AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1306200


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1306200 MtrunA17_Chr2g0317751 78.378 74 14 1 1 74 1 72 9.81e-38 120
Msa1306200 MtrunA17_Chr2g0317741 64.865 74 25 1 1 74 1 73 2.72e-23 84.0
Msa1306200 MtrunA17_Chr8g0385311 44.000 75 40 2 1 74 1 74 1.07e-12 57.0
Msa1306200 MtrunA17_Chr8g0337781 41.892 74 38 3 1 71 1 72 2.12e-12 56.2
Msa1306200 MtrunA17_Chr8g0337061 37.662 77 44 2 1 74 9 84 8.54e-11 52.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGCAAACACTTGTGAGAATT+TGG 0.253219 8_4:+986192 Msa1306200:CDS
GCCACTAACTAAATGCTCTT+TGG 0.345228 8_4:-986272 None:intergenic
CAAGCATGGATACATATATA+TGG 0.351007 8_4:+986362 Msa1306200:three_prime_UTR
GTGCACAAGAAACTGTTAAA+TGG 0.351514 8_4:+986321 Msa1306200:exon
ACCAAAGAGCATTTAGTTAG+TGG 0.385720 8_4:+986271 Msa1306200:CDS
ACATTCAAGGGACCATGTTT+CGG 0.416979 8_4:+986220 Msa1306200:CDS
TCATATTTATCATTAAGTTA+TGG 0.428066 8_4:+985473 Msa1306200:exon
ATTTAGTTAGTGGCAGGTGC+AGG 0.446134 8_4:+986281 Msa1306200:CDS
CAACAAAGAGAACGAGGAAG+AGG 0.464218 8_4:-985524 None:intergenic
AGAAACTGTTAAATGGATCA+TGG 0.482667 8_4:+986328 Msa1306200:exon
ATGGAGAAGAAATCATTAGT+TGG 0.488503 8_4:+985492 Msa1306200:CDS
GAATTTGGCTGGTACATTCA+AGG 0.488760 8_4:+986207 Msa1306200:CDS
AACACTTGTGAGAATTTGGC+TGG 0.492030 8_4:+986196 Msa1306200:CDS
ATATATGTATCCATGCTTGT+TGG 0.495303 8_4:-986358 None:intergenic
AAGAGCATTTAGTTAGTGGC+AGG 0.516402 8_4:+986275 Msa1306200:CDS
AATTTGGCTGGTACATTCAA+GGG 0.536130 8_4:+986208 Msa1306200:CDS
GCAGGGATGACTTTCGATGT+TGG 0.540207 8_4:+986299 Msa1306200:CDS
ATACGTTATGCACTATATTG+TGG 0.546559 8_4:-986484 None:intergenic
TTAAGTGTTTGTGTCTAGTG+TGG 0.553780 8_4:-985424 None:intergenic
CAGTTTGAGTTACCGAAACA+TGG 0.557423 8_4:-986232 None:intergenic
TTTAGTTAGTGGCAGGTGCA+GGG 0.572800 8_4:+986282 Msa1306200:CDS
TCTGAATGCAGAAGAAATTG+TGG 0.657378 8_4:+986162 Msa1306200:intron
AGAAGAAATTGTGGTGACTG+AGG 0.707441 8_4:+986171 Msa1306200:intron
TACGTGCAACAAAGAGAACG+AGG 0.716392 8_4:-985530 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATAAAAAATAATCAAATG+TGG + chr8_4:985837-985856 Msa1306200:intron 10.0%
!! TTATAAAAAATAATCAAATG+TGG + chr8_4:985837-985856 Msa1306200:intron 10.0%
!! TCATATTTATCATTAAGTTA+TGG + chr8_4:985473-985492 Msa1306200:exon 15.0%
!! ATATAATAATACACTAAGAA+TGG - chr8_4:985566-985585 None:intergenic 15.0%
!!! TGTTTTACGTTAATTTTTTT+AGG - chr8_4:985877-985896 None:intergenic 15.0%
!! TAATAATACAAATTGAACTT+TGG + chr8_4:985952-985971 Msa1306200:intron 15.0%
!! AAAAAAATACTTTCTAATAG+TGG - chr8_4:986006-986025 None:intergenic 15.0%
!! TCATATTTATCATTAAGTTA+TGG + chr8_4:985473-985492 Msa1306200:exon 15.0%
!! ATATAATAATACACTAAGAA+TGG - chr8_4:985566-985585 None:intergenic 15.0%
!!! TGTTTTACGTTAATTTTTTT+AGG - chr8_4:985877-985896 None:intergenic 15.0%
!! TAATAATACAAATTGAACTT+TGG + chr8_4:985952-985971 Msa1306200:intron 15.0%
!! AAAAAAATACTTTCTAATAG+TGG - chr8_4:986006-986025 None:intergenic 15.0%
