AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1460750


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1460750 MtrunA17_Chr8g0390061 89.855 207 21 0 24 230 1 207 6.68e-141 392
Msa1460750 MtrunA17_Chr8g0390051 60.924 238 62 3 24 230 1 238 5.33e-98 285
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 136 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTTGTCTTCCTTGTTCT+TGG 0.156350 tig0041068:+4916 None:intergenic
TAATGATATTGAAATGAATT+TGG 0.220117 tig0041068:-3836 Msa1460750:CDS
AAGACAGAAACAAAGAAATT+TGG 0.303541 tig0041068:-4222 Msa1460750:CDS
ATTGAAGATGATGCTACTTT+TGG 0.318948 tig0041068:-4277 Msa1460750:CDS
CAAAGCTTTCATGATGAAAA+TGG 0.325691 tig0041068:-3955 Msa1460750:CDS
CAGGTTTGCAATCAAGAAAT+AGG 0.331402 tig0041068:-3744 Msa1460750:CDS
ACTGTTCATGTTGATACTTC+AGG 0.350166 tig0041068:-3763 Msa1460750:CDS
ATTCAAATCAAGCTTGTTGC+TGG 0.398775 tig0041068:-4198 Msa1460750:CDS
ATCTATTACACCATTATTTG+CGG 0.399079 tig0041068:+3984 None:intergenic
GGATGTGGACATAAATTGTT+TGG 0.414508 tig0041068:-4177 Msa1460750:CDS
GAATCTACCTTTCCTGAGTC+AGG 0.424703 tig0041068:+4114 None:intergenic
AAAAGGGTCTAACGTAAAAC+AGG 0.453639 tig0041068:-4301 Msa1460750:CDS
ATCAAGCTTGTTGCTGGATG+TGG 0.461106 tig0041068:-4192 Msa1460750:CDS
GTGGAGAGTGCCGCAAATAA+TGG 0.466076 tig0041068:-3994 Msa1460750:CDS
AGAATGGAGTATCAATCTCT+TGG 0.471194 tig0041068:-4339 Msa1460750:CDS
CATAAATTGTTTGGACGGAA+AGG 0.490271 tig0041068:-4168 Msa1460750:CDS
GTTGAATTAATGCAGAAGAA+TGG 0.500286 tig0041068:-4355 Msa1460750:intron
GATATTGAAATGAATTTGGA+AGG 0.502773 tig0041068:-3832 Msa1460750:CDS
TCAGGAAAAGCTCTTTCATC+GGG 0.511579 tig0041068:+4132 None:intergenic
ATAAATTGTTTGGACGGAAA+GGG 0.528425 tig0041068:-4167 Msa1460750:CDS
GTCAGGAAAAGCTCTTTCAT+CGG 0.531583 tig0041068:+4131 None:intergenic
AGTATTTATGAAGTCACGTA+TGG 0.536293 tig0041068:-3865 Msa1460750:CDS
TCAGGAAAGGTAGATTCTGT+TGG 0.537763 tig0041068:-4108 Msa1460750:CDS
GTAGACGAAGAAATTAATAC+AGG 0.538396 tig0041068:-3790 Msa1460750:CDS
GTGGACATAAATTGTTTGGA+CGG 0.566125 tig0041068:-4173 Msa1460750:CDS
TGGAGTATCAATCTCTTGGA+AGG 0.588423 tig0041068:-4335 Msa1460750:CDS
ACAACTTGGAGTTGAAGAGA+AGG 0.600247 tig0041068:-4040 Msa1460750:CDS
CAACTTGGAGTTGAAGAGAA+GGG 0.601023 tig0041068:-4039 Msa1460750:CDS
AATACTGAACACCAAGAACA+AGG 0.614953 tig0041068:-4927 None:intergenic
CTTGATTTGATATAACAACC+AGG 0.620765 tig0041068:+4245 None:intergenic
