AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0794300


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0794300 MtrunA17_Chr5g0394361 97.143 210 5 1 1 210 1 209 9.60e-150 414
Msa0794300 MtrunA17_Chr1g0205591 89.888 89 9 0 122 210 1 89 3.30e-55 170
Msa0794300 MtrunA17_Chr1g0205601 49.533 107 29 3 1 100 1 89 1.10e-19 80.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0794300 AT1G03130.1 73.684 209 49 3 3 210 1 204 2.56e-105 302
Msa0794300 AT4G02770.1 72.770 213 48 4 3 210 1 208 7.72e-102 293

Find 62 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAATTGAAGTTAAGTTTAC+TGG 0.207430 5_3:-6168582 Msa0794300:CDS
AAGGGGTTGGTCAGAATTTC+AGG 0.236961 5_3:-6168626 Msa0794300:CDS
AAAGAACAGTGTTTGGCTTT+AGG 0.250321 5_3:-6168771 Msa0794300:CDS
GATGGTTGTTTCCATGGTTT+AGG 0.251347 5_3:+6169122 None:intergenic
CCAGTAAACTTAACTTCAAT+TGG 0.254455 5_3:+6168582 None:intergenic
TGGCTTTAGGAAATAGATTA+AGG 0.256198 5_3:-6168758 Msa0794300:CDS
AACACACCTTCACCAATCTT+TGG 0.314938 5_3:-6168942 Msa0794300:CDS
GTTAGGACCTTCTCTCATTA+TGG 0.318870 5_3:+6168812 None:intergenic
CGACCAGGGTTAACCTTCTC+AGG 0.322720 5_3:+6168651 None:intergenic
AAATATTGAACCTCACCATT+AGG 0.330180 5_3:+6168696 None:intergenic
ATGGTTGTTTCCATGGTTTA+GGG 0.335226 5_3:+6169123 None:intergenic
GGTCAGAATTTCAGGTCTAT+TGG 0.346075 5_3:-6168618 Msa0794300:CDS
CTTGCTAACTTAAGAAGGTT+AGG 0.358826 5_3:+6168795 None:intergenic
TGTTCTTGTTGTGAACTTGA+TGG 0.369555 5_3:+6169073 None:intergenic
AAGATTGGTGAAGGTGTGTT+TGG 0.388416 5_3:+6168945 None:intergenic
AATATTGAACCTCACCATTA+GGG 0.389009 5_3:+6168697 None:intergenic
AGCAAGGAAAGAACAGTGTT+TGG 0.399243 5_3:-6168778 Msa0794300:CDS
GAGATGAAGGATAAAGTTGA+TGG 0.402382 5_3:+6169104 None:intergenic
CTTTCCTTGCTAACTTAAGA+AGG 0.421239 5_3:+6168790 None:intergenic
GGTGTGTTTGGGTCTAGTTC+AGG 0.421350 5_3:+6168957 None:intergenic
CAGTAAACTTAACTTCAATT+GGG 0.432988 5_3:+6168583 None:intergenic
AAAGTTGATGGTTGTTTCCA+TGG 0.433796 5_3:+6169116 None:intergenic
GTTCTTGTTGTGAACTTGAT+GGG 0.443234 5_3:+6169074 None:intergenic
ATCTCAAAGATTTGTTCCTT+AGG 0.450732 5_3:+6168852 None:intergenic
GATGGGTTTGAGAGAGATGA+AGG 0.471436 5_3:+6169091 None:intergenic
TCAGGGTACACACCATCCTT+AGG 0.473133 5_3:+6168669 None:intergenic
CAAATCTTTGAGATGCCAAC+TGG 0.474824 5_3:-6168843 Msa0794300:CDS
GTGAAACCAACTGGTGCAGC+AGG 0.478227 5_3:+6168984 None:intergenic
AGATTGGTGAAGGTGTGTTT+GGG 0.480790 5_3:+6168946 None:intergenic
GTCAACCCTTACACATCAAA+AGG 0.481319 5_3:+6168552 None:intergenic
CCAATCTTTGGAGGAAGCAC+TGG 0.483310 5_3:-6168930 Msa0794300:CDS
CACTGGTGGTTTGTTACGTA+AGG 0.494140 5_3:-6168913 Msa0794300:CDS
CCAGTGCTTCCTCCAAAGAT+TGG 0.498438 5_3:+6168930 None:intergenic
TCAGGTGGAGTGAAACCAAC+TGG 0.512231 5_3:+6168975 None:intergenic
TGACCAACCCCTTCACGACC+AGG 0.514328 5_3:+6168636 None:intergenic
GGTTCAATATTTGCATCCTA+AGG 0.527977 5_3:-6168685 Msa0794300:CDS
CTAACCTTCTTAAGTTAGCA+AGG 0.531725 5_3:-6168794 Msa0794300:CDS
GAGAGGTGGAGTGAAGAGAG+AGG 0.532656 5_3:+6169151 None:intergenic
ACACCTTCACCAATCTTTGG+AGG 0.538603 5_3:-6168939 Msa0794300:CDS
GAAGCTCCTGCTGCACCAGT+TGG 0.541120 5_3:-6168990 Msa0794300:CDS
AAGGTTAACCCTGGTCGTGA+AGG 0.545203 5_3:-6168645 Msa0794300:CDS
ATCTTTGGAGGAAGCACTGG+TGG 0.547257 5_3:-6168927 Msa0794300:CDS