!!! TATCTTTGATTTTGTTTCCA+AGG + chr8_4:985662-985681 Msa1306200:intron 25.0%
!!! TGTATAATTTTGATGTCTTG+TGG - chr8_4:985718-985737 None:intergenic 25.0%
! TACCTAAATGTTCGAAAAAT+GGG - chr8_4:986561-986580 None:intergenic 25.0%
!!! TATCTTTGATTTTGTTTCCA+AGG + chr8_4:985662-985681 Msa1306200:intron 25.0%
!!! TGTATAATTTTGATGTCTTG+TGG - chr8_4:985718-985737 None:intergenic 25.0%
! TACCTAAATGTTCGAAAAAT+GGG - chr8_4:986561-986580 None:intergenic 25.0%
ATGGAGAAGAAATCATTAGT+TGG + chr8_4:985492-985511 Msa1306200:CDS 30.0%
AAATTGAACTTTGGATAGCA+TGG + chr8_4:985961-985980 Msa1306200:intron 30.0%
AATTGAACTTTGGATAGCAT+GGG + chr8_4:985962-985981 Msa1306200:intron 30.0%
AGAAACTGTTAAATGGATCA+TGG + chr8_4:986328-986347 Msa1306200:exon 30.0%
ATATATGTATCCATGCTTGT+TGG - chr8_4:986361-986380 None:intergenic 30.0%
CAAGCATGGATACATATATA+TGG + chr8_4:986362-986381 Msa1306200:three_prime_UTR 30.0%
ATACGTTATGCACTATATTG+TGG - chr8_4:986487-986506 None:intergenic 30.0%
!! ATCCCATTTTTCGAACATTT+AGG + chr8_4:986556-986575 Msa1306200:three_prime_UTR 30.0%
GTACCTAAATGTTCGAAAAA+TGG - chr8_4:986562-986581 None:intergenic 30.0%
ATGGAGAAGAAATCATTAGT+TGG + chr8_4:985492-985511 Msa1306200:CDS 30.0%
AAATTGAACTTTGGATAGCA+TGG + chr8_4:985961-985980 Msa1306200:intron 30.0%
AATTGAACTTTGGATAGCAT+GGG + chr8_4:985962-985981 Msa1306200:intron 30.0%
AGAAACTGTTAAATGGATCA+TGG + chr8_4:986328-986347 Msa1306200:exon 30.0%
ATATATGTATCCATGCTTGT+TGG - chr8_4:986361-986380 None:intergenic 30.0%
CAAGCATGGATACATATATA+TGG + chr8_4:986362-986381 Msa1306200:three_prime_UTR 30.0%
ATACGTTATGCACTATATTG+TGG - chr8_4:986487-986506 None:intergenic 30.0%
!! ATCCCATTTTTCGAACATTT+AGG + chr8_4:986556-986575 Msa1306200:three_prime_UTR 30.0%
GTACCTAAATGTTCGAAAAA+TGG - chr8_4:986562-986581 None:intergenic 30.0%
TTAAGTGTTTGTGTCTAGTG+TGG - chr8_4:985427-985446 None:intergenic 35.0%
TCTGAATGCAGAAGAAATTG+TGG + chr8_4:986162-986181 Msa1306200:intron 35.0%
AATTTGGCTGGTACATTCAA+GGG + chr8_4:986208-986227 Msa1306200:CDS 35.0%
!! ACCAAAGAGCATTTAGTTAG+TGG + chr8_4:986271-986290 Msa1306200:CDS 35.0%
GTGCACAAGAAACTGTTAAA+TGG + chr8_4:986321-986340 Msa1306200:exon 35.0%
TTAAGTGTTTGTGTCTAGTG+TGG - chr8_4:985427-985446 None:intergenic 35.0%
TCTGAATGCAGAAGAAATTG+TGG + chr8_4:986162-986181 Msa1306200:intron 35.0%
AATTTGGCTGGTACATTCAA+GGG + chr8_4:986208-986227 Msa1306200:CDS 35.0%
!! ACCAAAGAGCATTTAGTTAG+TGG + chr8_4:986271-986290 Msa1306200:CDS 35.0%
GTGCACAAGAAACTGTTAAA+TGG + chr8_4:986321-986340 Msa1306200:exon 35.0%
AGAAGAAATTGTGGTGACTG+AGG + chr8_4:986171-986190 Msa1306200:intron 40.0%
GGCAAACACTTGTGAGAATT+TGG + chr8_4:986192-986211 Msa1306200:CDS 40.0%
AACACTTGTGAGAATTTGGC+TGG + chr8_4:986196-986215 Msa1306200:CDS 40.0%
GAATTTGGCTGGTACATTCA+AGG + chr8_4:986207-986226 Msa1306200:CDS 40.0%
ACATTCAAGGGACCATGTTT+CGG + chr8_4:986220-986239 Msa1306200:CDS 40.0%
! CAGTTTGAGTTACCGAAACA+TGG - chr8_4:986235-986254 None:intergenic 40.0%
GCCACTAACTAAATGCTCTT+TGG - chr8_4:986275-986294 None:intergenic 40.0%
