AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0332290

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0332290 MtrunA17_Chr2g0315201 98.611 72 1 0 1 72 1 72 4.65e-48 155
Msa0332290 MtrunA17_Chr1g0154651 66.667 81 26 1 6 86 14 93 4.57e-30 107
Msa0332290 MtrunA17_Chr2g0315211 94.444 72 4 0 1 72 1 72 2.05e-28 104
Msa0332290 MtrunA17_Chr3g0141401 77.143 70 16 0 3 72 12 81 1.39e-23 91.7
Msa0332290 MtrunA17_Chr5g0403631 74.157 89 22 1 3 91 6 93 1.51e-22 89.0
Msa0332290 MtrunA17_Chr5g0408851 61.404 57 22 0 17 73 61 117 1.45e-18 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0332290 AT1G78700.1 91.667 72 6 0 1 72 1 72 4.68e-28 103
Msa0332290 AT4G18890.1 90.278 72 7 0 1 72 1 72 1.25e-26 99.4
Msa0332290 AT1G19350.5 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0332290 AT1G19350.1 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0332290 AT1G19350.6 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0332290 AT1G19350.4 73.973 73 19 0 6 78 22 94 8.25e-25 95.5
Msa0332290 AT3G50750.1 83.582 67 11 0 6 72 14 80 1.44e-24 94.0
Msa0332290 AT1G19350.3 73.973 73 19 0 6 78 44 116 1.67e-24 94.7
Msa0332290 AT4G36780.1 81.159 69 13 0 6 74 16 84 1.86e-24 93.2
Msa0332290 AT1G75080.2 72.603 73 20 0 6 78 23 95 1.14e-22 89.7
Msa0332290 AT1G75080.1 72.603 73 20 0 6 78 23 95 1.14e-22 89.7
Msa0332290 AT5G45300.1 61.290 62 22 1 17 78 97 156 5.03e-19 80.5
Msa0332290 AT5G45300.2 61.290 62 22 1 17 78 97 156 5.55e-19 80.5
Msa0332290 AT5G45300.3 61.290 62 22 1 17 78 111 170 6.12e-19 80.5
Msa0332290 AT2G45880.1 55.000 60 27 0 11 70 74 133 1.31e-15 70.9

Find 40 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGGGTGTAGTTAGTATATT+TGG 0.217831 2_4:+49195422 None:intergenic
GTTGATGTTAATGAGGATTA+TGG 0.283185 2_4:-49194626 Msa0332290:CDS
AGTATATTTGGAAATGGATT+TGG 0.293195 2_4:+49195434 None:intergenic
TCATTGTTATCACAATGTTT+AGG 0.355738 2_4:+49195183 None:intergenic
AATCCAAAGGTTGCATTTAG+TGG 0.362338 2_4:+49194656 None:intergenic
TTCTCTGGTTTGAGAATGTA+TGG 0.389954 2_4:-49195219 Msa0332290:CDS
GTAGTTAGTATATTTGGAAA+TGG 0.397691 2_4:+49195428 None:intergenic
ATGCCACTAAATGCAACCTT+TGG 0.398006 2_4:-49194659 Msa0332290:CDS
AGAAAAGAATTGAACTTTGA+AGG 0.412503 2_4:+49195367 None:intergenic
GAACTTTGAAGGAGAGAAAG+AGG 0.424311 2_4:+49195378 None:intergenic
TCAAAAGGGTGTTCACGAAA+TGG 0.427164 2_4:+49195344 None:intergenic
CATTGAGAGTAACTCTCAAA+AGG 0.443094 2_4:+49195329 None:intergenic
