Msa1456830:CDS 50.0%
CCGATACTGCGACCAACTTC+AGG - tig0037821:3155-3174 None:intergenic 55.0%
!! TGGAGGCAGAGGCACTTGTT+TGG + tig0037821:4412-4431 Msa1456830:intron 55.0%
GGCAAGATCCAGGAAAGGGT+CGG + tig0037821:4626-4645 Msa1456830:intron 55.0%
GCAAGATCCAGGAAAGGGTC+GGG + tig0037821:4627-4646 Msa1456830:intron 55.0%
GGAACCAGATTCCTCAGGAG+GGG + tig0037821:5103-5122 Msa1456830:CDS 55.0%
! TAACGGACCCGACCCTTTCC+TGG - tig0037821:4637-4656 None:intergenic 60.0%
! GGGTCGGGTCCGTTAGTCTA+TGG + tig0037821:4642-4661 Msa1456830:intron 60.0%
GGCTCCCCTCCTGAGGAATC+TGG - tig0037821:5110-5129 None:intergenic 65.0%
CTCAGATGGCTCCCCTCCTG+AGG - tig0037821:5117-5136 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0037821 gene 2804 5327 2804 ID=Msa1456830;Name=Msa1456830
tig0037821 mRNA 2804 5327 2804 ID=Msa1456830-mRNA-1;Parent=Msa1456830;Name=Msa1456830-mRNA-1;_AED=0.01;_eAED=0.01;_QI=78|1|1|1|1|1|2|122|150
tig0037821 exon 2804 3199 2804 ID=Msa1456830-mRNA-1:exon:20891;Parent=Msa1456830-mRNA-1
tig0037821 exon 5071 5327 5071 ID=Msa1456830-mRNA-1:exon:20892;Parent=Msa1456830-mRNA-1
tig0037821 five_prime_UTR 2804 2881 2804 ID=Msa1456830-mRNA-1:five_prime_utr;Parent=Msa1456830-mRNA-1
tig0037821 CDS 2882 3199 2882 ID=Msa1456830-mRNA-1:cds;Parent=Msa1456830-mRNA-1
tig0037821 CDS 5071 5205 5071 ID=Msa1456830-mRNA-1:cds;Parent=Msa1456830-mRNA-1
tig0037821 three_prime_UTR 5206 5327 5206 ID=Msa1456830-mRNA-1:three_prime_utr;Parent=Msa1456830-mRNA-1
Gene Sequence

>Msa1456830

ATGACGATGACGATGAACTGTGTTTCGTTTTGTTCGTCAATTTCAATTTCAATTCCAACCCCAATTGCATCAACACAACACCTCGCTTTCTCTTCTTCTTCATCTTTTTGTTCCATTTCAAGGGTTTCTATCAATCCTCCACGAAGAAGAAGAAGAAGAAGAAGAATAAACAATAATGGTTTCACTTGCAACGCACTTTTCGGATTAGGTGTACCTGAACTCGTTGTTATTGCTGGTGTTGCTGCCATCGTTTTTGGTCCCAAAAAATTGCCTGAAGTTGGTCGCAGTATCGGTAAAACTGTCAAAAGCTTTCAACAGGCAGCAAAGGAGTTTGAGTCTGAGCTTAAAAAGGAACCAGATTCCTCAGGAGGGGAGCCATCTGAGAAATCAATTGCTGTTAGCGAAGAGAAGAAGCAAGATACTGAGGTTTCTAGTTCTAAGGACAGTGTATGA

Protein sequence

>Msa1456830

MTMTMNCVSFCSSISISIPTPIASTQHLAFSSSSSFCSISRVSINPPRRRRRRRRINNNGFTCNALFGLGVPELVVIAGVAAIVFGPKKLPEVGRSIGKTVKSFQQAAKEFESELKKEPDSSGGEPSEKSIAVSEEKKQDTEVSSSKDSV*