GTTTGCAATCAAGAAATAGG+TGG 0.639196 tig0041068:-3741 Msa1460750:CDS
AAATAATGGTGTAATAGATG+AGG 0.639630 tig0041068:-3980 Msa1460750:CDS
GAAAATGGTGTTCCGCCTGA+CGG 0.653575 tig0041068:-3940 Msa1460750:CDS
AATGGTGTTCCGCCTGACGG+TGG 0.691121 tig0041068:-3937 Msa1460750:CDS
CCGTTGAGAAAACAAAACAA+AGG 0.712405 tig0041068:-4880 Msa1460750:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATGATATTGAAATGAATT+TGG - tig0041068:4822-4841 Msa1460750:intron 15.0%
!! TAATGATATTGAAATGAATT+TGG - tig0041068:4822-4841 Msa1460750:intron 15.0%
!! TTGTTACATAGAAAATTCAA+CGG + tig0041068:3846-3865 None:intergenic 20.0%
!! AAACTAAGAATCAAATCAAT+AGG + tig0041068:4049-4068 None:intergenic 20.0%
!!! CAACTTTTAGAATAGTAAAT+TGG - tig0041068:4758-4777 Msa1460750:intron 20.0%
!! TTGTTACATAGAAAATTCAA+CGG + tig0041068:3846-3865 None:intergenic 20.0%
!! AAACTAAGAATCAAATCAAT+AGG + tig0041068:4049-4068 None:intergenic 20.0%
!!! CAACTTTTAGAATAGTAAAT+TGG - tig0041068:4758-4777 Msa1460750:intron 20.0%
! GAAAATTCAACGGTAAAATA+AGG + tig0041068:3836-3855 None:intergenic 25.0%
! AAATCAATAGGCAAATATGT+TGG + tig0041068:4037-4056 None:intergenic 25.0%
!! AAAGAAAGACTTTTCTTTCA+TGG + tig0041068:4097-4116 None:intergenic 25.0%
! CATTAGTGTATATAGTTAGT+TGG - tig0041068:4166-4185 Msa1460750:CDS 25.0%
!!! AGTAACTTAACTTGTTGATT+TGG + tig0041068:4236-4255 None:intergenic 25.0%
! AAGACAGAAACAAAGAAATT+TGG - tig0041068:4436-4455 Msa1460750:intron 25.0%
!! AAAGAAAAAGAAGTACAACT+TGG - tig0041068:4604-4623 Msa1460750:intron 25.0%
! ATCTATTACACCATTATTTG+CGG + tig0041068:4677-4696 None:intergenic 25.0%
! AAATAATGGTGTAATAGATG+AGG - tig0041068:4678-4697 Msa1460750:intron 25.0%
! GATATTGAAATGAATTTGGA+AGG - tig0041068:4826-4845 Msa1460750:intron 25.0%
! GAAAATTCAACGGTAAAATA+AGG + tig0041068:3836-3855 None:intergenic 25.0%
! AAATCAATAGGCAAATATGT+TGG + tig0041068:4037-4056 None:intergenic 25.0%
!! AAAGAAAGACTTTTCTTTCA+TGG + tig0041068:4097-4116 None:intergenic 25.0%
! CATTAGTGTATATAGTTAGT+TGG - tig0041068:4166-4185 Msa1460750:CDS 25.0%
!!! AGTAACTTAACTTGTTGATT+TGG + tig0041068:4236-4255 None:intergenic 25.0%
! AAGACAGAAACAAAGAAATT+TGG - tig0041068:4436-4455 Msa1460750:intron 25.0%
!! AAAGAAAAAGAAGTACAACT+TGG - tig0041068:4604-4623 Msa1460750:intron 25.0%
! ATCTATTACACCATTATTTG+CGG + tig0041068:4677-4696 None:intergenic 25.0%
! AAATAATGGTGTAATAGATG+AGG - tig0041068:4678-4697 Msa1460750:intron 25.0%