TTCTCTCTCTCTTTCCATGT+TGG 0.450927 2_4:+49195288 None:intergenic
TTTGGAAATGGATTTGGAGG+TGG 0.455823 2_4:+49195440 None:intergenic
TTACGATAAGTTGTTCCATC+AGG 0.461183 2_4:+49195117 None:intergenic
AAATGCAACCTTTGGATTGA+CGG 0.466530 2_4:-49194651 Msa0332290:CDS
ATAGCTGCTAAGATCTTCTC+TGG 0.470421 2_4:-49195234 Msa0332290:CDS
AAAGCTCTTTGTAATGAAGC+TGG 0.472686 2_4:-49195153 Msa0332290:CDS
AGGTGGAGGGTGATCTTTGT+CGG 0.480030 2_4:+49195457 None:intergenic
GGAAATGGATTTGGAGGTGG+AGG 0.484848 2_4:+49195443 None:intergenic
GACGGTAGTTGATGTTAATG+AGG 0.487517 2_4:-49194633 Msa0332290:CDS
ATATTTGGAAATGGATTTGG+AGG 0.490012 2_4:+49195437 None:intergenic
TGTAATGAAAATAAAGGAAA+GGG 0.490496 2_4:+49195508 None:intergenic
AGGAGAGAAAGAGGGAGGTG+TGG 0.492949 2_4:+49195387 None:intergenic
AGGTGTGGAAGTAGAAGAAG+TGG 0.501319 2_4:+49195402 None:intergenic
AAAGTGTGTAATGAAAATAA+AGG 0.508090 2_4:+49195502 None:intergenic
GAGTTACTCTCAATGACATC+TGG 0.509973 2_4:-49195321 Msa0332290:exon
AACTTTGAAGGAGAGAAAGA+GGG 0.529635 2_4:+49195379 None:intergenic
GGTTGGTCTGTTGAACCTGA+TGG 0.545542 2_4:-49195132 Msa0332290:CDS
ATTGAGAGTAACTCTCAAAA+GGG 0.547709 2_4:+49195330 None:intergenic
CTCTTTGTAATGAAGCTGGT+TGG 0.548313 2_4:-49195149 Msa0332290:CDS
GTGTAATGAAAATAAAGGAA+AGG 0.558624 2_4:+49195507 None:intergenic
GGTGTGGAAGTAGAAGAAGT+GGG 0.575717 2_4:+49195403 None:intergenic
TTTGAAGGAGAGAAAGAGGG+AGG 0.577067 2_4:+49195382 None:intergenic
GAAATGGATTTGGAGGTGGA+GGG 0.584278 2_4:+49195444 None:intergenic
TGATGGAACAACTTATCGTA+AGG 0.588204 2_4:-49195115 Msa0332290:intron
CTGGTACAAGACTACCAACA+TGG 0.591004 2_4:-49195302 Msa0332290:CDS
AAGAGAGAGAGAACAACAAG+AGG 0.597645 2_4:-49195278 Msa0332290:CDS
GTGTGGAAGTAGAAGAAGTG+GGG 0.600322 2_4:+49195404 None:intergenic
ATCAACTACCGTCAATCCAA+AGG 0.603498 2_4:+49194643 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATATTATAATATAATTTGA+TGG - chr2_4:49195177-49195196 Msa0332290:CDS 10.0%
!! GATATTATAATATAATTTGA+TGG - chr2_4:49195177-49195196 Msa0332290:CDS 10.0%
!! GATATTATAATATGATTTGA+CGG - chr2_4:49195258-49195277 Msa0332290:CDS 15.0%
!! GATATTATAATATGATTTGA+CGG - chr2_4:49195258-49195277 Msa0332290:CDS 15.0%
!! TGTAATGAAAATAAAGGAAA+GGG + chr2_4:49194631-49194650 None:intergenic 20.0%
!! AAAGTGTGTAATGAAAATAA+AGG + chr2_4:49194637-49194656 None:intergenic 20.0%
!! TTCTTTGCATTATTACATTA+TGG - chr2_4:49195050-49195069 Msa0332290:intron 20.0%
