AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0311710

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0311710 MtrunA17_Chr2g0280901 92.188 128 4 2 1 128 1 122 1.98e-80 232
Msa0311710 MtrunA17_Chr2g0323271 45.588 136 52 2 1 114 1 136 2.17e-32 114
Msa0311710 MtrunA17_Chr2g0322971 49.153 59 30 0 3 61 29 87 1.38e-13 62.8
Msa0311710 MtrunA17_Chr4g0024021 45.763 59 32 0 5 63 36 94 1.08e-11 57.8
Msa0311710 MtrunA17_Chr4g0002211 46.552 58 31 0 3 60 6 63 4.74e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0311710 AT4G27310.1 48.624 109 52 1 1 105 1 109 8.93e-34 117
Msa0311710 AT5G54470.1 52.577 97 45 1 2 98 3 98 9.03e-32 112
Msa0311710 AT3G21890.1 52.941 51 24 0 4 54 30 80 1.07e-11 58.2
Msa0311710 AT3G21150.1 45.902 61 33 0 1 61 1 61 2.80e-11 58.9
Msa0311710 AT4G15248.1 41.176 68 37 1 5 69 32 99 4.09e-11 56.6

Find 24 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATTCACAAAACAACTTTGC+TGG 0.324029 2_4:-6606470 None:intergenic
ATCATTGTTGTTGTTATTGT+TGG 0.326101 2_4:-6606669 None:intergenic
GTGTTAGAGATTGACAAATA+TGG 0.391136 2_4:-6606580 None:intergenic
CAGATCAAGCAAGCCTTTGT+TGG 0.420231 2_4:+6606492 Msa0311710:CDS
GGAGATGGTGGGTACAAACT+TGG 0.425123 2_4:-6606621 None:intergenic
TTTGAAGAACAAGAAGAAAC+TGG 0.439733 2_4:-6606791 None:intergenic
AGATCAAGCAAGCCTTTGTT+GGG 0.466195 2_4:+6606493 Msa0311710:CDS
AAGAAAATCAAGTGGTTCCA+TGG 0.473604 2_4:+6606750 Msa0311710:CDS
TTGTTGGGAATGTGATGCTA+AGG 0.513214 2_4:+6606508 Msa0311710:CDS
CTAACACCTTGGCATGGCAC+TGG 0.516554 2_4:+6606596 Msa0311710:CDS
GAGATGGTGGGTACAAACTT+GGG 0.560143 2_4:-6606620 None:intergenic
GTGATTGCAAAGGGAGATGG+TGG 0.566393 2_4:-6606633 None:intergenic
AGTGACACAGTGATTGCAAA+GGG 0.569368 2_4:-6606642 None:intergenic
GGTGGAGTTGTAGATTTCCA+TGG 0.581275 2_4:-6606767 None:intergenic
TTTGTCAATCTCTAACACCT+TGG 0.584477 2_4:+6606585 Msa0311710:CDS
GAACAAGAAGAAACTGGTGG+TGG 0.609570 2_4:-6606785 None:intergenic
TTGGGTCCAGTGCCATGCCA+AGG 0.611081 2_4:-6606602 None:intergenic
ACAGTGATTGCAAAGGGAGA+TGG 0.619548 2_4:-6606636 None:intergenic
CAGTGACACAGTGATTGCAA+AGG 0.628505 2_4:-6606643 None:intergenic
TAGCATCACATTCCCAACAA+AGG 0.629004 2_4:-6606505 None:intergenic
CAATCTCTAACACCTTGGCA+TGG 0.658549 2_4:+6606590 Msa0311710:CDS
TGATGATGAAGAAAATCAAG+TGG 0.695519 2_4:+6606742 Msa0311710:CDS
GAAGAACAAGAAGAAACTGG+TGG 0.704625 2_4:-6606788 None:intergenic
TGATTGCAAAGGGAGATGGT+GGG 0.733841 2_4:-6606632 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCATTGTTGTTGTTATTGT+TGG - chr2_4:6606672-6606691 None:intergenic 25.0%
GTGTTAGAGATTGACAAATA+TGG - chr2_4:6606583-6606602 None:intergenic 30.0%