! GATATTGAAATGAATTTGGA+AGG - tig0041068:4826-4845 Msa1460750:intron 25.0%
!!! CCTTTGTTTTGTTTTCTCAA+CGG + tig0041068:3781-3800 None:intergenic 30.0%
GATAGATAGTTAAGAGTTGT+TGG - tig0041068:3987-4006 Msa1460750:CDS 30.0%
TAGATCAGATAAACATTCAG+AGG + tig0041068:4275-4294 None:intergenic 30.0%
GTTGAATTAATGCAGAAGAA+TGG - tig0041068:4303-4322 Msa1460750:CDS 30.0%
!!! ATTGAAGATGATGCTACTTT+TGG - tig0041068:4381-4400 Msa1460750:intron 30.0%
! CTTGATTTGATATAACAACC+AGG + tig0041068:4416-4435 None:intergenic 30.0%
ATAAATTGTTTGGACGGAAA+GGG - tig0041068:4491-4510 Msa1460750:intron 30.0%
AAACAAGATGCAGAAAAATG+AGG - tig0041068:4642-4661 Msa1460750:intron 30.0%
! CATTTTCATCATGAAAGCTT+TGG + tig0041068:4705-4724 None:intergenic 30.0%
CAAAGCTTTCATGATGAAAA+TGG - tig0041068:4703-4722 Msa1460750:intron 30.0%
AGTATTTATGAAGTCACGTA+TGG - tig0041068:4793-4812 Msa1460750:intron 30.0%
GTAGACGAAGAAATTAATAC+AGG - tig0041068:4868-4887 Msa1460750:intron 30.0%
!!! CCTTTGTTTTGTTTTCTCAA+CGG + tig0041068:3781-3800 None:intergenic 30.0%
GATAGATAGTTAAGAGTTGT+TGG - tig0041068:3987-4006 Msa1460750:CDS 30.0%
TAGATCAGATAAACATTCAG+AGG + tig0041068:4275-4294 None:intergenic 30.0%
GTTGAATTAATGCAGAAGAA+TGG - tig0041068:4303-4322 Msa1460750:CDS 30.0%
!!! ATTGAAGATGATGCTACTTT+TGG - tig0041068:4381-4400 Msa1460750:intron 30.0%
! CTTGATTTGATATAACAACC+AGG + tig0041068:4416-4435 None:intergenic 30.0%
ATAAATTGTTTGGACGGAAA+GGG - tig0041068:4491-4510 Msa1460750:intron 30.0%
AAACAAGATGCAGAAAAATG+AGG - tig0041068:4642-4661 Msa1460750:intron 30.0%
! CATTTTCATCATGAAAGCTT+TGG + tig0041068:4705-4724 None:intergenic 30.0%
CAAAGCTTTCATGATGAAAA+TGG - tig0041068:4703-4722 Msa1460750:intron 30.0%
AGTATTTATGAAGTCACGTA+TGG - tig0041068:4793-4812 Msa1460750:intron 30.0%
GTAGACGAAGAAATTAATAC+AGG - tig0041068:4868-4887 Msa1460750:intron 30.0%
TTTCTTGTCTTCCTTGTTCT+TGG + tig0041068:3745-3764 None:intergenic 35.0%
CCGTTGAGAAAACAAAACAA+AGG - tig0041068:3778-3797 Msa1460750:CDS 35.0%
CATGATGATTGATGGGAAAT+TGG + tig0041068:3923-3942 None:intergenic 35.0%
CAATTTCCCATCAATCATCA+TGG - tig0041068:3921-3940 Msa1460750:CDS 35.0%
TTGTAGCCATGATGATTGAT+GGG + tig0041068:3930-3949 None:intergenic 35.0%
ATTGTAGCCATGATGATTGA+TGG + tig0041068:3931-3950 None:intergenic 35.0%
GAGTTGTTGGAAATCATACT+TGG - tig0041068:4000-4019 Msa1460750:CDS 35.0%
! AGTCTTTCTTTTCCTACGTT+TGG - tig0041068:4106-4125 Msa1460750:CDS 35.0%