GTGTTTGGGTCTAGTTCAGG+TGG 0.547713 5_3:+6168960 None:intergenic
AGGTTAACCCTGGTCGTGAA+GGG 0.550600 5_3:-6168644 Msa0794300:CDS
CAATATTTGCATCCTAAGGA+TGG 0.551649 5_3:-6168681 Msa0794300:CDS
GGTTTAGGGCTTGAGAGAGG+TGG 0.569137 5_3:+6169137 None:intergenic
CATGGTTTAGGGCTTGAGAG+AGG 0.581991 5_3:+6169134 None:intergenic
AACCCTGGTCGTGAAGGGGT+TGG 0.582674 5_3:-6168639 Msa0794300:CDS
CTCTCTCAAGCCCTAAACCA+TGG 0.587901 5_3:-6169133 Msa0794300:CDS
GATCACATGGGAGTCACCTA+AGG 0.589857 5_3:-6168868 Msa0794300:CDS
GGATGGTGTGTACCCTGAGA+AGG 0.597067 5_3:-6168664 Msa0794300:CDS
AAGAATTCTATGTGATCACA+TGG 0.598132 5_3:-6168881 Msa0794300:CDS
CTTCCTCCAAAGATTGGTGA+AGG 0.600903 5_3:+6168936 None:intergenic
ATTATGGCTGCACCACCAGT+TGG 0.609110 5_3:+6168828 None:intergenic
GACCAACCCCTTCACGACCA+GGG 0.637725 5_3:+6168637 None:intergenic
GGTGCAGCCATAATGAGAGA+AGG 0.648728 5_3:-6168819 Msa0794300:CDS
GGTTAACCCTGGTCGTGAAG+GGG 0.649178 5_3:-6168643 Msa0794300:CDS
TACCCTGAGAAGGTTAACCC+TGG 0.651425 5_3:-6168654 Msa0794300:CDS
ATTCATCAACAACATGGCAA+TGG 0.658103 5_3:-6169183 None:intergenic
GACCAGGGTTAACCTTCTCA+GGG 0.658939 5_3:+6168652 None:intergenic
ATCTTTGAGATGCCAACTGG+TGG 0.674480 5_3:-6168840 Msa0794300:CDS
AGAATTCTATGTGATCACAT+GGG 0.727784 5_3:-6168880 Msa0794300:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATTAAGTATCAGTTTTAC+AGG - chr5_3:6169005-6169024 Msa0794300:CDS 25.0%
!! GATTAAGTATCAGTTTTACA+GGG - chr5_3:6169006-6169025 Msa0794300:CDS 25.0%
! CAGTAAACTTAACTTCAATT+GGG + chr5_3:6169150-6169169 None:intergenic 25.0%
AAGAATTCTATGTGATCACA+TGG - chr5_3:6168849-6168868 Msa0794300:CDS 30.0%
AGAATTCTATGTGATCACAT+GGG - chr5_3:6168850-6168869 Msa0794300:CDS 30.0%
! ATCTCAAAGATTTGTTCCTT+AGG + chr5_3:6168881-6168900 None:intergenic 30.0%
!! TGGCTTTAGGAAATAGATTA+AGG - chr5_3:6168972-6168991 Msa0794300:CDS 30.0%
AATATTGAACCTCACCATTA+GGG + chr5_3:6169036-6169055 None:intergenic 30.0%
AAATATTGAACCTCACCATT+AGG + chr5_3:6169037-6169056 None:intergenic 30.0%
CCAGTAAACTTAACTTCAAT+TGG + chr5_3:6169151-6169170 None:intergenic 30.0%
CCAATTGAAGTTAAGTTTAC+TGG - chr5_3:6169148-6169167 Msa0794300:CDS 30.0%
! ATGGTTGTTTCCATGGTTTA+GGG + chr5_3:6168610-6168629 None:intergenic 35.0%
!! AAAGTTGATGGTTGTTTCCA+TGG + chr5_3:6168617-6168636 None:intergenic 35.0%
GAGATGAAGGATAAAGTTGA+TGG + chr5_3:6168629-6168648 None:intergenic 35.0%
! GTTCTTGTTGTGAACTTGAT+GGG + chr5_3:6168659-6168678 None:intergenic 35.0%
! TGTTCTTGTTGTGAACTTGA+TGG + chr5_3:6168660-6168679 None:intergenic 35.0%
CTTGCTAACTTAAGAAGGTT+AGG + chr5_3:6168938-6168957 None:intergenic 35.0%
CTAACCTTCTTAAGTTAGCA+AGG - chr5_3:6168936-6168955 Msa0794300:CDS 35.0%
CTTTCCTTGCTAACTTAAGA+AGG + chr5_3:6168943-6168962 None:intergenic 35.0%
!! AAAGAACAGTGTTTGGCTTT+AGG - chr5_3:6168959-6168978 Msa0794300:CDS 35.0%
! TTTTACAGGGTTTTCCCTAA+TGG - chr5_3:6169019-6169038 Msa0794300:CDS 35.0%
GGTTCAATATTTGCATCCTA+AGG - chr5_3:6169045-6169064 Msa0794300:CDS 35.0%
CAATATTTGCATCCTAAGGA+TGG - chr5_3:6169049-6169068 Msa0794300:CDS 35.0%
! GATGGTTGTTTCCATGGTTT+AGG + chr5_3:6168611-6168630 None:intergenic 40.0%
! GCTTCTTCTTTTGTTGCAAC+TGG + chr5_3:6168725-6168744 None:intergenic 40.0%
! AGATTGGTGAAGGTGTGTTT+GGG + chr5_3:6168787-6168806 None:intergenic 40.0%
