AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1418060


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1418060 MtrunA17_Chr3g0144631 100.000 81 0 0 1 81 1 81 1.61e-56 169
Msa1418060 MtrunA17_Chr1g0155181 71.014 69 20 0 14 82 5 73 1.80e-34 113
Msa1418060 MtrunA17_Chr3g0141601 69.565 69 21 0 14 82 5 73 7.05e-32 107
Msa1418060 MtrunA17_Chr7g0255841 72.308 65 18 0 19 83 15 79 1.70e-30 103
Msa1418060 MtrunA17_Chr3g0081631 62.963 81 23 2 1 80 1 75 6.13e-29 99.8
Msa1418060 MtrunA17_Chr8g0373131 62.687 67 24 1 16 82 5 70 2.39e-27 95.1
Msa1418060 MtrunA17_Chr8g0373111 62.687 67 24 1 16 82 5 70 2.43e-27 95.1
Msa1418060 MtrunA17_Chr8g0373121 62.687 67 24 1 16 82 5 70 2.43e-27 95.1
Msa1418060 MtrunA17_Chr5g0404101 60.938 64 25 0 16 79 19 82 7.98e-26 92.0
Msa1418060 MtrunA17_Chr6g0449111 60.000 65 26 0 14 78 8 72 1.71e-25 90.5
Msa1418060 MtrunA17_Chr5g0404301 68.852 61 18 1 16 76 4 63 2.05e-25 89.7
Msa1418060 MtrunA17_Chr8g0373101 63.492 63 22 1 14 76 3 64 3.83e-25 89.4
Msa1418060 MtrunA17_Chr3g0141641 52.239 67 32 0 16 82 3 69 8.41e-22 81.6
Msa1418060 MtrunA17_Chr8g0364741 45.122 82 39 1 16 91 10 91 2.68e-21 81.3
Msa1418060 MtrunA17_Chr5g0429521 53.623 69 32 0 16 84 29 97 6.49e-21 84.3
Msa1418060 MtrunA17_Chr8g0365011 52.239 67 32 0 14 80 6 72 2.33e-20 82.4
Msa1418060 MtrunA17_Chr3g0104071 56.522 69 30 0 16 84 43 111 1.56e-19 80.5
Msa1418060 MtrunA17_Chr7g0241761 50.000 70 35 0 14 83 33 102 2.66e-18 77.0
Msa1418060 MtrunA17_Chr5g0436501 50.000 68 34 0 16 83 27 94 4.44e-18 76.3
Msa1418060 MtrunA17_Chr1g0162081 45.455 77 42 0 14 90 10 86 8.36e-18 75.9
Msa1418060 MtrunA17_Chr7g0270711 50.000 80 33 2 16 88 11 90 1.69e-16 68.2
Msa1418060 MtrunA17_Chr1g0194071 59.649 57 22 1 16 71 11 67 7.93e-16 66.6
Msa1418060 MtrunA17_Chr1g0210471 47.619 63 33 0 16 78 24 86 1.14e-15 69.3
Msa1418060 MtrunA17_Chr4g0062741 40.000 70 39 1 12 78 4 73 2.70e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1418060 AT1G75250.1 67.500 80 22 1 1 80 1 76 3.36e-35 117
Msa1418060 AT1G75250.2 67.500 80 22 1 1 80 1 76 5.01e-35 115
Msa1418060 AT4G39250.1 69.697 66 20 0 16 81 14 79 1.46e-33 112
Msa1418060 AT2G21650.1 65.672 67 23 0 16 82 14 80 2.14e-30 103
Msa1418060 AT1G19510.1 71.429 63 18 0 19 81 15 77 1.68e-29 101
Msa1418060 AT2G18328.1 69.841 63 19 0 19 81 14 76 9.69e-29 99.0
Msa1418060 AT4G36570.1 77.273 44 10 0 16 59 12 55 3.13e-21 79.3
Msa1418060 AT5G05790.2 52.941 68 32 0 14 81 29 96 6.05e-18 76.3
Msa1418060 AT5G05790.1 52.941 68 32 0 14 81 29 96 6.05e-18 76.3
Msa1418060 AT2G38090.1 53.846 65 30 0 16 80 29 93 1.46e-17 75.5
Msa1418060 AT5G58900.1 49.231 65 33 0 14 78 32 96 2.53e-17 74.7
Msa1418060 AT3G11280.2 47.826 69 36 0 16 84 33 101 4.83e-17 73.6
Msa1418060 AT3G11280.1 47.826 69 36 0 16 84 33 101 4.83e-17 73.6
Msa1418060 AT5G08520.1 49.254 67 34 0 14 80 10 76 3.80e-16 71.6
Msa1418060 AT5G04760.1 41.791 67 38 1 12 78 2 67 3.23e-13 62.8
Msa1418060 AT1G49010.1 42.647 68 36 1 14 78 6 73 1.58e-12 61.6
Msa1418060 AT5G01200.1 43.284 67 37 1 13 78 27 93 3.84e-12 60.5
Msa1418060 AT5G23650.1 39.189 74 45 0 5 78 2 75 3.52e-11 58.2

