AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0491770


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0491770 MtrunA17_Chr3g0084011 93.506 77 5 0 1 77 1 77 1.20e-49 151
Msa0491770 MtrunA17_Chr3g0083921 98.630 73 1 0 1 73 1 73 5.20e-47 151
Msa0491770 MtrunA17_Chr8g0352591 76.712 73 17 0 1 73 1 73 5.46e-35 120
Msa0491770 MtrunA17_Chr3g0083901 72.603 73 20 0 1 73 1 73 3.60e-32 113
Msa0491770 MtrunA17_Chr8g0352611 69.863 73 22 0 1 73 1 73 7.68e-32 112
Msa0491770 MtrunA17_Chr8g0352621 69.863 73 21 1 1 73 1 72 2.60e-31 110
Msa0491770 MtrunA17_Chr2g0293441 56.164 73 32 0 1 73 1 73 1.26e-24 93.2
Msa0491770 MtrunA17_Chr8g0382281 55.405 74 32 1 1 73 1 74 3.80e-20 81.3
Msa0491770 MtrunA17_Chr5g0425971 52.703 74 34 1 1 73 1 74 8.24e-20 80.5
Msa0491770 MtrunA17_Chr8g0393281 54.054 74 33 1 1 73 1 74 1.90e-19 79.3
Msa0491770 MtrunA17_Chr8g0352571 54.795 73 32 1 1 72 1 73 1.23e-18 77.4
Msa0491770 MtrunA17_Chr6g0479421 53.333 75 34 1 1 74 1 75 1.67e-17 74.3
Msa0491770 MtrunA17_Chr1g0210981 49.333 75 37 1 1 74 1 75 1.09e-15 69.3
Msa0491770 MtrunA17_Chr6g0479411 50.000 74 36 1 1 73 28 101 3.29e-15 68.2
Msa0491770 MtrunA17_Chr1g0162071 44.595 74 40 1 1 73 1 74 1.26e-14 66.2
Msa0491770 MtrunA17_Chr6g0479391 52.459 61 29 0 14 74 15 75 5.93e-14 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0491770 AT5G12380.1 61.644 73 28 0 1 73 1 73 4.55e-27 100
Msa0491770 AT5G10220.1 58.108 74 30 1 1 73 1 74 1.57e-21 85.5
Msa0491770 AT5G65020.1 58.108 74 30 1 1 73 1 74 1.72e-21 85.5
Msa0491770 AT5G10230.1 58.108 74 30 1 1 73 1 74 2.00e-21 85.1
Msa0491770 AT2G38760.1 52.055 73 34 1 1 72 1 73 5.95e-21 84.0
Msa0491770 AT1G35720.1 55.405 74 32 1 1 73 1 74 3.17e-20 82.0
Msa0491770 AT5G65020.2 61.224 49 19 0 25 73 11 59 9.87e-15 67.0
Msa0491770 AT1G68090.2 50.704 71 34 1 1 70 1 71 9.38e-14 63.9
Msa0491770 AT1G68090.1 50.704 71 34 1 1 70 1 71 1.39e-13 63.9

Find 16 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTCTTGAGTCTGAGCTTTC+AGG 0.157675 3_4:+14707763 Msa0491770:CDS
ATGACCTAATATTGCTATAA+TGG 0.265808 3_4:-14707671 None:intergenic
CTTGTCTGATTTGAGTCCTT+TGG 0.274325 3_4:-14707705 None:intergenic
AGTGGTTGGAAGGAGCAATA+AGG 0.292571 3_4:-14706899 None:intergenic
AAAGCCATTATAGCAATATT+AGG 0.311002 3_4:+14707667 Msa0491770:CDS
GCTCTTCAAAGGGCTGTTAA+AGG 0.314120 3_4:+14706942 Msa0491770:CDS
TTGTCTGATTTGAGTCCTTT+GGG 0.385685 3_4:-14707704 None:intergenic