! GTCTTTCTTTTCCTACGTTT+GGG - tig0041068:4107-4126 Msa1460750:CDS 35.0%
! TTTTGCATTTGCAACAAGAG+AGG + tig0041068:4202-4221 None:intergenic 35.0%
! AGAATGGAGTATCAATCTCT+TGG - tig0041068:4319-4338 Msa1460750:CDS 35.0%
!! GAAGGTACCAAAAACCAAAA+GGG - tig0041068:4341-4360 Msa1460750:CDS 35.0%
! TGTTTTACGTTAGACCCTTT+TGG + tig0041068:4358-4377 None:intergenic 35.0%
AAAAGGGTCTAACGTAAAAC+AGG - tig0041068:4357-4376 Msa1460750:intron 35.0%
!! ATTCAAATCAAGCTTGTTGC+TGG - tig0041068:4460-4479 Msa1460750:intron 35.0%
GGATGTGGACATAAATTGTT+TGG - tig0041068:4481-4500 Msa1460750:intron 35.0%
GTGGACATAAATTGTTTGGA+CGG - tig0041068:4485-4504 Msa1460750:intron 35.0%
CATAAATTGTTTGGACGGAA+AGG - tig0041068:4490-4509 Msa1460750:intron 35.0%
ACTGTTCATGTTGATACTTC+AGG - tig0041068:4895-4914 Msa1460750:CDS 35.0%
CAGGTTTGCAATCAAGAAAT+AGG - tig0041068:4914-4933 Msa1460750:CDS 35.0%
GTTTGCAATCAAGAAATAGG+TGG - tig0041068:4917-4936 Msa1460750:CDS 35.0%
TTTCTTGTCTTCCTTGTTCT+TGG + tig0041068:3745-3764 None:intergenic 35.0%
CCGTTGAGAAAACAAAACAA+AGG - tig0041068:3778-3797 Msa1460750:CDS 35.0%
CATGATGATTGATGGGAAAT+TGG + tig0041068:3923-3942 None:intergenic 35.0%
CAATTTCCCATCAATCATCA+TGG - tig0041068:3921-3940 Msa1460750:CDS 35.0%
TTGTAGCCATGATGATTGAT+GGG + tig0041068:3930-3949 None:intergenic 35.0%
ATTGTAGCCATGATGATTGA+TGG + tig0041068:3931-3950 None:intergenic 35.0%
GAGTTGTTGGAAATCATACT+TGG - tig0041068:4000-4019 Msa1460750:CDS 35.0%
! AGTCTTTCTTTTCCTACGTT+TGG - tig0041068:4106-4125 Msa1460750:CDS 35.0%
! GTCTTTCTTTTCCTACGTTT+GGG - tig0041068:4107-4126 Msa1460750:CDS 35.0%
! TTTTGCATTTGCAACAAGAG+AGG + tig0041068:4202-4221 None:intergenic 35.0%
! AGAATGGAGTATCAATCTCT+TGG - tig0041068:4319-4338 Msa1460750:CDS 35.0%
!! GAAGGTACCAAAAACCAAAA+GGG - tig0041068:4341-4360 Msa1460750:CDS 35.0%
! TGTTTTACGTTAGACCCTTT+TGG + tig0041068:4358-4377 None:intergenic 35.0%
AAAAGGGTCTAACGTAAAAC+AGG - tig0041068:4357-4376 Msa1460750:intron 35.0%
!! ATTCAAATCAAGCTTGTTGC+TGG - tig0041068:4460-4479 Msa1460750:intron 35.0%
GGATGTGGACATAAATTGTT+TGG - tig0041068:4481-4500 Msa1460750:intron 35.0%
GTGGACATAAATTGTTTGGA+CGG - tig0041068:4485-4504 Msa1460750:intron 35.0%
CATAAATTGTTTGGACGGAA+AGG - tig0041068:4490-4509 Msa1460750:intron 35.0%
ACTGTTCATGTTGATACTTC+AGG - tig0041068:4895-4914 Msa1460750:CDS 35.0%
CAGGTTTGCAATCAAGAAAT+AGG - tig0041068:4914-4933 Msa1460750:CDS 35.0%
