AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1169250


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1169250 MtrunA17_Chr7g0263811 86.364 88 3 4 1 80 1 87 9.75e-46 142
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1169250 AT5G03120.2 38.372 86 40 2 16 94 10 89 1.24e-12 59.3
Msa1169250 AT5G03120.1 40.625 64 31 1 16 72 10 73 1.11e-11 55.8

Find 32 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATCATTGTGTGATTTAT+AGG 0.229909 7_4:-62188536 None:intergenic
GACAAACCTCTAGAGAAATA+TGG 0.278570 7_4:-62188697 None:intergenic
AGATCATTGTGTGATTTATA+GGG 0.390485 7_4:-62188535 None:intergenic
AGCATCAACACCCGTAGCTT+TGG 0.412256 7_4:-62189177 None:intergenic
TCATTATCATCACAGGATCT+AGG 0.434501 7_4:+62189240 Msa1169250:CDS
ACAAACCTCTAGAGAAATAT+GGG 0.461398 7_4:-62188696 None:intergenic
AAGAAAGAGAAAGAAACAAT+TGG 0.485064 7_4:-62188662 None:intergenic
GAAACAATTGGCGATGAAGA+TGG 0.489266 7_4:-62188650 None:intergenic
GGCACAAACGAGTGAGTCTC+AGG 0.492086 7_4:-62189089 None:intergenic
GACATGCACAAATTTCTTGA+GGG 0.493470 7_4:-62188607 None:intergenic
AAATTTGTGCATGTCATACA+TGG 0.499981 7_4:+62188615 Msa1169250:exon
ATTTATGAGATCGATTATAG+AGG 0.512251 7_4:+62189065 Msa1169250:CDS
GGCTTACCATGGGAATGATC+AGG 0.514926 7_4:-62189116 None:intergenic
TGCAGCTGCAACCAAAGCTA+CGG 0.523815 7_4:+62189166 Msa1169250:CDS
GATTTATAGGGTGGAAAGAA+AGG 0.525657 7_4:-62188523 None:intergenic
GACTAATGTATGCAAGTTCA+CGG 0.529375 7_4:-62188465 None:intergenic
TGATGCTACCATGAAACAAA+AGG 0.546319 7_4:+62189193 Msa1169250:CDS
TGACATGCACAAATTTCTTG+AGG 0.548150 7_4:-62188608 None:intergenic
TCATTGTGTGATTTATAGGG+TGG 0.550522 7_4:-62188532 None:intergenic
CTCTTGTCATGAGCTGAATG+AGG 0.554978 7_4:-62189137 None:intergenic
CAACTACTCATTATCATCAC+AGG 0.565467 7_4:+62189233 Msa1169250:CDS
ACTCTCCCATATTTCTCTAG+AGG 0.566327 7_4:+62188691 Msa1169250:CDS
GAGCTGAATGAGGCTTACCA+TGG 0.584782 7_4:-62189127 None:intergenic
GCAGCTGCAACCAAAGCTAC+GGG 0.602211 7_4:+62189167 Msa1169250:CDS
CCATGGGAATGATCAGGTGG+AGG 0.610610 7_4:-62189110 None:intergenic
CCTCCACCTGATCATTCCCA+TGG 0.611138 7_4:+62189110 Msa1169250:CDS
ACAATTGGCGATGAAGATGG+AGG 0.611543 7_4:-62188647 None:intergenic
AGCTGAATGAGGCTTACCAT+GGG 0.626115 7_4:-62189126 None:intergenic
GAAGAAACATAACATGGTCA+AGG 0.648058 7_4:-62188443 None:intergenic
CAATTGGCGATGAAGATGGA+GGG 0.648695 7_4:-62188646 None:intergenic
TTCACGGAAGAAACATAACA+TGG 0.691093 7_4:-62188449 None:intergenic
TTACCATGGGAATGATCAGG+TGG 0.701175 7_4:-62189113 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTATAAAATTTATGAGAG+TGG - chr7_4:62188756-62188775 None:intergenic 15.0%
