AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0010780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0010780 MtrunA17_Chr1g0211101 94.012 167 7 2 1 165 1 166 8.54e-114 320
Msa0010780 MtrunA17_Chr3g0132441 38.835 103 58 4 29 129 22 121 3.03e-19 80.1
Msa0010780 MtrunA17_Chr8g0335531 35.484 124 71 6 9 128 2 120 5.33e-17 74.3
Msa0010780 MtrunA17_Chr8g0380901 35.897 117 68 5 15 128 8 120 8.33e-17 72.0
Msa0010780 MtrunA17_Chr6g0453801 35.833 120 72 4 14 129 14 132 1.57e-16 72.8
Msa0010780 MtrunA17_Chr8g0335571 37.097 124 69 6 9 128 2 120 1.81e-16 73.2
Msa0010780 MtrunA17_Chr3g0132511 35.000 120 69 5 18 130 7 124 7.19e-16 72.0
Msa0010780 MtrunA17_Chr1g0205701 33.065 124 73 5 13 132 9 126 1.32e-15 70.5
Msa0010780 MtrunA17_Chr1g0196801 32.787 122 69 5 30 149 20 130 1.44e-14 67.8
Msa0010780 MtrunA17_Chr7g0253761 30.645 124 78 4 14 133 7 126 2.32e-14 67.0
Msa0010780 MtrunA17_Chr4g0064041 36.275 102 57 4 33 128 191 290 7.11e-14 68.2
Msa0010780 MtrunA17_Chr4g0064041 30.263 152 86 6 7 152 5 142 2.14e-13 66.6
Msa0010780 MtrunA17_Chr8g0380711 36.275 102 61 3 28 128 23 121 3.55e-13 62.8
Msa0010780 MtrunA17_Chr6g0481491 30.579 121 77 5 17 134 12 128 1.12e-12 63.2
Msa0010780 MtrunA17_Chr3g0125791 36.735 98 57 4 30 126 30 123 1.44e-12 61.2
Msa0010780 MtrunA17_Chr7g0253731 31.356 118 76 4 14 128 6 121 3.96e-12 60.8
Msa0010780 MtrunA17_Chr7g0253701 32.743 113 69 4 8 118 4 111 4.25e-12 60.8
Msa0010780 MtrunA17_Chr7g0253671 32.743 113 69 4 8 118 4 111 4.25e-12 60.8
Msa0010780 MtrunA17_Chr4g0001571 34.286 105 64 4 28 130 24 125 6.71e-12 60.5
Msa0010780 MtrunA17_Chr8g0360371 28.099 121 81 4 12 128 3 121 2.91e-11 60.5
Msa0010780 MtrunA17_Chr7g0253631 31.707 123 76 4 13 131 6 124 5.02e-11 59.3
Msa0010780 MtrunA17_Chr2g0306461 30.894 123 75 6 14 129 7 126 5.50e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0010780 AT2G31050.1 38.194 144 73 6 11 151 8 138 6.18e-21 85.1
Msa0010780 AT5G26330.1 34.951 103 61 4 30 128 21 121 4.90e-16 72.0
Msa0010780 AT3G17675.1 32.500 120 73 4 15 128 10 127 1.02e-15 69.7
Msa0010780 AT2G26720.1 35.938 128 76 5 8 132 5 129 1.17e-14 68.9
Msa0010780 AT2G02850.1 34.211 114 66 5 14 126 21 126 1.20e-14 67.0
Msa0010780 AT1G72230.1 31.061 132 81 5 8 137 3 126 6.78e-14 66.2
Msa0010780 AT5G07475.1 28.571 147 98 5 12 154 9 152 1.17e-13 65.9
Msa0010780 AT1G22480.1 33.058 121 74 5 18 135 4 120 3.38e-11 58.9
Msa0010780 AT1G17800.1 32.231 121 74 5 13 127 17 135 4.05e-11 58.2
Msa0010780 AT2G27035.1 28.205 117 79 4 36 149 32 146 4.30e-11 58.5
