AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1039390


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1039390 MtrunA17_Chr5g0426561 67.857 56 16 1 8 61 1 56 1.58e-22 81.3
Msa1039390 MtrunA17_Chr5g0420451 84.783 46 7 0 8 53 2 47 3.74e-22 84.7
Msa1039390 MtrunA17_Chr1g0172341 77.083 48 11 0 6 53 1 48 6.60e-22 81.3
Msa1039390 MtrunA17_Chr8g0372151 74.000 50 13 0 5 54 3 52 1.32e-20 80.5
Msa1039390 MtrunA17_Chr5g0393801 76.087 46 11 0 8 53 1 46 1.36e-20 77.8
Msa1039390 MtrunA17_Chr6g0453011 63.793 58 21 0 6 63 31 88 1.71e-20 78.2
Msa1039390 MtrunA17_Chr2g0304851 70.833 48 14 0 6 53 3 50 3.67e-19 79.0
Msa1039390 MtrunA17_Chr6g0481111 71.739 46 13 0 8 53 1 46 1.16e-18 73.9
Msa1039390 MtrunA17_Chr1g0167871 77.273 44 10 0 10 53 208 251 2.77e-18 76.6
Msa1039390 MtrunA17_Chr7g0223511 60.784 51 20 0 3 53 19 69 1.05e-17 73.6
Msa1039390 MtrunA17_Chr5g0393531 73.913 46 12 0 8 53 1 46 1.11e-17 73.2
Msa1039390 MtrunA17_Chr7g0231491 75.556 45 11 0 9 53 36 80 1.25e-17 73.6
Msa1039390 MtrunA17_Chr8g0347361 62.745 51 19 0 3 53 6 56 2.26e-17 72.0
Msa1039390 MtrunA17_Chr6g0464321 72.093 43 12 0 8 50 1 43 8.38e-17 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAACCCAAAGAAGGATTTC+TGG 0.203063 7_1:-76531445 Msa1039390:CDS
AGCTTCCAGAAATCCTTCTT+TGG 0.249300 7_1:+76531440 None:intergenic
AACAATTCTTCATGGGAAAC+AGG 0.366959 7_1:-76532045 None:intergenic
GCAAGACCAGTTCAATTTAT+CGG 0.369808 7_1:-76531473 Msa1039390:CDS
AGACAAATGGGTTGTTGTTA+AGG 0.378712 7_1:-76531402 Msa1039390:CDS
GCTTCCAGAAATCCTTCTTT+GGG 0.413903 7_1:+76531441 None:intergenic
AATTGAACTGGTCTTGCCAT+TGG 0.425041 7_1:+76531479 None:intergenic
AAATGGGTTGTTGTTAAGGA+TGG 0.435334 7_1:-76531398 Msa1039390:CDS
ATTGAACTGGTCTTGCCATT+GGG 0.450658 7_1:+76531480 None:intergenic
CGGTGATATTAACCCAAAGA+AGG 0.479855 7_1:-76531453 Msa1039390:CDS
TAAGGATGGGAGGGAGCACT+TGG 0.492942 7_1:-76531384 Msa1039390:CDS
CTGTGAGGGTGAAAGACAAA+TGG 0.494992 7_1:-76531415 Msa1039390:CDS
ATATCACCGATAAATTGAAC+TGG 0.497635 7_1:+76531467 None:intergenic
GATGGTTATCGTTGATGCCA+AGG 0.528606 7_1:-76531360 Msa1039390:CDS
AATGGGTTGTTGTTAAGGAT+GGG 0.540007 7_1:-76531397 Msa1039390:CDS
TGGGAGGGAGCACTTGGAGA+TGG 0.552726 7_1:-76531378 Msa1039390:CDS
TAAAGATACACATAAAACCT+TGG 0.574092 7_1:+76531343 None:intergenic
GGTTGTTGTTAAGGATGGGA+GGG 0.576229 7_1:-76531393 Msa1039390:CDS
GGGTTGTTGTTAAGGATGGG+AGG 0.583709 7_1:-76531394 Msa1039390:CDS
TGTGAGGGTGAAAGACAAAT+GGG 0.607479 7_1:-76531414 Msa1039390:CDS
ATTTCTGGAAGCTGACTGTG+AGG 0.675527 7_1:-76531430 Msa1039390:CDS
TGTTCTCAGAGCAATCCCAA+TGG 0.678231 7_1:-76531495 Msa1039390:intron