!! ATTAATTGTCTATTGTAAAT+AGG - chr7_4:62188868-62188887 None:intergenic 15.0%
!!! GTGTTATGTTTTTAAATTTT+AGG + chr7_4:62189017-62189036 Msa1169250:intron 15.0%
!!! TTATGTTTTTAAATTTTAGG+TGG + chr7_4:62189020-62189039 Msa1169250:intron 15.0%
!! TATTATAAAATTTATGAGAG+TGG - chr7_4:62188756-62188775 None:intergenic 15.0%
!! ATTAATTGTCTATTGTAAAT+AGG - chr7_4:62188868-62188887 None:intergenic 15.0%
!!! GTGTTATGTTTTTAAATTTT+AGG + chr7_4:62189017-62189036 Msa1169250:intron 15.0%
!!! TTATGTTTTTAAATTTTAGG+TGG + chr7_4:62189020-62189039 Msa1169250:intron 15.0%
!! GAGTAATATTGTAGAAAAAA+AGG - chr7_4:62188837-62188856 None:intergenic 20.0%
!!! TTTTTAAATTTTAGGTGGAT+CGG + chr7_4:62189025-62189044 Msa1169250:intron 20.0%
!! GAGTAATATTGTAGAAAAAA+AGG - chr7_4:62188837-62188856 None:intergenic 20.0%
!!! TTTTTAAATTTTAGGTGGAT+CGG + chr7_4:62189025-62189044 Msa1169250:intron 20.0%
! AGGAAATGAAAAAAGAAGAA+GGG - chr7_4:62188506-62188525 None:intergenic 25.0%
! AAGGAAATGAAAAAAGAAGA+AGG - chr7_4:62188507-62188526 None:intergenic 25.0%
! AGATCATTGTGTGATTTATA+GGG - chr7_4:62188538-62188557 None:intergenic 25.0%
! AAGATCATTGTGTGATTTAT+AGG - chr7_4:62188539-62188558 None:intergenic 25.0%
! AAGAAAGAGAAAGAAACAAT+TGG - chr7_4:62188665-62188684 None:intergenic 25.0%
! TATAAAATTTATGAGAGTGG+TGG - chr7_4:62188753-62188772 None:intergenic 25.0%
! ATTTATGAGATCGATTATAG+AGG + chr7_4:62189065-62189084 Msa1169250:CDS 25.0%
! AGGAAATGAAAAAAGAAGAA+GGG - chr7_4:62188506-62188525 None:intergenic 25.0%
! AAGGAAATGAAAAAAGAAGA+AGG - chr7_4:62188507-62188526 None:intergenic 25.0%
! AGATCATTGTGTGATTTATA+GGG - chr7_4:62188538-62188557 None:intergenic 25.0%
! AAGATCATTGTGTGATTTAT+AGG - chr7_4:62188539-62188558 None:intergenic 25.0%
! AAGAAAGAGAAAGAAACAAT+TGG - chr7_4:62188665-62188684 None:intergenic 25.0%
! TATAAAATTTATGAGAGTGG+TGG - chr7_4:62188753-62188772 None:intergenic 25.0%
! ATTTATGAGATCGATTATAG+AGG + chr7_4:62189065-62189084 Msa1169250:CDS 25.0%
! AAAAAGAAGAAGGGGTTTTA+AGG - chr7_4:62188497-62188516 None:intergenic 30.0%
GGAAATGAAAAAAGAAGAAG+GGG - chr7_4:62188505-62188524 None:intergenic 30.0%
AAATTTGTGCATGTCATACA+TGG + chr7_4:62188615-62188634 Msa1169250:exon 30.0%
! ACAAACCTCTAGAGAAATAT+GGG - chr7_4:62188699-62188718 None:intergenic 30.0%
GAAAGAGGGTTTGTAAAATT+CGG - chr7_4:62188724-62188743 None:intergenic 30.0%
TTGTCTATTGTAAATAGGAC+CGG - chr7_4:62188863-62188882 None:intergenic 30.0%
GTCAACTTTCTCTTGTAAAT+AGG + chr7_4:62188966-62188985 Msa1169250:intron 30.0%
CTTTCTCTTGTAAATAGGAT+CGG + chr7_4:62188971-62188990 Msa1169250:intron 30.0%