Msa0010780 AT5G20230.1 30.400 125 80 4 33 152 25 147 5.98e-11 58.5

Find 33 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCCTTGGAGGAATGAGGTT+TGG 0.332332 1_1:+16308424 Msa0010780:CDS
CCCATGTAGCATAATTTGTT+TGG 0.336122 1_1:-16307915 None:intergenic
GCCTTGGAGGAATGAGGTTT+GGG 0.340464 1_1:+16308425 Msa0010780:CDS
AGATCAAGTGGTTCTAAATA+AGG 0.343342 1_1:+16308363 Msa0010780:CDS
TAAATAAGGTGAAGAGATAT+TGG 0.384569 1_1:+16308377 Msa0010780:intron
TCTCAAAGATGGAGAGTGAT+TGG 0.389696 1_1:+16308544 Msa0010780:CDS
TTTAGCCGTGGAGATGTTCT+TGG 0.401037 1_1:+16307952 Msa0010780:CDS
GATGGAGTTGGTTGAATTTG+TGG 0.412161 1_1:-16308505 None:intergenic
TGGTTCATTTGCAATATAGC+TGG 0.431102 1_1:+16308397 Msa0010780:CDS
ATAGCTGGACATTGCCTTGG+AGG 0.459542 1_1:+16308412 Msa0010780:CDS
ATGGCTAGTGTTTATGCTGT+TGG 0.480177 1_1:+16307871 Msa0010780:CDS
TGGATTTAAAGCACCGTCCA+TGG 0.481063 1_1:-16308485 None:intergenic
CTCAAAGATGGAGAGTGATT+GGG 0.483596 1_1:+16308545 Msa0010780:CDS
ATTCTTGTATCTCTCAAAGA+TGG 0.491476 1_1:+16308533 Msa0010780:CDS
GACATTGCCTTGGAGGAATG+AGG 0.494262 1_1:+16308419 Msa0010780:CDS
CAAGAATTTAGTGATGGAGT+TGG 0.498793 1_1:-16308517 None:intergenic
GCCAAACAAATTATGCTACA+TGG 0.511548 1_1:+16307914 Msa0010780:CDS
GAGATACAAGAATTTAGTGA+TGG 0.532359 1_1:-16308523 None:intergenic
CAACAATGGTACTAATTCCA+TGG 0.540787 1_1:+16308468 Msa0010780:CDS
AATATAGCTGGACATTGCCT+TGG 0.550956 1_1:+16308409 Msa0010780:CDS
CTGTTGGTGATCAAGATGAA+TGG 0.566698 1_1:+16307887 Msa0010780:CDS
AATAAGAATTGAGAGTATGA+AGG 0.571197 1_1:-16307818 None:intergenic
GTGTTGGCTAAGTATGAAAG+TGG 0.577082 1_1:+16308337 Msa0010780:CDS
GTCAAAGAAGATAGCAACAA+TGG 0.584763 1_1:+16308454 Msa0010780:CDS
TAATGTGTATGAAGTGAGAG+AGG 0.584918 1_1:+16308282 Msa0010780:CDS
CCAAACAAATTATGCTACAT+GGG 0.597055 1_1:+16307915 Msa0010780:CDS
TGAAACAAGTAGTGGAGTGT+TGG 0.609215 1_1:+16308321 Msa0010780:CDS
AGATCATGTGAAACAAGTAG+TGG 0.611448 1_1:+16308313 Msa0010780:CDS
AATGGTACTAATTCCATGGA+CGG 0.621827 1_1:+16308472 Msa0010780:CDS
GAGAGATACAACTTTAGCCG+TGG 0.623416 1_1:+16307940 Msa0010780:CDS
TCCCAAACCTCATTCCTCCA+AGG 0.624087 1_1:-16308426 None:intergenic
TGAAAGTGGAGAAGATCAAG+TGG 0.654735 1_1:+16308351 Msa0010780:CDS
TACTACCAAGAACATCTCCA+CGG 0.676544 1_1:-16307957 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTAATTAAATTATATTTT+TGG + chr1_1:16308218-16308237 Msa0010780:intron 0.0%
!!! TTTTAATTAAATTATATTTT+TGG + chr1_1:16308218-16308237 Msa0010780:intron 0.0%
!!! TTATATTTTTGGTGTTGTAT+TGG + chr1_1:16308229-16308248 Msa0010780:intron 20.0%