GTGGTTGGAAGGAGCAATAA+GGG 0.389381 3_4:-14706898 None:intergenic
AGAGCTTCTGCATCTTCAAC+TGG 0.416203 3_4:-14706924 None:intergenic
CTGCATCTTCAACTGGAGAG+TGG 0.522358 3_4:-14706917 None:intergenic
AAGATGCAGAAGCTCTTCAA+AGG 0.524239 3_4:+14706931 Msa0491770:CDS
ATCTTCAACTGGAGAGTGGT+TGG 0.525012 3_4:-14706913 None:intergenic
TCAACTGGAGAGTGGTTGGA+AGG 0.576644 3_4:-14706909 None:intergenic
AGATGCAGAAGCTCTTCAAA+GGG 0.589809 3_4:+14706932 Msa0491770:CDS
ATACTATGAACTCTATCAAG+AGG 0.590523 3_4:+14707729 Msa0491770:CDS
GTCATAGAAATGCTACCCAA+AGG 0.630775 3_4:+14707689 Msa0491770:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATTATTAATTAAAATTT+GGG - chr3_4:14707103-14707122 None:intergenic 0.0%
!! ATTAATTATTAATTAAAATT+TGG - chr3_4:14707104-14707123 None:intergenic 0.0%
!! TAATTAATAATAATTAATTA+AGG + chr3_4:14707116-14707135 Msa0491770:intron 0.0%
!! TTAATTATTAATTAAAATTT+GGG - chr3_4:14707103-14707122 None:intergenic 0.0%
!! ATTAATTATTAATTAAAATT+TGG - chr3_4:14707104-14707123 None:intergenic 0.0%
!! TAATTAATAATAATTAATTA+AGG + chr3_4:14707116-14707135 Msa0491770:intron 0.0%
!! TTGAAATTGATTAAATTACT+GGG + chr3_4:14707611-14707630 Msa0491770:intron 15.0%
!! TTGAAATTGATTAAATTACT+GGG + chr3_4:14707611-14707630 Msa0491770:intron 15.0%
!! TTAATTAAGGTCATATTTGT+TGG + chr3_4:14707129-14707148 Msa0491770:intron 20.0%
!! TAATTAAGGTCATATTTGTT+GGG + chr3_4:14707130-14707149 Msa0491770:intron 20.0%
!! CTTGAAATTGATTAAATTAC+TGG + chr3_4:14707610-14707629 Msa0491770:intron 20.0%
!! TTAATTAAGGTCATATTTGT+TGG + chr3_4:14707129-14707148 Msa0491770:intron 20.0%
!! TAATTAAGGTCATATTTGTT+GGG + chr3_4:14707130-14707149 Msa0491770:intron 20.0%
!! CTTGAAATTGATTAAATTAC+TGG + chr3_4:14707610-14707629 Msa0491770:intron 20.0%
! AAGAAATGAAAAGATGGATA+TGG - chr3_4:14706977-14706996 None:intergenic 25.0%
! TCAAAGAAGAAATGAAAAGA+TGG - chr3_4:14706983-14707002 None:intergenic 25.0%
! TATTCTTATGTGTGAATGAA+AGG - chr3_4:14707051-14707070 None:intergenic 25.0%
! TGTTGTTCTTAGTTAAAAGT+TGG + chr3_4:14707192-14707211 Msa0491770:intron 25.0%
! ACAACAATACGTTAGAAAAA+TGG - chr3_4:14707402-14707421 None:intergenic 25.0%
! TTATAATCGGTGAGTTTATA+TGG + chr3_4:14707545-14707564 Msa0491770:intron 25.0%
! TATAATCGGTGAGTTTATAT+GGG + chr3_4:14707546-14707565 Msa0491770:intron 25.0%
! AAAGCCATTATAGCAATATT+AGG + chr3_4:14707667-14707686 Msa0491770:CDS 25.0%