Find 23 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCACGTGGATTTGTAATT+TGG 0.099924 tig0024534:-24432 None:intergenic
ACAAGCCTTGTGATTCAATT+TGG 0.187124 tig0024534:+24232 Msa1418060:CDS
GTGGATTTGTAATTTGGAAT+AGG 0.364725 tig0024534:-24426 None:intergenic
TCAAAATTACAAAATCAGAT+AGG 0.377429 tig0024534:-24705 None:intergenic
CTTATATAGATGCTTGCCTC+AGG 0.419615 tig0024534:+24614 Msa1418060:intron
AGCACTTGCAAAATTTGATA+AGG 0.422428 tig0024534:+24284 Msa1418060:CDS
CTGAAGTATCTAAAGTTGAA+TGG 0.424280 tig0024534:+24640 Msa1418060:CDS
CACAAGGCTTGTGTTTGCTA+AGG 0.474591 tig0024534:-24221 None:intergenic
CAAAATTACAAAATCAGATA+GGG 0.481920 tig0024534:-24704 None:intergenic
GATCTCAAACACATTGAGTC+TGG 0.498892 tig0024534:+24396 Msa1418060:CDS
AGACAGATGGAGGAACAAAC+AGG 0.503947 tig0024534:-24681 None:intergenic
GAGACACTATGAGCTACTCT+TGG 0.504426 tig0024534:+24371 Msa1418060:CDS
ACAAGGCTTGTGTTTGCTAA+GGG 0.544579 tig0024534:-24220 None:intergenic
ACACTATGAGCTACTCTTGG+AGG 0.567606 tig0024534:+24374 Msa1418060:CDS
GTGTTTGCTAAGGGAACTTG+AGG 0.586339 tig0024534:-24211 None:intergenic
AATGTAGCAAAAGCAGTTGG+TGG 0.597235 tig0024534:+24327 Msa1418060:CDS
CAAAATGTAGCAAAAGCAGT+TGG 0.599555 tig0024534:+24324 Msa1418060:CDS
GGAGTCCAAATTGAATCACA+AGG 0.603739 tig0024534:-24237 None:intergenic
ATAAGGATACCCCTGACCGT+TGG 0.605106 tig0024534:+24301 Msa1418060:CDS
AAATCAGATAGGGAGACAGA+TGG 0.611076 tig0024534:-24694 None:intergenic
AGTTGGTGGTAAATCAGTTG+AGG 0.635333 tig0024534:+24341 Msa1418060:CDS
TTAGATACTTCAGAAGCCTG+AGG 0.659984 tig0024534:-24630 None:intergenic
TCAGATAGGGAGACAGATGG+AGG 0.662436 tig0024534:-24691 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGAAAAAAAATATCATA+AGG + tig0024534:24479-24498 Msa1418060:intron 10.0%
!!! TCAAACAACTTGTTTTGTTT+TGG - tig0024534:24261-24280 None:intergenic 25.0%
! GAAACATGAACAAAAAATAG+TGG - tig0024534:24550-24569 None:intergenic 25.0%
AGCACTTGCAAAATTTGATA+AGG + tig0024534:24284-24303 Msa1418060:CDS 30.0%
! GTGGATTTGTAATTTGGAAT+AGG - tig0024534:24429-24448 None:intergenic 30.0%
ATGAACAAAAAATAGTGGCA+TGG - tig0024534:24545-24564 None:intergenic 30.0%
! CTGAAGTATCTAAAGTTGAA+TGG + tig0024534:24640-24659 Msa1418060:CDS 30.0%
! ACAAGCCTTGTGATTCAATT+TGG + tig0024534:24232-24251 Msa1418060:CDS 35.0%
! CTTTTGCTACATTTTGCCAA+CGG - tig0024534:24320-24339 None:intergenic 35.0%
CAAAATGTAGCAAAAGCAGT+TGG + tig0024534:24324-24343 Msa1418060:CDS 35.0%
CTTCACGTGGATTTGTAATT+TGG - tig0024534:24435-24454 None:intergenic 35.0%
TAGTGGCATGGTACATAATT+TGG - tig0024534:24533-24552 None:intergenic 35.0%