GTTTGCAATCAAGAAATAGG+TGG - tig0041068:4917-4936 Msa1460750:CDS 35.0%
! TGTTTTCTCAACGGAGAAAG+TGG + tig0041068:3772-3791 None:intergenic 40.0%
AAGTCAAACAACCCAAACGT+AGG + tig0041068:4121-4140 None:intergenic 40.0%
! TGGAGTATCAATCTCTTGGA+AGG - tig0041068:4323-4342 Msa1460750:CDS 40.0%
!! GGAAGGTACCAAAAACCAAA+AGG - tig0041068:4340-4359 Msa1460750:CDS 40.0%
!!! CGTTAGACCCTTTTGGTTTT+TGG + tig0041068:4351-4370 None:intergenic 40.0%
TCAGGAAAAGCTCTTTCATC+GGG + tig0041068:4529-4548 None:intergenic 40.0%
GTCAGGAAAAGCTCTTTCAT+CGG + tig0041068:4530-4549 None:intergenic 40.0%
TCAGGAAAGGTAGATTCTGT+TGG - tig0041068:4550-4569 Msa1460750:intron 40.0%
ACAACTTGGAGTTGAAGAGA+AGG - tig0041068:4618-4637 Msa1460750:intron 40.0%
CAACTTGGAGTTGAAGAGAA+GGG - tig0041068:4619-4638 Msa1460750:intron 40.0%
CAAGATGCAGAAAAATGAGG+TGG - tig0041068:4645-4664 Msa1460750:intron 40.0%
! TGTTTTCTCAACGGAGAAAG+TGG + tig0041068:3772-3791 None:intergenic 40.0%
AAGTCAAACAACCCAAACGT+AGG + tig0041068:4121-4140 None:intergenic 40.0%
! TGGAGTATCAATCTCTTGGA+AGG - tig0041068:4323-4342 Msa1460750:CDS 40.0%
!! GGAAGGTACCAAAAACCAAA+AGG - tig0041068:4340-4359 Msa1460750:CDS 40.0%
!!! CGTTAGACCCTTTTGGTTTT+TGG + tig0041068:4351-4370 None:intergenic 40.0%
TCAGGAAAAGCTCTTTCATC+GGG + tig0041068:4529-4548 None:intergenic 40.0%
GTCAGGAAAAGCTCTTTCAT+CGG + tig0041068:4530-4549 None:intergenic 40.0%
TCAGGAAAGGTAGATTCTGT+TGG - tig0041068:4550-4569 Msa1460750:intron 40.0%
ACAACTTGGAGTTGAAGAGA+AGG - tig0041068:4618-4637 Msa1460750:intron 40.0%
CAACTTGGAGTTGAAGAGAA+GGG - tig0041068:4619-4638 Msa1460750:intron 40.0%
CAAGATGCAGAAAAATGAGG+TGG - tig0041068:4645-4664 Msa1460750:intron 40.0%
!! TACTTTTGGCTGTTTGTGCC+TGG - tig0041068:4395-4414 Msa1460750:intron 45.0%
!! ATCAAGCTTGTTGCTGGATG+TGG - tig0041068:4466-4485 Msa1460750:intron 45.0%
! GAAAGAGCTTTTCCTGACTC+AGG - tig0041068:4532-4551 Msa1460750:intron 45.0%
! AGCTTTTCCTGACTCAGGAA+AGG - tig0041068:4537-4556 Msa1460750:intron 45.0%
GAATCTACCTTTCCTGAGTC+AGG + tig0041068:4547-4566 None:intergenic 45.0%
! ATGTTTTCTTCACCACCGTC+AGG + tig0041068:4736-4755 None:intergenic 45.0%
!! TACTTTTGGCTGTTTGTGCC+TGG - tig0041068:4395-4414 Msa1460750:intron 45.0%
!! ATCAAGCTTGTTGCTGGATG+TGG - tig0041068:4466-4485 Msa1460750:intron 45.0%
! GAAAGAGCTTTTCCTGACTC+AGG - tig0041068:4532-4551 Msa1460750:intron 45.0%