! ATGACCTAATATTGCTATAA+TGG - chr3_4:14707674-14707693 None:intergenic 25.0%
! AAGAAATGAAAAGATGGATA+TGG - chr3_4:14706977-14706996 None:intergenic 25.0%
! TCAAAGAAGAAATGAAAAGA+TGG - chr3_4:14706983-14707002 None:intergenic 25.0%
! TATTCTTATGTGTGAATGAA+AGG - chr3_4:14707051-14707070 None:intergenic 25.0%
! TGTTGTTCTTAGTTAAAAGT+TGG + chr3_4:14707192-14707211 Msa0491770:intron 25.0%
! ACAACAATACGTTAGAAAAA+TGG - chr3_4:14707402-14707421 None:intergenic 25.0%
! TTATAATCGGTGAGTTTATA+TGG + chr3_4:14707545-14707564 Msa0491770:intron 25.0%
! TATAATCGGTGAGTTTATAT+GGG + chr3_4:14707546-14707565 Msa0491770:intron 25.0%
! AAAGCCATTATAGCAATATT+AGG + chr3_4:14707667-14707686 Msa0491770:CDS 25.0%
! ATGACCTAATATTGCTATAA+TGG - chr3_4:14707674-14707693 None:intergenic 25.0%
!! GGTTTGATGAATTTTCAAGA+TGG - chr3_4:14707030-14707049 None:intergenic 30.0%
ACGATTCCATGTGTTATAAT+CGG + chr3_4:14707532-14707551 Msa0491770:intron 30.0%
ATACTATGAACTCTATCAAG+AGG + chr3_4:14707729-14707748 Msa0491770:CDS 30.0%
!! GGTTTGATGAATTTTCAAGA+TGG - chr3_4:14707030-14707049 None:intergenic 30.0%
ACGATTCCATGTGTTATAAT+CGG + chr3_4:14707532-14707551 Msa0491770:intron 30.0%
ATACTATGAACTCTATCAAG+AGG + chr3_4:14707729-14707748 Msa0491770:CDS 30.0%
TTTAGTCCTTTACCTTCGAT+GGG - chr3_4:14707311-14707330 None:intergenic 35.0%
ATCGAAGGTAAAGGACTAAA+GGG + chr3_4:14707311-14707330 Msa0491770:intron 35.0%
! ATAGCTTAGATCCTTTTTCC+TGG + chr3_4:14707353-14707372 Msa0491770:intron 35.0%
GGTGTAACATGTCAGAATAT+TGG - chr3_4:14707381-14707400 None:intergenic 35.0%
! AACTCACCGATTATAACACA+TGG - chr3_4:14707541-14707560 None:intergenic 35.0%
! GCTTCGAAATTTTGTAGGTT+GGG + chr3_4:14707633-14707652 Msa0491770:intron 35.0%
! CTTCGAAATTTTGTAGGTTG+GGG + chr3_4:14707634-14707653 Msa0491770:intron 35.0%
! TTGTCTGATTTGAGTCCTTT+GGG - chr3_4:14707707-14707726 None:intergenic 35.0%
TTTAGTCCTTTACCTTCGAT+GGG - chr3_4:14707311-14707330 None:intergenic 35.0%
ATCGAAGGTAAAGGACTAAA+GGG + chr3_4:14707311-14707330 Msa0491770:intron 35.0%
! ATAGCTTAGATCCTTTTTCC+TGG + chr3_4:14707353-14707372 Msa0491770:intron 35.0%
GGTGTAACATGTCAGAATAT+TGG - chr3_4:14707381-14707400 None:intergenic 35.0%
! AACTCACCGATTATAACACA+TGG - chr3_4:14707541-14707560 None:intergenic 35.0%
! GCTTCGAAATTTTGTAGGTT+GGG + chr3_4:14707633-14707652 Msa0491770:intron 35.0%
! CTTCGAAATTTTGTAGGTTG+GGG + chr3_4:14707634-14707653 Msa0491770:intron 35.0%