! TGATGATGAAGAAAATCAAG+TGG + chr2_4:6606742-6606761 Msa0311710:CDS 30.0%
TTTGAAGAACAAGAAGAAAC+TGG - chr2_4:6606794-6606813 None:intergenic 30.0%
GATTCACAAAACAACTTTGC+TGG - chr2_4:6606473-6606492 None:intergenic 35.0%
TTTGTCAATCTCTAACACCT+TGG + chr2_4:6606585-6606604 Msa0311710:CDS 35.0%
! TGATGATGATGATGATACTG+AGG + chr2_4:6606715-6606734 Msa0311710:CDS 35.0%
AAGAAAATCAAGTGGTTCCA+TGG + chr2_4:6606750-6606769 Msa0311710:CDS 35.0%
AGATCAAGCAAGCCTTTGTT+GGG + chr2_4:6606493-6606512 Msa0311710:CDS 40.0%
TAGCATCACATTCCCAACAA+AGG - chr2_4:6606508-6606527 None:intergenic 40.0%
TTGTTGGGAATGTGATGCTA+AGG + chr2_4:6606508-6606527 Msa0311710:CDS 40.0%
AGTGACACAGTGATTGCAAA+GGG - chr2_4:6606645-6606664 None:intergenic 40.0%
GAAGAACAAGAAGAAACTGG+TGG - chr2_4:6606791-6606810 None:intergenic 40.0%
CAGATCAAGCAAGCCTTTGT+TGG + chr2_4:6606492-6606511 Msa0311710:CDS 45.0%
CAATCTCTAACACCTTGGCA+TGG + chr2_4:6606590-6606609 Msa0311710:CDS 45.0%
!! GAGATGGTGGGTACAAACTT+GGG - chr2_4:6606623-6606642 None:intergenic 45.0%
TGATTGCAAAGGGAGATGGT+GGG - chr2_4:6606635-6606654 None:intergenic 45.0%
ACAGTGATTGCAAAGGGAGA+TGG - chr2_4:6606639-6606658 None:intergenic 45.0%
CAGTGACACAGTGATTGCAA+AGG - chr2_4:6606646-6606665 None:intergenic 45.0%
GGTGGAGTTGTAGATTTCCA+TGG - chr2_4:6606770-6606789 None:intergenic 45.0%
GAACAAGAAGAAACTGGTGG+TGG - chr2_4:6606788-6606807 None:intergenic 45.0%
!! GGAGATGGTGGGTACAAACT+TGG - chr2_4:6606624-6606643 None:intergenic 50.0%
GTGATTGCAAAGGGAGATGG+TGG - chr2_4:6606636-6606655 None:intergenic 50.0%
CTAACACCTTGGCATGGCAC+TGG + chr2_4:6606596-6606615 Msa0311710:CDS 55.0%
TTGGGTCCAGTGCCATGCCA+AGG - chr2_4:6606605-6606624 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 6606440 6606826 6606440 ID=Msa0311710;Name=Msa0311710
chr2_4 mRNA 6606440 6606826 6606440 ID=Msa0311710-mRNA-1;Parent=Msa0311710;Name=Msa0311710-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|128
chr2_4 exon 6606440 6606826 6606440 ID=Msa0311710-mRNA-1:exon:2540;Parent=Msa0311710-mRNA-1
chr2_4 CDS 6606440 6606826 6606440 ID=Msa0311710-mRNA-1:cds;Parent=Msa0311710-mRNA-1
Gene Sequence

>Msa0311710

ATGAAGAAGAAATGTGAGCTATGCAAAAGTCCAGCAAAGTTGTTTTGTGAATCAGATCAAGCAAGCCTTTGTTGGGAATGTGATGCTAAGGTTCACACTGCAAACTTCATAGTCACAAAGCATCACAGATTTCTTCTCTGCCATATTTGTCAATCTCTAACACCTTGGCATGGCACTGGACCCAAGTTTGTACCCACCATCTCCCTTTGCAATCACTGTGTCACTGCTACCAACAATAACAACAACAATGATGATGAAGATAATGATCAAGATGATGATGATGATGATGATACTGAGGATGATGATGATGAAGAAAATCAAGTGGTTCCATGGAAATCTACAACTCCACCACCAGTTTCTTCTTGTTCTTCAAATAGTGCAAACTAA
Protein sequence

>Msa0311710

MKKKCELCKSPAKLFCESDQASLCWECDAKVHTANFIVTKHHRFLLCHICQSLTPWHGTGPKFVPTISLCNHCVTATNNNNNNDDEDNDQDDDDDDDTEDDDDEENQVVPWKSTTPPPVSSCSSNSAN*