! AGCTTTTCCTGACTCAGGAA+AGG - tig0041068:4537-4556 Msa1460750:intron 45.0%
GAATCTACCTTTCCTGAGTC+AGG + tig0041068:4547-4566 None:intergenic 45.0%
! ATGTTTTCTTCACCACCGTC+AGG + tig0041068:4736-4755 None:intergenic 45.0%
!! GTGGAGAGTGCCGCAAATAA+TGG - tig0041068:4664-4683 Msa1460750:intron 50.0%
GAAAATGGTGTTCCGCCTGA+CGG - tig0041068:4718-4737 Msa1460750:intron 50.0%
! TTTTCTTCACCACCGTCAGG+CGG + tig0041068:4733-4752 None:intergenic 50.0%
!! GTGGAGAGTGCCGCAAATAA+TGG - tig0041068:4664-4683 Msa1460750:intron 50.0%
GAAAATGGTGTTCCGCCTGA+CGG - tig0041068:4718-4737 Msa1460750:intron 50.0%
! TTTTCTTCACCACCGTCAGG+CGG + tig0041068:4733-4752 None:intergenic 50.0%
AATGGTGTTCCGCCTGACGG+TGG - tig0041068:4721-4740 Msa1460750:intron 60.0%
AATGGTGTTCCGCCTGACGG+TGG - tig0041068:4721-4740 Msa1460750:intron 60.0%
Chromosome Type Strat End Strand Name
tig0041068 gene 3735 4945 3735 ID=Msa1460750;Name=Msa1460750
tig0041068 mRNA 3735 4945 3735 ID=Msa1460750-mRNA-1;Parent=Msa1460750;Name=Msa1460750-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|1|0|1|0|0|2|0|230
tig0041068 exon 4881 4945 4881 ID=Msa1460750-mRNA-1:exon:22885;Parent=Msa1460750-mRNA-1
tig0041068 exon 3735 4362 3735 ID=Msa1460750-mRNA-1:exon:22884;Parent=Msa1460750-mRNA-1
tig0041068 CDS 4881 4945 4881 ID=Msa1460750-mRNA-1:cds;Parent=Msa1460750-mRNA-1
tig0041068 CDS 3735 4362 3735 ID=Msa1460750-mRNA-1:cds;Parent=Msa1460750-mRNA-1
Gene Sequence

>Msa1460750

CTGAACACCAAGAACAAGGAAGACAAGAAAGAAACCACTTTCTCCGTTGAGAAAACAAAACAAAGAAGAATGGAGTATCAATCTCTTGGAAGGTACCAAAAACCAAAAGGGTCTAACGTAAAACAGGTATTGAAGATGATGCTACTTTTGGCTGTTTGTGCCTGGTTGTTATATCAAATCAAGAAGACAGAAACAAAGAAATTTGGTATTCAAATCAAGCTTGTTGCTGGATGTGGACATAAATTGTTTGGACGGAAAGGGATGCTATCACGTCCCGATGAAAGAGCTTTTCCTGACTCAGGAAAGGTAGATTCTGTTGGAGAAGTAACAAATGAGTTTAAAAGTAATGACAAAGAAAAAGAAGTACAACTTGGAGTTGAAGAGAAGGGAAACAAGATGCAGAAAAATGAGGTGGAGAGTGCCGCAAATAATGGTGTAATAGATGAGGTCCAAAGCTTTCATGATGAAAATGGTGTTCCGCCTGACGGTGGTGAAGAAAACATGTCAACTTTTAGAATAGTAAATTGGCTTAAAAAGATCAGTATTTATGAAGTCACGTATGGAGAAGATAATGATATTGAAATGAATTTGGAAGGAACGACGAATGCTACAACAGTAGACGAAGAAATTAATACAGGAACTACTGTTCATGTTGATACTTCAGGTTTGCAATCAAGAAATAGGTGGAGATAA

Protein sequence

>Msa1460750

LNTKNKEDKKETTFSVEKTKQRRMEYQSLGRYQKPKGSNVKQVLKMMLLLAVCAWLLYQIKKTETKKFGIQIKLVAGCGHKLFGRKGMLSRPDERAFPDSGKVDSVGEVTNEFKSNDKEKEVQLGVEEKGNKMQKNEVESAANNGVIDEVQSFHDENGVPPDGGEENMSTFRIVNWLKKISIYEVTYGEDNDIEMNLEGTTNATTVDEEINTGTTVHVDTSGLQSRNRWR*