! TTGTCTGATTTGAGTCCTTT+GGG - chr3_4:14707707-14707726 None:intergenic 35.0%
AAGATGCAGAAGCTCTTCAA+AGG + chr3_4:14706931-14706950 Msa0491770:CDS 40.0%
AGATGCAGAAGCTCTTCAAA+GGG + chr3_4:14706932-14706951 Msa0491770:CDS 40.0%
CGATGGGGCTATTAGTATTT+CGG - chr3_4:14707295-14707314 None:intergenic 40.0%
AATACTAATAGCCCCATCGA+AGG + chr3_4:14707296-14707315 Msa0491770:intron 40.0%
TTAGTCCTTTACCTTCGATG+GGG - chr3_4:14707310-14707329 None:intergenic 40.0%
CTTTAGTCCTTTACCTTCGA+TGG - chr3_4:14707312-14707331 None:intergenic 40.0%
CATCGAAGGTAAAGGACTAA+AGG + chr3_4:14707310-14707329 Msa0491770:intron 40.0%
GAATATTGGCACCAGGAAAA+AGG - chr3_4:14707367-14707386 None:intergenic 40.0%
! ACTGGGCTTCGAAATTTTGT+AGG + chr3_4:14707628-14707647 Msa0491770:intron 40.0%
! GGCTTCGAAATTTTGTAGGT+TGG + chr3_4:14707632-14707651 Msa0491770:intron 40.0%
GTCATAGAAATGCTACCCAA+AGG + chr3_4:14707689-14707708 Msa0491770:CDS 40.0%
! CTTGTCTGATTTGAGTCCTT+TGG - chr3_4:14707708-14707727 None:intergenic 40.0%
!! TGAGCTTTCAGGTGATTTTG+AGG + chr3_4:14707774-14707793 Msa0491770:CDS 40.0%
!!! GTGATTTTGAGGTACATCCA+CGG + chr3_4:14707785-14707804 Msa0491770:CDS 40.0%
AAGATGCAGAAGCTCTTCAA+AGG + chr3_4:14706931-14706950 Msa0491770:CDS 40.0%
AGATGCAGAAGCTCTTCAAA+GGG + chr3_4:14706932-14706951 Msa0491770:CDS 40.0%
CGATGGGGCTATTAGTATTT+CGG - chr3_4:14707295-14707314 None:intergenic 40.0%
AATACTAATAGCCCCATCGA+AGG + chr3_4:14707296-14707315 Msa0491770:intron 40.0%
TTAGTCCTTTACCTTCGATG+GGG - chr3_4:14707310-14707329 None:intergenic 40.0%
CTTTAGTCCTTTACCTTCGA+TGG - chr3_4:14707312-14707331 None:intergenic 40.0%
CATCGAAGGTAAAGGACTAA+AGG + chr3_4:14707310-14707329 Msa0491770:intron 40.0%
GAATATTGGCACCAGGAAAA+AGG - chr3_4:14707367-14707386 None:intergenic 40.0%
! ACTGGGCTTCGAAATTTTGT+AGG + chr3_4:14707628-14707647 Msa0491770:intron 40.0%
! GGCTTCGAAATTTTGTAGGT+TGG + chr3_4:14707632-14707651 Msa0491770:intron 40.0%
GTCATAGAAATGCTACCCAA+AGG + chr3_4:14707689-14707708 Msa0491770:CDS 40.0%
! CTTGTCTGATTTGAGTCCTT+TGG - chr3_4:14707708-14707727 None:intergenic 40.0%
!! TGAGCTTTCAGGTGATTTTG+AGG + chr3_4:14707774-14707793 Msa0491770:CDS 40.0%
!!! GTGATTTTGAGGTACATCCA+CGG + chr3_4:14707785-14707804 Msa0491770:CDS 40.0%
GTGGTTGGAAGGAGCAATAA+GGG - chr3_4:14706901-14706920 None:intergenic 45.0%
AGTGGTTGGAAGGAGCAATA+AGG - chr3_4:14706902-14706921 None:intergenic 45.0%