!!! GAAACCATAAATGTTTTAAA+AGG - chr2_4:49195402-49195421 Msa0332290:five_prime_UTR 20.0%
!! TGTAATGAAAATAAAGGAAA+GGG + chr2_4:49194631-49194650 None:intergenic 20.0%
!! AAAGTGTGTAATGAAAATAA+AGG + chr2_4:49194637-49194656 None:intergenic 20.0%
!! TTCTTTGCATTATTACATTA+TGG - chr2_4:49195050-49195069 Msa0332290:intron 20.0%
!!! GAAACCATAAATGTTTTAAA+AGG - chr2_4:49195402-49195421 Msa0332290:five_prime_UTR 20.0%
! GTGTAATGAAAATAAAGGAA+AGG + chr2_4:49194632-49194651 None:intergenic 25.0%
!! AGTATATTTGGAAATGGATT+TGG + chr2_4:49194705-49194724 None:intergenic 25.0%
! GTAGTTAGTATATTTGGAAA+TGG + chr2_4:49194711-49194730 None:intergenic 25.0%
! AGAAAAGAATTGAACTTTGA+AGG + chr2_4:49194772-49194791 None:intergenic 25.0%
! TCATTGTTATCACAATGTTT+AGG + chr2_4:49194956-49194975 None:intergenic 25.0%
! TAGTTTCAAAAATATCTAGG+TGG + chr2_4:49195227-49195246 None:intergenic 25.0%
!!! GGTTAGTTTCAAAAATATCT+AGG + chr2_4:49195230-49195249 None:intergenic 25.0%
!!! ACCATAAATGTTTTAAAAGG+TGG - chr2_4:49195405-49195424 Msa0332290:five_prime_UTR 25.0%
!!! ACCACCTTTTAAAACATTTA+TGG + chr2_4:49195409-49195428 None:intergenic 25.0%
! GTGTAATGAAAATAAAGGAA+AGG + chr2_4:49194632-49194651 None:intergenic 25.0%
!! AGTATATTTGGAAATGGATT+TGG + chr2_4:49194705-49194724 None:intergenic 25.0%
! GTAGTTAGTATATTTGGAAA+TGG + chr2_4:49194711-49194730 None:intergenic 25.0%
! AGAAAAGAATTGAACTTTGA+AGG + chr2_4:49194772-49194791 None:intergenic 25.0%
! TCATTGTTATCACAATGTTT+AGG + chr2_4:49194956-49194975 None:intergenic 25.0%
! TAGTTTCAAAAATATCTAGG+TGG + chr2_4:49195227-49195246 None:intergenic 25.0%
!!! GGTTAGTTTCAAAAATATCT+AGG + chr2_4:49195230-49195249 None:intergenic 25.0%
!!! ACCATAAATGTTTTAAAAGG+TGG - chr2_4:49195405-49195424 Msa0332290:five_prime_UTR 25.0%
!!! ACCACCTTTTAAAACATTTA+TGG + chr2_4:49195409-49195428 None:intergenic 25.0%
! ATATTTGGAAATGGATTTGG+AGG + chr2_4:49194702-49194721 None:intergenic 30.0%
ATTGAGAGTAACTCTCAAAA+GGG + chr2_4:49194809-49194828 None:intergenic 30.0%
! TGTAAAAAGTTTTGCACAGT+CGG - chr2_4:49195288-49195307 Msa0332290:CDS 30.0%
!!! AATGTTTTAAAAGGTGGTTG+TGG - chr2_4:49195411-49195430 Msa0332290:five_prime_UTR 30.0%
GTTGATGTTAATGAGGATTA+TGG - chr2_4:49195510-49195529 Msa0332290:five_prime_UTR 30.0%
! ATATTTGGAAATGGATTTGG+AGG + chr2_4:49194702-49194721 None:intergenic 30.0%
ATTGAGAGTAACTCTCAAAA+GGG + chr2_4:49194809-49194828 None:intergenic 30.0%