!!! TTATATTTTTGGTGTTGTAT+TGG + chr1_1:16308229-16308248 Msa0010780:intron 20.0%
!! AATAAGAATTGAGAGTATGA+AGG - chr1_1:16307821-16307840 None:intergenic 25.0%
!! ATCACATGGATATCTTTTAT+TGG - chr1_1:16308052-16308071 None:intergenic 25.0%
! AAGATAATGTTATGATCACA+TGG - chr1_1:16308066-16308085 None:intergenic 25.0%
!!! TATAGTTTTCAAGTATGTGA+AGG + chr1_1:16308252-16308271 Msa0010780:intron 25.0%
!!! ATAGTTTTCAAGTATGTGAA+GGG + chr1_1:16308253-16308272 Msa0010780:intron 25.0%
! TAAATAAGGTGAAGAGATAT+TGG + chr1_1:16308377-16308396 Msa0010780:intron 25.0%
!! AATAAGAATTGAGAGTATGA+AGG - chr1_1:16307821-16307840 None:intergenic 25.0%
!! ATCACATGGATATCTTTTAT+TGG - chr1_1:16308052-16308071 None:intergenic 25.0%
! AAGATAATGTTATGATCACA+TGG - chr1_1:16308066-16308085 None:intergenic 25.0%
!!! TATAGTTTTCAAGTATGTGA+AGG + chr1_1:16308252-16308271 Msa0010780:intron 25.0%
!!! ATAGTTTTCAAGTATGTGAA+GGG + chr1_1:16308253-16308272 Msa0010780:intron 25.0%
! TAAATAAGGTGAAGAGATAT+TGG + chr1_1:16308377-16308396 Msa0010780:intron 25.0%
! TTTTCTCTTGAATTGTGTCA+TGG + chr1_1:16307852-16307871 Msa0010780:CDS 30.0%
CCAAACAAATTATGCTACAT+GGG + chr1_1:16307915-16307934 Msa0010780:CDS 30.0%
!!! TAGTTTTCAAGTATGTGAAG+GGG + chr1_1:16308254-16308273 Msa0010780:intron 30.0%
!! AGATCAAGTGGTTCTAAATA+AGG + chr1_1:16308363-16308382 Msa0010780:CDS 30.0%
GAGATACAAGAATTTAGTGA+TGG - chr1_1:16308526-16308545 None:intergenic 30.0%
ATTCTTGTATCTCTCAAAGA+TGG + chr1_1:16308533-16308552 Msa0010780:CDS 30.0%
! TTTTCTCTTGAATTGTGTCA+TGG + chr1_1:16307852-16307871 Msa0010780:CDS 30.0%
CCAAACAAATTATGCTACAT+GGG + chr1_1:16307915-16307934 Msa0010780:CDS 30.0%
!!! TAGTTTTCAAGTATGTGAAG+GGG + chr1_1:16308254-16308273 Msa0010780:intron 30.0%
!! AGATCAAGTGGTTCTAAATA+AGG + chr1_1:16308363-16308382 Msa0010780:CDS 30.0%
GAGATACAAGAATTTAGTGA+TGG - chr1_1:16308526-16308545 None:intergenic 30.0%
ATTCTTGTATCTCTCAAAGA+TGG + chr1_1:16308533-16308552 Msa0010780:CDS 30.0%
GCCAAACAAATTATGCTACA+TGG + chr1_1:16307914-16307933 Msa0010780:CDS 35.0%
!! CCCATGTAGCATAATTTGTT+TGG - chr1_1:16307918-16307937 None:intergenic 35.0%
TAATGTGTATGAAGTGAGAG+AGG + chr1_1:16308282-16308301 Msa0010780:CDS 35.0%
AGATCATGTGAAACAAGTAG+TGG + chr1_1:16308313-16308332 Msa0010780:CDS 35.0%
TGGTTCATTTGCAATATAGC+TGG + chr1_1:16308397-16308416 Msa0010780:CDS 35.0%
GTCAAAGAAGATAGCAACAA+TGG + chr1_1:16308454-16308473 Msa0010780:CDS 35.0%
CAACAATGGTACTAATTCCA+TGG + chr1_1:16308468-16308487 Msa0010780:CDS 35.0%