ATCTTCAACTGGAGAGTGGT+TGG - chr3_4:14706916-14706935 None:intergenic 45.0%
AGAGCTTCTGCATCTTCAAC+TGG - chr3_4:14706927-14706946 None:intergenic 45.0%
GCTCTTCAAAGGGCTGTTAA+AGG + chr3_4:14706942-14706961 Msa0491770:CDS 45.0%
AATAGCCCCATCGAAGGTAA+AGG + chr3_4:14707302-14707321 Msa0491770:intron 45.0%
CATGTCAGAATATTGGCACC+AGG - chr3_4:14707374-14707393 None:intergenic 45.0%
GTGGTTGGAAGGAGCAATAA+GGG - chr3_4:14706901-14706920 None:intergenic 45.0%
AGTGGTTGGAAGGAGCAATA+AGG - chr3_4:14706902-14706921 None:intergenic 45.0%
ATCTTCAACTGGAGAGTGGT+TGG - chr3_4:14706916-14706935 None:intergenic 45.0%
AGAGCTTCTGCATCTTCAAC+TGG - chr3_4:14706927-14706946 None:intergenic 45.0%
GCTCTTCAAAGGGCTGTTAA+AGG + chr3_4:14706942-14706961 Msa0491770:CDS 45.0%
AATAGCCCCATCGAAGGTAA+AGG + chr3_4:14707302-14707321 Msa0491770:intron 45.0%
CATGTCAGAATATTGGCACC+AGG - chr3_4:14707374-14707393 None:intergenic 45.0%
TCAACTGGAGAGTGGTTGGA+AGG - chr3_4:14706912-14706931 None:intergenic 50.0%
CTGCATCTTCAACTGGAGAG+TGG - chr3_4:14706920-14706939 None:intergenic 50.0%
CGTCTTGAGTCTGAGCTTTC+AGG + chr3_4:14707763-14707782 Msa0491770:CDS 50.0%
TCAACTGGAGAGTGGTTGGA+AGG - chr3_4:14706912-14706931 None:intergenic 50.0%
CTGCATCTTCAACTGGAGAG+TGG - chr3_4:14706920-14706939 None:intergenic 50.0%
CGTCTTGAGTCTGAGCTTTC+AGG + chr3_4:14707763-14707782 Msa0491770:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 14706891 14707810 14706891 ID=Msa0491770;Name=Msa0491770
chr3_4 mRNA 14706891 14707810 14706891 ID=Msa0491770-mRNA-1;Parent=Msa0491770;Name=Msa0491770-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|0|0|1|1|1|2|0|77
chr3_4 exon 14706891 14706963 14706891 ID=Msa0491770-mRNA-1:exon:4356;Parent=Msa0491770-mRNA-1
chr3_4 exon 14707650 14707810 14707650 ID=Msa0491770-mRNA-1:exon:4357;Parent=Msa0491770-mRNA-1
chr3_4 CDS 14706891 14706963 14706891 ID=Msa0491770-mRNA-1:cds;Parent=Msa0491770-mRNA-1
chr3_4 CDS 14707650 14707810 14707650 ID=Msa0491770-mRNA-1:cds;Parent=Msa0491770-mRNA-1
Gene Sequence

>Msa0491770

ATGGCTTCCCTTATTGCTCCTTCCAACCACTCTCCAGTTGAAGATGCAGAAGCTCTTCAAAGGGCTGTTAAAGGTTGGGGAGCTGATGAAAAAGCCATTATAGCAATATTAGGTCATAGAAATGCTACCCAAAGGACTCAAATCAGACAAGCATACTATGAACTCTATCAAGAGGATCTCATCAAACGTCTTGAGTCTGAGCTTTCAGGTGATTTTGAGGTACATCCACGGTAA

Protein sequence

>Msa0491770

MASLIAPSNHSPVEDAEALQRAVKGWGADEKAIIAILGHRNATQRTQIRQAYYELYQEDLIKRLESELSGDFEVHPR*