! AAGATTGGTGAAGGTGTGTT+TGG + chr5_3:6168788-6168807 None:intergenic 40.0%
AACACACCTTCACCAATCTT+TGG - chr5_3:6168788-6168807 Msa0794300:CDS 40.0%
!! CAAATCTTTGAGATGCCAAC+TGG - chr5_3:6168887-6168906 Msa0794300:CDS 40.0%
GTTAGGACCTTCTCTCATTA+TGG + chr5_3:6168921-6168940 None:intergenic 40.0%
AGCAAGGAAAGAACAGTGTT+TGG - chr5_3:6168952-6168971 Msa0794300:CDS 40.0%
! GGTCAGAATTTCAGGTCTAT+TGG - chr5_3:6169112-6169131 Msa0794300:CDS 40.0%
! GATGGGTTTGAGAGAGATGA+AGG + chr5_3:6168642-6168661 None:intergenic 45.0%
ACACCTTCACCAATCTTTGG+AGG - chr5_3:6168791-6168810 Msa0794300:CDS 45.0%
CTTCCTCCAAAGATTGGTGA+AGG + chr5_3:6168797-6168816 None:intergenic 45.0%
!! CACTGGTGGTTTGTTACGTA+AGG - chr5_3:6168817-6168836 Msa0794300:CDS 45.0%
!! ATCTTTGAGATGCCAACTGG+TGG - chr5_3:6168890-6168909 Msa0794300:CDS 45.0%
!! AAGGGGTTGGTCAGAATTTC+AGG - chr5_3:6169104-6169123 Msa0794300:CDS 45.0%
! CATGGTTTAGGGCTTGAGAG+AGG + chr5_3:6168599-6168618 None:intergenic 50.0%
CTCTCTCAAGCCCTAAACCA+TGG - chr5_3:6168597-6168616 Msa0794300:CDS 50.0%
TCAGGTGGAGTGAAACCAAC+TGG + chr5_3:6168758-6168777 None:intergenic 50.0%
! GTGTTTGGGTCTAGTTCAGG+TGG + chr5_3:6168773-6168792 None:intergenic 50.0%
! GGTGTGTTTGGGTCTAGTTC+AGG + chr5_3:6168776-6168795 None:intergenic 50.0%
CCAGTGCTTCCTCCAAAGAT+TGG + chr5_3:6168803-6168822 None:intergenic 50.0%
! CCAATCTTTGGAGGAAGCAC+TGG - chr5_3:6168800-6168819 Msa0794300:CDS 50.0%
!! ATCTTTGGAGGAAGCACTGG+TGG - chr5_3:6168803-6168822 Msa0794300:CDS 50.0%
GATCACATGGGAGTCACCTA+AGG - chr5_3:6168862-6168881 Msa0794300:CDS 50.0%
ATTATGGCTGCACCACCAGT+TGG + chr5_3:6168905-6168924 None:intergenic 50.0%
GGTGCAGCCATAATGAGAGA+AGG - chr5_3:6168911-6168930 Msa0794300:CDS 50.0%
! CAGGGTTTTCCCTAATGGTG+AGG - chr5_3:6169024-6169043 Msa0794300:CDS 50.0%
TCAGGGTACACACCATCCTT+AGG + chr5_3:6169064-6169083 None:intergenic 50.0%
TACCCTGAGAAGGTTAACCC+TGG - chr5_3:6169076-6169095 Msa0794300:CDS 50.0%
GACCAGGGTTAACCTTCTCA+GGG + chr5_3:6169081-6169100 None:intergenic 50.0%
AAGGTTAACCCTGGTCGTGA+AGG - chr5_3:6169085-6169104 Msa0794300:CDS 50.0%
AGGTTAACCCTGGTCGTGAA+GGG - chr5_3:6169086-6169105 Msa0794300:CDS 50.0%
GAGAGGTGGAGTGAAGAGAG+AGG + chr5_3:6168582-6168601 None:intergenic 55.0%
! GGTTTAGGGCTTGAGAGAGG+TGG + chr5_3:6168596-6168615 None:intergenic 55.0%
GTGAAACCAACTGGTGCAGC+AGG + chr5_3:6168749-6168768 None:intergenic 55.0%
GGATGGTGTGTACCCTGAGA+AGG - chr5_3:6169066-6169085 Msa0794300:CDS 55.0%
CGACCAGGGTTAACCTTCTC+AGG + chr5_3:6169082-6169101 None:intergenic 55.0%
GGTTAACCCTGGTCGTGAAG+GGG - chr5_3:6169087-6169106 Msa0794300:CDS 55.0%
GAAGCTCCTGCTGCACCAGT+TGG - chr5_3:6168740-6168759 Msa0794300:CDS 60.0%
AACCCTGGTCGTGAAGGGGT+TGG - chr5_3:6169091-6169110 Msa0794300:CDS 60.0%
GACCAACCCCTTCACGACCA+GGG + chr5_3:6169096-6169115 None:intergenic 60.0%
TGACCAACCCCTTCACGACC+AGG + chr5_3:6169097-6169116 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 6168560 6169192 6168560 ID=Msa0794300;Name=Msa0794300
chr5_3 mRNA 6168560 6169192 6168560 ID=Msa0794300-mRNA-1;Parent=Msa0794300;Name=Msa0794300-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|210
chr5_3 exon 6168560 6169192 6168560 ID=Msa0794300-mRNA-1:exon:2472;Parent=Msa0794300-mRNA-1
chr5_3 CDS 6168560 6169192 6168560 ID=Msa0794300-mRNA-1:cds;Parent=Msa0794300-mRNA-1
Gene Sequence