AATGGTACTAATTCCATGGA+CGG + chr1_1:16308472-16308491 Msa0010780:CDS 35.0%
! CAAGAATTTAGTGATGGAGT+TGG - chr1_1:16308520-16308539 None:intergenic 35.0%
GCCAAACAAATTATGCTACA+TGG + chr1_1:16307914-16307933 Msa0010780:CDS 35.0%
!! CCCATGTAGCATAATTTGTT+TGG - chr1_1:16307918-16307937 None:intergenic 35.0%
TAATGTGTATGAAGTGAGAG+AGG + chr1_1:16308282-16308301 Msa0010780:CDS 35.0%
AGATCATGTGAAACAAGTAG+TGG + chr1_1:16308313-16308332 Msa0010780:CDS 35.0%
TGGTTCATTTGCAATATAGC+TGG + chr1_1:16308397-16308416 Msa0010780:CDS 35.0%
GTCAAAGAAGATAGCAACAA+TGG + chr1_1:16308454-16308473 Msa0010780:CDS 35.0%
CAACAATGGTACTAATTCCA+TGG + chr1_1:16308468-16308487 Msa0010780:CDS 35.0%
AATGGTACTAATTCCATGGA+CGG + chr1_1:16308472-16308491 Msa0010780:CDS 35.0%
! CAAGAATTTAGTGATGGAGT+TGG - chr1_1:16308520-16308539 None:intergenic 35.0%
ATGGCTAGTGTTTATGCTGT+TGG + chr1_1:16307871-16307890 Msa0010780:CDS 40.0%
!! CTGTTGGTGATCAAGATGAA+TGG + chr1_1:16307887-16307906 Msa0010780:CDS 40.0%
TACTACCAAGAACATCTCCA+CGG - chr1_1:16307960-16307979 None:intergenic 40.0%
! TGAAACAAGTAGTGGAGTGT+TGG + chr1_1:16308321-16308340 Msa0010780:CDS 40.0%
!! GTGTTGGCTAAGTATGAAAG+TGG + chr1_1:16308337-16308356 Msa0010780:CDS 40.0%
TGAAAGTGGAGAAGATCAAG+TGG + chr1_1:16308351-16308370 Msa0010780:CDS 40.0%
AATATAGCTGGACATTGCCT+TGG + chr1_1:16308409-16308428 Msa0010780:CDS 40.0%
! GATGGAGTTGGTTGAATTTG+TGG - chr1_1:16308508-16308527 None:intergenic 40.0%
TCTCAAAGATGGAGAGTGAT+TGG + chr1_1:16308544-16308563 Msa0010780:CDS 40.0%
CTCAAAGATGGAGAGTGATT+GGG + chr1_1:16308545-16308564 Msa0010780:CDS 40.0%
ATGGCTAGTGTTTATGCTGT+TGG + chr1_1:16307871-16307890 Msa0010780:CDS 40.0%
!! CTGTTGGTGATCAAGATGAA+TGG + chr1_1:16307887-16307906 Msa0010780:CDS 40.0%
TACTACCAAGAACATCTCCA+CGG - chr1_1:16307960-16307979 None:intergenic 40.0%
! TGAAACAAGTAGTGGAGTGT+TGG + chr1_1:16308321-16308340 Msa0010780:CDS 40.0%
!! GTGTTGGCTAAGTATGAAAG+TGG + chr1_1:16308337-16308356 Msa0010780:CDS 40.0%
TGAAAGTGGAGAAGATCAAG+TGG + chr1_1:16308351-16308370 Msa0010780:CDS 40.0%
AATATAGCTGGACATTGCCT+TGG + chr1_1:16308409-16308428 Msa0010780:CDS 40.0%
! GATGGAGTTGGTTGAATTTG+TGG - chr1_1:16308508-16308527 None:intergenic 40.0%
TCTCAAAGATGGAGAGTGAT+TGG + chr1_1:16308544-16308563 Msa0010780:CDS 40.0%
GAGAGATACAACTTTAGCCG+TGG + chr1_1:16307940-16307959 Msa0010780:CDS 45.0%
TTTAGCCGTGGAGATGTTCT+TGG + chr1_1:16307952-16307971 Msa0010780:CDS 45.0%
!! TGGATTTAAAGCACCGTCCA+TGG - chr1_1:16308488-16308507 None:intergenic 45.0%