! TGTAAAAAGTTTTGCACAGT+CGG - chr2_4:49195288-49195307 Msa0332290:CDS 30.0%
!!! AATGTTTTAAAAGGTGGTTG+TGG - chr2_4:49195411-49195430 Msa0332290:five_prime_UTR 30.0%
GTTGATGTTAATGAGGATTA+TGG - chr2_4:49195510-49195529 Msa0332290:five_prime_UTR 30.0%
AAAGGAAAGGGAAAAAGTGA+AGG + chr2_4:49194619-49194638 None:intergenic 35.0%
TGGGGTGTAGTTAGTATATT+TGG + chr2_4:49194717-49194736 None:intergenic 35.0%
! AACTTTGAAGGAGAGAAAGA+GGG + chr2_4:49194760-49194779 None:intergenic 35.0%
CATTGAGAGTAACTCTCAAA+AGG + chr2_4:49194810-49194829 None:intergenic 35.0%
! TTCTCTGGTTTGAGAATGTA+TGG - chr2_4:49194917-49194936 Msa0332290:intron 35.0%
AAAGCTCTTTGTAATGAAGC+TGG - chr2_4:49194983-49195002 Msa0332290:intron 35.0%
TTACGATAAGTTGTTCCATC+AGG + chr2_4:49195022-49195041 None:intergenic 35.0%
TGATGGAACAACTTATCGTA+AGG - chr2_4:49195021-49195040 Msa0332290:intron 35.0%
TTAAAAGGTGGTTGTGGTAA+TGG - chr2_4:49195417-49195436 Msa0332290:five_prime_UTR 35.0%
AATCCAAAGGTTGCATTTAG+TGG + chr2_4:49195483-49195502 None:intergenic 35.0%
AAATGCAACCTTTGGATTGA+CGG - chr2_4:49195485-49195504 Msa0332290:five_prime_UTR 35.0%
AAAGGAAAGGGAAAAAGTGA+AGG + chr2_4:49194619-49194638 None:intergenic 35.0%
TGGGGTGTAGTTAGTATATT+TGG + chr2_4:49194717-49194736 None:intergenic 35.0%
! AACTTTGAAGGAGAGAAAGA+GGG + chr2_4:49194760-49194779 None:intergenic 35.0%
CATTGAGAGTAACTCTCAAA+AGG + chr2_4:49194810-49194829 None:intergenic 35.0%
! TTCTCTGGTTTGAGAATGTA+TGG - chr2_4:49194917-49194936 Msa0332290:intron 35.0%
AAAGCTCTTTGTAATGAAGC+TGG - chr2_4:49194983-49195002 Msa0332290:intron 35.0%
TTACGATAAGTTGTTCCATC+AGG + chr2_4:49195022-49195041 None:intergenic 35.0%
TGATGGAACAACTTATCGTA+AGG - chr2_4:49195021-49195040 Msa0332290:intron 35.0%
TTAAAAGGTGGTTGTGGTAA+TGG - chr2_4:49195417-49195436 Msa0332290:five_prime_UTR 35.0%
AATCCAAAGGTTGCATTTAG+TGG + chr2_4:49195483-49195502 None:intergenic 35.0%
AAATGCAACCTTTGGATTGA+CGG - chr2_4:49195485-49195504 Msa0332290:five_prime_UTR 35.0%
! TTTGGAAATGGATTTGGAGG+TGG + chr2_4:49194699-49194718 None:intergenic 40.0%
! GAACTTTGAAGGAGAGAAAG+AGG + chr2_4:49194761-49194780 None:intergenic 40.0%
!! TCAAAAGGGTGTTCACGAAA+TGG + chr2_4:49194795-49194814 None:intergenic 40.0%
GAGTTACTCTCAATGACATC+TGG - chr2_4:49194815-49194834 Msa0332290:intron 40.0%
TTCTCTCTCTCTTTCCATGT+TGG + chr2_4:49194851-49194870 None:intergenic 40.0%
AAGAGAGAGAGAACAACAAG+AGG - chr2_4:49194858-49194877 Msa0332290:intron 40.0%