!! AAGAGCATTTAGTTAGTGGC+AGG + chr8_4:986275-986294 Msa1306200:CDS 40.0%
! TGGATTTTCTCCAACAAGCA+TGG + chr8_4:986348-986367 Msa1306200:three_prime_UTR 40.0%
AGAAGAAATTGTGGTGACTG+AGG + chr8_4:986171-986190 Msa1306200:intron 40.0%
GGCAAACACTTGTGAGAATT+TGG + chr8_4:986192-986211 Msa1306200:CDS 40.0%
AACACTTGTGAGAATTTGGC+TGG + chr8_4:986196-986215 Msa1306200:CDS 40.0%
GAATTTGGCTGGTACATTCA+AGG + chr8_4:986207-986226 Msa1306200:CDS 40.0%
ACATTCAAGGGACCATGTTT+CGG + chr8_4:986220-986239 Msa1306200:CDS 40.0%
! CAGTTTGAGTTACCGAAACA+TGG - chr8_4:986235-986254 None:intergenic 40.0%
GCCACTAACTAAATGCTCTT+TGG - chr8_4:986275-986294 None:intergenic 40.0%
!! AAGAGCATTTAGTTAGTGGC+AGG + chr8_4:986275-986294 Msa1306200:CDS 40.0%
! TGGATTTTCTCCAACAAGCA+TGG + chr8_4:986348-986367 Msa1306200:three_prime_UTR 40.0%
CAACAAAGAGAACGAGGAAG+AGG - chr8_4:985527-985546 None:intergenic 45.0%
TACGTGCAACAAAGAGAACG+AGG - chr8_4:985533-985552 None:intergenic 45.0%
CGCATGATGTCTTTAAGCCT+TGG - chr8_4:985682-985701 None:intergenic 45.0%
ATTTAGTTAGTGGCAGGTGC+AGG + chr8_4:986281-986300 Msa1306200:CDS 45.0%
TTTAGTTAGTGGCAGGTGCA+GGG + chr8_4:986282-986301 Msa1306200:CDS 45.0%
CAACAAAGAGAACGAGGAAG+AGG - chr8_4:985527-985546 None:intergenic 45.0%
TACGTGCAACAAAGAGAACG+AGG - chr8_4:985533-985552 None:intergenic 45.0%
CGCATGATGTCTTTAAGCCT+TGG - chr8_4:985682-985701 None:intergenic 45.0%
ATTTAGTTAGTGGCAGGTGC+AGG + chr8_4:986281-986300 Msa1306200:CDS 45.0%
TTTAGTTAGTGGCAGGTGCA+GGG + chr8_4:986282-986301 Msa1306200:CDS 45.0%
!!! ACTTTAATTTTTTTTAATAA+TGG + chr8_4:985759-985778 Msa1306200:intron 5.0%
!!! ACTTTAATTTTTTTTAATAA+TGG + chr8_4:985759-985778 Msa1306200:intron 5.0%
GCAGGGATGACTTTCGATGT+TGG + chr8_4:986299-986318 Msa1306200:CDS 50.0%
GCAGGGATGACTTTCGATGT+TGG + chr8_4:986299-986318 Msa1306200:CDS 50.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 985417 986583 985417 ID=Msa1306200;Name=Msa1306200
chr8_4 mRNA 985417 986583 985417 ID=Msa1306200-mRNA-1;Parent=Msa1306200;Name=Msa1306200-mRNA-1;_AED=0.27;_eAED=0.27;_QI=75|1|1|1|0|0|2|244|74
chr8_4 exon 985417 985549 985417 ID=Msa1306200-mRNA-1:exon:164;Parent=Msa1306200-mRNA-1
chr8_4 exon 986173 986583 986173 ID=Msa1306200-mRNA-1:exon:165;Parent=Msa1306200-mRNA-1
chr8_4 five_prime_UTR 985417 985491 985417 ID=Msa1306200-mRNA-1:five_prime_utr;Parent=Msa1306200-mRNA-1
chr8_4 CDS 985492 985549 985492 ID=Msa1306200-mRNA-1:cds;Parent=Msa1306200-mRNA-1
chr8_4 CDS 986173 986339 986173 ID=Msa1306200-mRNA-1:cds;Parent=Msa1306200-mRNA-1
chr8_4 three_prime_UTR 986340 986583 986340 ID=Msa1306200-mRNA-1:three_prime_utr;Parent=Msa1306200-mRNA-1
Gene Sequence

>Msa1306200

ATGGAGAAGAAATCATTAGTTGGCATGTGCTTCCTCTTCCTCGTTCTCTTTGTTGCACAAGAAATTGTGGTGACTGAGGCAAACACTTGTGAGAATTTGGCTGGTACATTCAAGGGACCATGTTTCGGTAACTCAAACTGTGACTTTCACTGCAGAACCAAAGAGCATTTAGTTAGTGGCAGGTGCAGGGATGACTTTCGATGTTGGTGCACAAGAAACTGTTAA

Protein sequence

>Msa1306200

MEKKSLVGMCFLFLVLFVAQEIVVTEANTCENLAGTFKGPCFGNSNCDFHCRTKEHLVSGRCRDDFRCWCTRNC*