GAGAGATACAACTTTAGCCG+TGG + chr1_1:16307940-16307959 Msa0010780:CDS 45.0%
TTTAGCCGTGGAGATGTTCT+TGG + chr1_1:16307952-16307971 Msa0010780:CDS 45.0%
!! TGGATTTAAAGCACCGTCCA+TGG - chr1_1:16308488-16308507 None:intergenic 45.0%
ATAGCTGGACATTGCCTTGG+AGG + chr1_1:16308412-16308431 Msa0010780:CDS 50.0%
GACATTGCCTTGGAGGAATG+AGG + chr1_1:16308419-16308438 Msa0010780:CDS 50.0%
TGCCTTGGAGGAATGAGGTT+TGG + chr1_1:16308424-16308443 Msa0010780:CDS 50.0%
GCCTTGGAGGAATGAGGTTT+GGG + chr1_1:16308425-16308444 Msa0010780:CDS 50.0%
TCCCAAACCTCATTCCTCCA+AGG - chr1_1:16308429-16308448 None:intergenic 50.0%
ATAGCTGGACATTGCCTTGG+AGG + chr1_1:16308412-16308431 Msa0010780:CDS 50.0%
GACATTGCCTTGGAGGAATG+AGG + chr1_1:16308419-16308438 Msa0010780:CDS 50.0%
TGCCTTGGAGGAATGAGGTT+TGG + chr1_1:16308424-16308443 Msa0010780:CDS 50.0%
GCCTTGGAGGAATGAGGTTT+GGG + chr1_1:16308425-16308444 Msa0010780:CDS 50.0%
TCCCAAACCTCATTCCTCCA+AGG - chr1_1:16308429-16308448 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 16307787 16308567 16307787 ID=Msa0010780;Name=Msa0010780
chr1_1 mRNA 16307787 16308567 16307787 ID=Msa0010780-mRNA-1;Parent=Msa0010780;Name=Msa0010780-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|0|0|1|0|0|3|0|165
chr1_1 exon 16307787 16307976 16307787 ID=Msa0010780-mRNA-1:exon:5989;Parent=Msa0010780-mRNA-1
chr1_1 exon 16308257 16308384 16308257 ID=Msa0010780-mRNA-1:exon:5990;Parent=Msa0010780-mRNA-1
chr1_1 exon 16308391 16308567 16308391 ID=Msa0010780-mRNA-1:exon:5991;Parent=Msa0010780-mRNA-1
chr1_1 CDS 16307787 16307976 16307787 ID=Msa0010780-mRNA-1:cds;Parent=Msa0010780-mRNA-1
chr1_1 CDS 16308257 16308384 16308257 ID=Msa0010780-mRNA-1:cds;Parent=Msa0010780-mRNA-1
chr1_1 CDS 16308391 16308567 16308391 ID=Msa0010780-mRNA-1:cds;Parent=Msa0010780-mRNA-1
Gene Sequence

>Msa0010780

ATGGTGATCACAAATTTCTTCAACAACTGTACCTTCATACTCTCAATTCTTATTTTGCTATGTAGTTTTCTCTTGAATTGTGTCATGGCTAGTGTTTATGCTGTTGGTGATCAAGATGAATGGAGTAGCCAAACAAATTATGCTACATGGGCAGAGAGATACAACTTTAGCCGTGGAGATGTTCTTGGTATTTTCAAGTATGTGAAGGGGCAACATAATGTGTATGAAGTGAGAGAGGAAACTTTTAGATCATGTGAAACAAGTAGTGGAGTGTTGGCTAAGTATGAAAGTGGAGAAGATCAAGTGGTTCTAAATAAGAGATATTGGTTCATTTGCAATATAGCTGGACATTGCCTTGGAGGAATGAGGTTTGGGATTGAAGTCAAAGAAGATAGCAACAATGGTACTAATTCCATGGACGGTGCTTTAAATCCACAAATTCAACCAACTCCATCACTAAATTCTTGTATCTCTCAAAGATGGAGAGTGATTGGG

Protein sequence

>Msa0010780

MVITNFFNNCTFILSILILLCSFLLNCVMASVYAVGDQDEWSSQTNYATWAERYNFSRGDVLGIFKYVKGQHNVYEVREETFRSCETSSGVLAKYESGEDQVVLNKRYWFICNIAGHCLGGMRFGIEVKEDSNNGTNSMDGALNPQIQPTPSLNSCISQRWRVIG