!! GGGAGTATTAATTTGTTTCT+TGG + chr7_4:62188995-62189014 Msa1169250:intron 30.0%
!! AAAACTTGCCTTTTGTTTCA+TGG - chr7_4:62189204-62189223 None:intergenic 30.0%
! AAAAAGAAGAAGGGGTTTTA+AGG - chr7_4:62188497-62188516 None:intergenic 30.0%
GGAAATGAAAAAAGAAGAAG+GGG - chr7_4:62188505-62188524 None:intergenic 30.0%
AAATTTGTGCATGTCATACA+TGG + chr7_4:62188615-62188634 Msa1169250:exon 30.0%
! ACAAACCTCTAGAGAAATAT+GGG - chr7_4:62188699-62188718 None:intergenic 30.0%
GAAAGAGGGTTTGTAAAATT+CGG - chr7_4:62188724-62188743 None:intergenic 30.0%
TTGTCTATTGTAAATAGGAC+CGG - chr7_4:62188863-62188882 None:intergenic 30.0%
GTCAACTTTCTCTTGTAAAT+AGG + chr7_4:62188966-62188985 Msa1169250:intron 30.0%
CTTTCTCTTGTAAATAGGAT+CGG + chr7_4:62188971-62188990 Msa1169250:intron 30.0%
!! GGGAGTATTAATTTGTTTCT+TGG + chr7_4:62188995-62189014 Msa1169250:intron 30.0%
!! AAAACTTGCCTTTTGTTTCA+TGG - chr7_4:62189204-62189223 None:intergenic 30.0%
TTCACGGAAGAAACATAACA+TGG - chr7_4:62188452-62188471 None:intergenic 35.0%
GACTAATGTATGCAAGTTCA+CGG - chr7_4:62188468-62188487 None:intergenic 35.0%
GATTTATAGGGTGGAAAGAA+AGG - chr7_4:62188526-62188545 None:intergenic 35.0%
TCATTGTGTGATTTATAGGG+TGG - chr7_4:62188535-62188554 None:intergenic 35.0%
GACATGCACAAATTTCTTGA+GGG - chr7_4:62188610-62188629 None:intergenic 35.0%
TGACATGCACAAATTTCTTG+AGG - chr7_4:62188611-62188630 None:intergenic 35.0%
! GACAAACCTCTAGAGAAATA+TGG - chr7_4:62188700-62188719 None:intergenic 35.0%
! TTTATGAGAGTGGTGGAAAT+TGG - chr7_4:62188746-62188765 None:intergenic 35.0%
TTCTACAATATTACTCCCTC+CGG + chr7_4:62188841-62188860 Msa1169250:intron 35.0%
TGATGCTACCATGAAACAAA+AGG + chr7_4:62189193-62189212 Msa1169250:CDS 35.0%
CAACTACTCATTATCATCAC+AGG + chr7_4:62189233-62189252 Msa1169250:CDS 35.0%
TCATTATCATCACAGGATCT+AGG + chr7_4:62189240-62189259 Msa1169250:CDS 35.0%
TTCACGGAAGAAACATAACA+TGG - chr7_4:62188452-62188471 None:intergenic 35.0%
GACTAATGTATGCAAGTTCA+CGG - chr7_4:62188468-62188487 None:intergenic 35.0%
GATTTATAGGGTGGAAAGAA+AGG - chr7_4:62188526-62188545 None:intergenic 35.0%
TCATTGTGTGATTTATAGGG+TGG - chr7_4:62188535-62188554 None:intergenic 35.0%
GACATGCACAAATTTCTTGA+GGG - chr7_4:62188610-62188629 None:intergenic 35.0%
TGACATGCACAAATTTCTTG+AGG - chr7_4:62188611-62188630 None:intergenic 35.0%
! GACAAACCTCTAGAGAAATA+TGG - chr7_4:62188700-62188719 None:intergenic 35.0%
! TTTATGAGAGTGGTGGAAAT+TGG - chr7_4:62188746-62188765 None:intergenic 35.0%
TTCTACAATATTACTCCCTC+CGG + chr7_4:62188841-62188860 Msa1169250:intron 35.0%
TGATGCTACCATGAAACAAA+AGG + chr7_4:62189193-62189212 Msa1169250:CDS 35.0%