TTTCTGGAAGCTGACTGTGA+GGG 0.678677 7_1:-76531429 Msa1039390:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATATTTAAATATTAGTGA+TGG + chr7_1:76531427-76531446 None:intergenic 10.0%
!! AAAAGATTTATAATGTTATA+GGG + chr7_1:76531458-76531477 None:intergenic 10.0%
!! TAAAAGATTTATAATGTTAT+AGG + chr7_1:76531459-76531478 None:intergenic 10.0%
!!! AATTTTTATCTTACTTTAAT+TGG - chr7_1:76531488-76531507 Msa1039390:CDS 10.0%
!! AAAGATTTATAATGTTATAG+GGG + chr7_1:76531457-76531476 None:intergenic 15.0%
!! AAGTAAGATAAAAATTGTTA+TGG + chr7_1:76531484-76531503 None:intergenic 15.0%
!!! CTTTGCTACATAATTTTTAT+TGG - chr7_1:76531775-76531794 Msa1039390:intron 20.0%
!! AAGTGTTATAAAAATCTTGT+AGG + chr7_1:76531820-76531839 None:intergenic 20.0%
! TGCAAAAGCAATAAGTTATA+TGG + chr7_1:76531580-76531599 None:intergenic 25.0%
! ATCTAGAAACAAAATTAGGA+TGG + chr7_1:76531703-76531722 None:intergenic 25.0%
! AAATTATGTAGCAAAGTGTA+AGG + chr7_1:76531771-76531790 None:intergenic 25.0%
! TAAAGATACACATAAAACCT+TGG + chr7_1:76532007-76532026 None:intergenic 25.0%
TATATTCACACTCATCTACA+TGG - chr7_1:76531383-76531402 Msa1039390:CDS 30.0%
ATATTCACACTCATCTACAT+GGG - chr7_1:76531384-76531403 Msa1039390:CDS 30.0%
!! GGTATGGTACTATTTTAAGA+GGG + chr7_1:76531546-76531565 None:intergenic 30.0%
AGTTATATGGTGTACAATGT+GGG + chr7_1:76531567-76531586 None:intergenic 30.0%
AAGTTATATGGTGTACAATG+TGG + chr7_1:76531568-76531587 None:intergenic 30.0%
GCAGATCTAGAAACAAAATT+AGG + chr7_1:76531707-76531726 None:intergenic 30.0%
AAGTGTAAGGACTTAAAAGA+AGG + chr7_1:76531758-76531777 None:intergenic 30.0%
ATATCACCGATAAATTGAAC+TGG + chr7_1:76531883-76531902 None:intergenic 30.0%
!! GGGTATGGTACTATTTTAAG+AGG + chr7_1:76531547-76531566 None:intergenic 35.0%
!! CCTTTTAGCTATTGTACGAA+GGG + chr7_1:76531630-76531649 None:intergenic 35.0%
!! TCCTTTTAGCTATTGTACGA+AGG + chr7_1:76531631-76531650 None:intergenic 35.0%
ATGAGAGAAGTGGTTAGAAA+AGG + chr7_1:76531663-76531682 None:intergenic 35.0%
GCAAGACCAGTTCAATTTAT+CGG - chr7_1:76531874-76531893 Msa1039390:intron 35.0%
TTAACCCAAAGAAGGATTTC+TGG - chr7_1:76531902-76531921 Msa1039390:intron 35.0%
!! AGACAAATGGGTTGTTGTTA+AGG - chr7_1:76531945-76531964 Msa1039390:intron 35.0%
!! AAATGGGTTGTTGTTAAGGA+TGG - chr7_1:76531949-76531968 Msa1039390:intron 35.0%
!! AATGGGTTGTTGTTAAGGAT+GGG - chr7_1:76531950-76531969 Msa1039390:intron 35.0%
CATGCGCAATAACAGTGTTA+TGG - chr7_1:76531330-76531349 Msa1039390:CDS 40.0%
GATAGTGTCAGAGAGAATGT+TGG + chr7_1:76531524-76531543 None:intergenic 40.0%
TATGGTGTACAATGTGGGTA+TGG + chr7_1:76531562-76531581 None:intergenic 40.0%
! AGCTATTGTACGAAGGGTAT+GGG + chr7_1:76531624-76531643 None:intergenic 40.0%