>Msa0794300

ATGGCAATGGCAACTCAAGCCTCTCTCTTCACTCCACCTCTCTCAAGCCCTAAACCATGGAAACAACCATCAACTTTATCCTTCATCTCTCTCAAACCCATCAAGTTCACAACAAGAACAACAAAAATCTCAGCTGCAGATGACAAAACAGAAGCAGCAGCACCAGTTGCAACAAAAGAAGAAGCTCCTGCTGCACCAGTTGGTTTCACTCCACCTGAACTAGACCCAAACACACCTTCACCAATCTTTGGAGGAAGCACTGGTGGTTTGTTACGTAAGGCACAAGTTGAAGAATTCTATGTGATCACATGGGAGTCACCTAAGGAACAAATCTTTGAGATGCCAACTGGTGGTGCAGCCATAATGAGAGAAGGTCCTAACCTTCTTAAGTTAGCAAGGAAAGAACAGTGTTTGGCTTTAGGAAATAGATTAAGGTCTAAGTACAAGATTAAGTATCAGTTTTACAGGGTTTTCCCTAATGGTGAGGTTCAATATTTGCATCCTAAGGATGGTGTGTACCCTGAGAAGGTTAACCCTGGTCGTGAAGGGGTTGGTCAGAATTTCAGGTCTATTGGAAAGAATGTTAGCCCAATTGAAGTTAAGTTTACTGGTAAGCAACCTTTTGATGTGTAA

Protein sequence

>Msa0794300

MAMATQASLFTPPLSSPKPWKQPSTLSFISLKPIKFTTRTTKISAADDKTEAAAPVATKEEAPAAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGNRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNFRSIGKNVSPIEVKFTGKQPFDV*