CAACTACTCATTATCATCAC+AGG + chr7_4:62189233-62189252 Msa1169250:CDS 35.0%
TCATTATCATCACAGGATCT+AGG + chr7_4:62189240-62189259 Msa1169250:CDS 35.0%
!!! AAGAAGGGGTTTTAAGGAGT+GGG - chr7_4:62188491-62188510 None:intergenic 40.0%
GAAACAATTGGCGATGAAGA+TGG - chr7_4:62188653-62188672 None:intergenic 40.0%
ACTCTCCCATATTTCTCTAG+AGG + chr7_4:62188691-62188710 Msa1169250:CDS 40.0%
! AGTGGTGGAAATTGGAAAGA+GGG - chr7_4:62188738-62188757 None:intergenic 40.0%
CTATTGTAAATAGGACCGGA+GGG - chr7_4:62188859-62188878 None:intergenic 40.0%
TCTATTGTAAATAGGACCGG+AGG - chr7_4:62188860-62188879 None:intergenic 40.0%
TCTCTTGTAAATAGGATCGG+AGG + chr7_4:62188974-62188993 Msa1169250:intron 40.0%
CTCTTGTAAATAGGATCGGA+GGG + chr7_4:62188975-62188994 Msa1169250:intron 40.0%
!!! AAGAAGGGGTTTTAAGGAGT+GGG - chr7_4:62188491-62188510 None:intergenic 40.0%
GAAACAATTGGCGATGAAGA+TGG - chr7_4:62188653-62188672 None:intergenic 40.0%
ACTCTCCCATATTTCTCTAG+AGG + chr7_4:62188691-62188710 Msa1169250:CDS 40.0%
! AGTGGTGGAAATTGGAAAGA+GGG - chr7_4:62188738-62188757 None:intergenic 40.0%
CTATTGTAAATAGGACCGGA+GGG - chr7_4:62188859-62188878 None:intergenic 40.0%
TCTATTGTAAATAGGACCGG+AGG - chr7_4:62188860-62188879 None:intergenic 40.0%
TCTCTTGTAAATAGGATCGG+AGG + chr7_4:62188974-62188993 Msa1169250:intron 40.0%
CTCTTGTAAATAGGATCGGA+GGG + chr7_4:62188975-62188994 Msa1169250:intron 40.0%
!!! AGAAGGGGTTTTAAGGAGTG+GGG - chr7_4:62188490-62188509 None:intergenic 45.0%
!!! GAAGAAGGGGTTTTAAGGAG+TGG - chr7_4:62188492-62188511 None:intergenic 45.0%
CAATTGGCGATGAAGATGGA+GGG - chr7_4:62188649-62188668 None:intergenic 45.0%
ACAATTGGCGATGAAGATGG+AGG - chr7_4:62188650-62188669 None:intergenic 45.0%
! GAGTGGTGGAAATTGGAAAG+AGG - chr7_4:62188739-62188758 None:intergenic 45.0%
! TTTAGGTGGATCGGAAGCAT+TGG + chr7_4:62189034-62189053 Msa1169250:intron 45.0%
TTACCATGGGAATGATCAGG+TGG - chr7_4:62189116-62189135 None:intergenic 45.0%
AGCTGAATGAGGCTTACCAT+GGG - chr7_4:62189129-62189148 None:intergenic 45.0%
CTCTTGTCATGAGCTGAATG+AGG - chr7_4:62189140-62189159 None:intergenic 45.0%
!!! AGAAGGGGTTTTAAGGAGTG+GGG - chr7_4:62188490-62188509 None:intergenic 45.0%
!!! GAAGAAGGGGTTTTAAGGAG+TGG - chr7_4:62188492-62188511 None:intergenic 45.0%
CAATTGGCGATGAAGATGGA+GGG - chr7_4:62188649-62188668 None:intergenic 45.0%
ACAATTGGCGATGAAGATGG+AGG - chr7_4:62188650-62188669 None:intergenic 45.0%
! GAGTGGTGGAAATTGGAAAG+AGG - chr7_4:62188739-62188758 None:intergenic 45.0%
! TTTAGGTGGATCGGAAGCAT+TGG + chr7_4:62189034-62189053 Msa1169250:intron 45.0%
TTACCATGGGAATGATCAGG+TGG - chr7_4:62189116-62189135 None:intergenic 45.0%