ATAGCTGCTAAGATCTTCTC+TGG - chr2_4:49194902-49194921 Msa0332290:intron 40.0%
CTCTTTGTAATGAAGCTGGT+TGG - chr2_4:49194987-49195006 Msa0332290:intron 40.0%
ATGCCACTAAATGCAACCTT+TGG - chr2_4:49195477-49195496 Msa0332290:five_prime_UTR 40.0%
ATCAACTACCGTCAATCCAA+AGG + chr2_4:49195496-49195515 None:intergenic 40.0%
! GACGGTAGTTGATGTTAATG+AGG - chr2_4:49195503-49195522 Msa0332290:five_prime_UTR 40.0%
! TTTGGAAATGGATTTGGAGG+TGG + chr2_4:49194699-49194718 None:intergenic 40.0%
! GAACTTTGAAGGAGAGAAAG+AGG + chr2_4:49194761-49194780 None:intergenic 40.0%
!! TCAAAAGGGTGTTCACGAAA+TGG + chr2_4:49194795-49194814 None:intergenic 40.0%
GAGTTACTCTCAATGACATC+TGG - chr2_4:49194815-49194834 Msa0332290:intron 40.0%
TTCTCTCTCTCTTTCCATGT+TGG + chr2_4:49194851-49194870 None:intergenic 40.0%
AAGAGAGAGAGAACAACAAG+AGG - chr2_4:49194858-49194877 Msa0332290:intron 40.0%
ATAGCTGCTAAGATCTTCTC+TGG - chr2_4:49194902-49194921 Msa0332290:intron 40.0%
CTCTTTGTAATGAAGCTGGT+TGG - chr2_4:49194987-49195006 Msa0332290:intron 40.0%
ATGCCACTAAATGCAACCTT+TGG - chr2_4:49195477-49195496 Msa0332290:five_prime_UTR 40.0%
ATCAACTACCGTCAATCCAA+AGG + chr2_4:49195496-49195515 None:intergenic 40.0%
! GACGGTAGTTGATGTTAATG+AGG - chr2_4:49195503-49195522 Msa0332290:five_prime_UTR 40.0%
CGGAAAAATGAGAGAGTGAG+AGG + chr2_4:49194662-49194681 None:intergenic 45.0%
! GAAATGGATTTGGAGGTGGA+GGG + chr2_4:49194695-49194714 None:intergenic 45.0%
GTGTGGAAGTAGAAGAAGTG+GGG + chr2_4:49194735-49194754 None:intergenic 45.0%
GGTGTGGAAGTAGAAGAAGT+GGG + chr2_4:49194736-49194755 None:intergenic 45.0%
AGGTGTGGAAGTAGAAGAAG+TGG + chr2_4:49194737-49194756 None:intergenic 45.0%
TTTGAAGGAGAGAAAGAGGG+AGG + chr2_4:49194757-49194776 None:intergenic 45.0%
CTGGTACAAGACTACCAACA+TGG - chr2_4:49194834-49194853 Msa0332290:intron 45.0%
!! TTGTGGTAATGGTTGTGGCT+CGG - chr2_4:49195428-49195447 Msa0332290:five_prime_UTR 45.0%
CGGAAAAATGAGAGAGTGAG+AGG + chr2_4:49194662-49194681 None:intergenic 45.0%
! GAAATGGATTTGGAGGTGGA+GGG + chr2_4:49194695-49194714 None:intergenic 45.0%
GTGTGGAAGTAGAAGAAGTG+GGG + chr2_4:49194735-49194754 None:intergenic 45.0%
GGTGTGGAAGTAGAAGAAGT+GGG + chr2_4:49194736-49194755 None:intergenic 45.0%
AGGTGTGGAAGTAGAAGAAG+TGG + chr2_4:49194737-49194756 None:intergenic 45.0%
TTTGAAGGAGAGAAAGAGGG+AGG + chr2_4:49194757-49194776 None:intergenic 45.0%
CTGGTACAAGACTACCAACA+TGG - chr2_4:49194834-49194853 Msa0332290:intron 45.0%