! ACAAGGCTTGTGTTTGCTAA+GGG - tig0024534:24223-24242 None:intergenic 40.0%
GGAGTCCAAATTGAATCACA+AGG - tig0024534:24240-24259 None:intergenic 40.0%
AATGTAGCAAAAGCAGTTGG+TGG + tig0024534:24327-24346 Msa1418060:CDS 40.0%
!! AGTTGGTGGTAAATCAGTTG+AGG + tig0024534:24341-24360 Msa1418060:CDS 40.0%
GATCTCAAACACATTGAGTC+TGG + tig0024534:24396-24415 Msa1418060:CDS 40.0%
!! CTAATTTGCTACACTTCACG+TGG - tig0024534:24448-24467 None:intergenic 40.0%
CTTATATAGATGCTTGCCTC+AGG + tig0024534:24614-24633 Msa1418060:intron 40.0%
TTAGATACTTCAGAAGCCTG+AGG - tig0024534:24633-24652 None:intergenic 40.0%
AAATCAGATAGGGAGACAGA+TGG - tig0024534:24697-24716 None:intergenic 40.0%
! GTGTTTGCTAAGGGAACTTG+AGG - tig0024534:24214-24233 None:intergenic 45.0%
! CACAAGGCTTGTGTTTGCTA+AGG - tig0024534:24224-24243 None:intergenic 45.0%
! TACATTTTGCCAACGGTCAG+GGG - tig0024534:24313-24332 None:intergenic 45.0%
! CTACATTTTGCCAACGGTCA+GGG - tig0024534:24314-24333 None:intergenic 45.0%
GAGACACTATGAGCTACTCT+TGG + tig0024534:24371-24390 Msa1418060:CDS 45.0%
ACACTATGAGCTACTCTTGG+AGG + tig0024534:24374-24393 Msa1418060:CDS 45.0%
AGACAGATGGAGGAACAAAC+AGG - tig0024534:24684-24703 None:intergenic 45.0%
ATAAGGATACCCCTGACCGT+TGG + tig0024534:24301-24320 Msa1418060:CDS 50.0%
! GCTACATTTTGCCAACGGTC+AGG - tig0024534:24315-24334 None:intergenic 50.0%
TCAGATAGGGAGACAGATGG+AGG - tig0024534:24694-24713 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0024534 gene 24207 24718 24207 ID=Msa1418060;Name=Msa1418060
tig0024534 mRNA 24207 24718 24207 ID=Msa1418060-mRNA-1;Parent=Msa1418060;Name=Msa1418060-mRNA-1;_AED=0.16;_eAED=0.16;_QI=0|0|0.5|1|1|1|2|50|95
tig0024534 exon 24207 24448 24207 ID=Msa1418060-mRNA-1:exon:179;Parent=Msa1418060-mRNA-1
tig0024534 exon 24623 24718 24623 ID=Msa1418060-mRNA-1:exon:180;Parent=Msa1418060-mRNA-1
tig0024534 CDS 24207 24448 24207 ID=Msa1418060-mRNA-1:cds;Parent=Msa1418060-mRNA-1
tig0024534 CDS 24623 24668 24623 ID=Msa1418060-mRNA-1:cds;Parent=Msa1418060-mRNA-1
tig0024534 three_prime_UTR 24669 24718 24669 ID=Msa1418060-mRNA-1:three_prime_utr;Parent=Msa1418060-mRNA-1
Gene Sequence

>Msa1418060

ATGGCCTCAAGTTCCCTTAGCAAACACAAGCCTTGTGATTCAATTTGGACTCCAAAACAAAACAAGTTGTTTGAAAAAGCACTTGCAAAATTTGATAAGGATACCCCTGACCGTTGGCAAAATGTAGCAAAAGCAGTTGGTGGTAAATCAGTTGAGGAAGTTAAGAGACACTATGAGCTACTCTTGGAGGATCTCAAACACATTGAGTCTGGTCATGTTCCTATTCCAAATTACAAATCCACATGCTTGCCTCAGGCTTCTGAAGTATCTAAAGTTGAATGGATTTGA

Protein sequence

>Msa1418060

MASSSLSKHKPCDSIWTPKQNKLFEKALAKFDKDTPDRWQNVAKAVGGKSVEEVKRHYELLLEDLKHIESGHVPIPNYKSTCLPQASEVSKVEWI*