AGCTGAATGAGGCTTACCAT+GGG - chr7_4:62189129-62189148 None:intergenic 45.0%
CTCTTGTCATGAGCTGAATG+AGG - chr7_4:62189140-62189159 None:intergenic 45.0%
GGCTTACCATGGGAATGATC+AGG - chr7_4:62189119-62189138 None:intergenic 50.0%
GAGCTGAATGAGGCTTACCA+TGG - chr7_4:62189130-62189149 None:intergenic 50.0%
TGCAGCTGCAACCAAAGCTA+CGG + chr7_4:62189166-62189185 Msa1169250:CDS 50.0%
AGCATCAACACCCGTAGCTT+TGG - chr7_4:62189180-62189199 None:intergenic 50.0%
GGCTTACCATGGGAATGATC+AGG - chr7_4:62189119-62189138 None:intergenic 50.0%
GAGCTGAATGAGGCTTACCA+TGG - chr7_4:62189130-62189149 None:intergenic 50.0%
TGCAGCTGCAACCAAAGCTA+CGG + chr7_4:62189166-62189185 Msa1169250:CDS 50.0%
AGCATCAACACCCGTAGCTT+TGG - chr7_4:62189180-62189199 None:intergenic 50.0%
GGCACAAACGAGTGAGTCTC+AGG - chr7_4:62189092-62189111 None:intergenic 55.0%
CCATGGGAATGATCAGGTGG+AGG - chr7_4:62189113-62189132 None:intergenic 55.0%
CCTCCACCTGATCATTCCCA+TGG + chr7_4:62189110-62189129 Msa1169250:CDS 55.0%
GCAGCTGCAACCAAAGCTAC+GGG + chr7_4:62189167-62189186 Msa1169250:CDS 55.0%
GGCACAAACGAGTGAGTCTC+AGG - chr7_4:62189092-62189111 None:intergenic 55.0%
CCATGGGAATGATCAGGTGG+AGG - chr7_4:62189113-62189132 None:intergenic 55.0%
CCTCCACCTGATCATTCCCA+TGG + chr7_4:62189110-62189129 Msa1169250:CDS 55.0%
GCAGCTGCAACCAAAGCTAC+GGG + chr7_4:62189167-62189186 Msa1169250:CDS 55.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 62188444 62189280 62188444 ID=Msa1169250;Name=Msa1169250
chr7_4 mRNA 62188444 62189280 62188444 ID=Msa1169250-mRNA-1;Parent=Msa1169250;Name=Msa1169250-mRNA-1;_AED=0.05;_eAED=0.18;_QI=181|0|0.5|1|0|0|2|0|101
chr7_4 exon 62188444 62188712 62188444 ID=Msa1169250-mRNA-1:exon:19707;Parent=Msa1169250-mRNA-1
chr7_4 exon 62189063 62189280 62189063 ID=Msa1169250-mRNA-1:exon:19708;Parent=Msa1169250-mRNA-1
chr7_4 five_prime_UTR 62188444 62188624 62188444 ID=Msa1169250-mRNA-1:five_prime_utr;Parent=Msa1169250-mRNA-1
chr7_4 CDS 62188625 62188712 62188625 ID=Msa1169250-mRNA-1:cds;Parent=Msa1169250-mRNA-1
chr7_4 CDS 62189063 62189280 62189063 ID=Msa1169250-mRNA-1:cds;Parent=Msa1169250-mRNA-1
Gene Sequence

>Msa1169250

ATGTCATACATGGATCTAAGACCCTCCATCTTCATCGCCAATTGTTTCTTTCTCTTTCTTATACTCACTCTCCCATATTTCTCTAGAGAAATTTATGAGATCGATTATAGAGGTCCTGAGACTCACTCGTTTGTGCCTCCACCTGATCATTCCCATGGTAAGCCTCATTCAGCTCATGACAAGAGCTCTACTGCAGCTGCAACCAAAGCTACGGGTGTTGATGCTACCATGAAACAAAAGGCAAGTTTTGAATTAAATCAACTACTCATTATCATCACAGGATCTAGGAAATTTTATTTCGTATAA

Protein sequence

>Msa1169250

MSYMDLRPSIFIANCFFLFLILTLPYFSREIYEIDYRGPETHSFVPPPDHSHGKPHSAHDKSSTAAATKATGVDATMKQKASFELNQLLIIITGSRKFYFV*