!! TTGTGGTAATGGTTGTGGCT+CGG - chr2_4:49195428-49195447 Msa0332290:five_prime_UTR 45.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_4:49195170-49195189 None:intergenic 5.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_4:49195170-49195189 None:intergenic 5.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_4:49195170-49195189 None:intergenic 5.0%
!!! ATATTATAATATCATTTTAT+AGG + chr2_4:49195170-49195189 None:intergenic 5.0%
AGGTGGAGGGTGATCTTTGT+CGG + chr2_4:49194682-49194701 None:intergenic 50.0%
! GGAAATGGATTTGGAGGTGG+AGG + chr2_4:49194696-49194715 None:intergenic 50.0%
!! GGTTGGTCTGTTGAACCTGA+TGG - chr2_4:49195004-49195023 Msa0332290:intron 50.0%
!! GGTGGTTGTGGTAATGGTTG+TGG - chr2_4:49195423-49195442 Msa0332290:five_prime_UTR 50.0%
AGGTGGAGGGTGATCTTTGT+CGG + chr2_4:49194682-49194701 None:intergenic 50.0%
! GGAAATGGATTTGGAGGTGG+AGG + chr2_4:49194696-49194715 None:intergenic 50.0%
!! GGTTGGTCTGTTGAACCTGA+TGG - chr2_4:49195004-49195023 Msa0332290:intron 50.0%
!! GGTGGTTGTGGTAATGGTTG+TGG - chr2_4:49195423-49195442 Msa0332290:five_prime_UTR 50.0%
AGGAGAGAAAGAGGGAGGTG+TGG + chr2_4:49194752-49194771 None:intergenic 55.0%
AGGAGAGAAAGAGGGAGGTG+TGG + chr2_4:49194752-49194771 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 49194616 49195542 49194616 ID=Msa0332290;Name=Msa0332290
chr2_4 mRNA 49194616 49195542 49194616 ID=Msa0332290-mRNA-1;Parent=Msa0332290;Name=Msa0332290-mRNA-1;_AED=0.52;_eAED=0.52;_QI=211|0|0.5|0.5|1|1|2|0|97
chr2_4 exon 49194616 49194693 49194616 ID=Msa0332290-mRNA-1:exon:14763;Parent=Msa0332290-mRNA-1
chr2_4 exon 49195116 49195542 49195116 ID=Msa0332290-mRNA-1:exon:14762;Parent=Msa0332290-mRNA-1
chr2_4 five_prime_UTR 49195332 49195542 49195332 ID=Msa0332290-mRNA-1:five_prime_utr;Parent=Msa0332290-mRNA-1
chr2_4 CDS 49195116 49195331 49195116 ID=Msa0332290-mRNA-1:cds;Parent=Msa0332290-mRNA-1
chr2_4 CDS 49194616 49194693 49194616 ID=Msa0332290-mRNA-1:cds;Parent=Msa0332290-mRNA-1
Gene Sequence

>Msa0332290

ATGACATCTGGTACAAGACTACCAACATGGAAAGAGAGAGAGAACAACAAGAGGAGAGAGAGAAGAAGAAGAGCTATAGCTGCTAAGATCTTCTCTGGTTTGAGAATGTATGGTAACTTTAGATTACCTAAACATTGTGATAACAATGAAGTTCTTAAAGCTCTTTGTAATGAAGCTGGTTGGTCTGTTGAACCTGATGGAACAACTTATCGTAAGTGTTACAGTCAAATGCCACTAAATGCAACCTTTGGATTGACGGTAGTTGATGTTAATGAGGATTATGGTCGAATGTGA
Protein sequence

>Msa0332290

MTSGTRLPTWKERENNKRRERRRRAIAAKIFSGLRMYGNFRLPKHCDNNEVLKALCNEAGWSVEPDGTTYRKCYSQMPLNATFGLTVVDVNEDYGRM*