TAGCTATTGTACGAAGGGTA+TGG + chr7_1:76531625-76531644 None:intergenic 40.0%
CCCTTCGTACAATAGCTAAA+AGG - chr7_1:76531627-76531646 Msa1039390:intron 40.0%
TCTCATCCATTGAGCTCTTT+AGG - chr7_1:76531677-76531696 Msa1039390:intron 40.0%
!! ATTGAACTGGTCTTGCCATT+GGG + chr7_1:76531870-76531889 None:intergenic 40.0%
!! AATTGAACTGGTCTTGCCAT+TGG + chr7_1:76531871-76531890 None:intergenic 40.0%
CGGTGATATTAACCCAAAGA+AGG - chr7_1:76531894-76531913 Msa1039390:intron 40.0%
GCTTCCAGAAATCCTTCTTT+GGG + chr7_1:76531909-76531928 None:intergenic 40.0%
AGCTTCCAGAAATCCTTCTT+TGG + chr7_1:76531910-76531929 None:intergenic 40.0%
TGTGAGGGTGAAAGACAAAT+GGG - chr7_1:76531933-76531952 Msa1039390:intron 40.0%
AGCTCAATGGATGAGAGAAG+TGG + chr7_1:76531673-76531692 None:intergenic 45.0%
TGTTCTCAGAGCAATCCCAA+TGG - chr7_1:76531852-76531871 Msa1039390:intron 45.0%
! ATTTCTGGAAGCTGACTGTG+AGG - chr7_1:76531917-76531936 Msa1039390:intron 45.0%
! TTTCTGGAAGCTGACTGTGA+GGG - chr7_1:76531918-76531937 Msa1039390:intron 45.0%
CTGTGAGGGTGAAAGACAAA+TGG - chr7_1:76531932-76531951 Msa1039390:intron 45.0%
! GGTTGTTGTTAAGGATGGGA+GGG - chr7_1:76531954-76531973 Msa1039390:intron 45.0%
GATGGTTATCGTTGATGCCA+AGG - chr7_1:76531987-76532006 Msa1039390:intron 45.0%
! GAAGGGTATGGGCAATGCAA+TGG + chr7_1:76531613-76531632 None:intergenic 50.0%
GGATGGCCTAAAGAGCTCAA+TGG + chr7_1:76531686-76531705 None:intergenic 50.0%
! GGGTTGTTGTTAAGGATGGG+AGG - chr7_1:76531953-76531972 Msa1039390:intron 50.0%
!! TAAGGATGGGAGGGAGCACT+TGG - chr7_1:76531963-76531982 Msa1039390:intron 55.0%
!! TGGGAGGGAGCACTTGGAGA+TGG - chr7_1:76531969-76531988 Msa1039390:intron 60.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 76531313 76532056 76531313 ID=Msa1039390;Name=Msa1039390
chr7_1 mRNA 76531313 76532056 76531313 ID=Msa1039390-mRNA-1;Parent=Msa1039390;Name=Msa1039390-mRNA-1;_AED=0.39;_eAED=0.41;_QI=0|0|0|1|0|0.5|2|0|68
chr7_1 exon 76532046 76532056 76532046 ID=Msa1039390-mRNA-1:exon:19906;Parent=Msa1039390-mRNA-1
chr7_1 exon 76531313 76531508 76531313 ID=Msa1039390-mRNA-1:exon:19905;Parent=Msa1039390-mRNA-1
chr7_1 CDS 76532046 76532056 76532046 ID=Msa1039390-mRNA-1:cds;Parent=Msa1039390-mRNA-1
chr7_1 CDS 76531313 76531508 76531313 ID=Msa1039390-mRNA-1:cds;Parent=Msa1039390-mRNA-1
Gene Sequence

>Msa1039390

ATGGGAAACAGAGCAATCCCAATGGCAAGACCAGTTCAATTTATCGGTGATATTAACCCAAAGAAGGATTTCTGGAAGCTGACTGTGAGGGTGAAAGACAAATGGGTTGTTGTTAAGGATGGGAGGGAGCACTTGGAGATGGTTATCGTTGATGCCAAGGTTTTATGTGTATCTTTAGCTGTTGTAATATTAATTATTTCAACATAG

Protein sequence

>Msa1039390

MGNRAIPMARPVQFIGDINPKKDFWKLTVRVKDKWVVVKDGREHLEMVIVDAKVLCVSLAVVILIIST*