AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0568610


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0568610 MtrunA17_Chr8g0383481 93.506 77 4 1 1 76 36 112 2.70e-48 148
Msa0568610 MtrunA17_Chr3g0129411 50.588 85 33 3 1 76 35 119 1.34e-19 75.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 34 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTGTCTGCCTAGAAAATA+TGG 0.191697 4_1:-70237869 None:intergenic
AAATATTTGTAGCTCCTTCT+AGG 0.236923 4_1:-70238004 None:intergenic
ACCTCTACTATACGTGTATT+TGG 0.243926 4_1:-70237791 None:intergenic
AAAATATGGGTATGTGCTAT+TGG 0.285709 4_1:-70237855 None:intergenic
ATCGGTGGCTTCCTTCTTGC+TGG 0.286574 4_1:-70238495 None:intergenic
TAAGGTAGATCATATGTTTA+AGG 0.311443 4_1:+70238422 Msa0568610:CDS
AAATATGGGTATGTGCTATT+GGG 0.333544 4_1:-70237854 None:intergenic
AATGAGTAATACTCATAATA+AGG 0.356818 4_1:+70238404 Msa0568610:CDS
GCATTAAACTTCGTGGCAAT+TGG 0.368027 4_1:+70237964 Msa0568610:five_prime_UTR
ATAGTAGAGGTTGACATTCA+TGG 0.371098 4_1:+70237803 Msa0568610:five_prime_UTR
AAAAGTCGAATTATTTAAGA+TGG 0.436642 4_1:+70238130 Msa0568610:exon
CCTCTACTATACGTGTATTT+GGG 0.444033 4_1:-70237790 None:intergenic
ACAATATTTCAATTGTGAAT+CGG 0.450645 4_1:-70238513 None:intergenic
TGCATAATACCACAATCATA+TGG 0.494409 4_1:+70237939 Msa0568610:five_prime_UTR
ATAACTTAATACCTCTAGCT+TGG 0.497100 4_1:-70238214 None:intergenic
TATGGTTGCATTAAACTTCG+TGG 0.508843 4_1:+70237957 Msa0568610:five_prime_UTR
TAACTTAATACCTCTAGCTT+GGG 0.523329 4_1:-70238213 None:intergenic
GAAGGAATAGAACCACTACT+AGG 0.529646 4_1:-70238175 None:intergenic
CTTGTCTGCCTAGAAAATAT+GGG 0.530731 4_1:-70237868 None:intergenic
AATATGGGTATGTGCTATTG+GGG 0.541039 4_1:-70237853 None:intergenic
GGCAAAAGAAGAACATAATG+TGG 0.544421 4_1:+70238443 Msa0568610:CDS
AAACAAACGTTTCCTAGTAG+TGG 0.554374 4_1:+70238163 Msa0568610:CDS
TGGGTATGTGCTATTGGGGA+AGG 0.558645 4_1:-70237849 None:intergenic
TGGTGCAGCACGAACTCTGA+AGG 0.582207 4_1:+70238365 Msa0568610:intron
GGGTATGTGCTATTGGGGAA+GGG 0.584361 4_1:-70237848 None:intergenic
ATATTTCAATTGTGAATCGG+TGG 0.587562 4_1:-70238510 None:intergenic
TTAATGCAACCATATGATTG+TGG 0.591100 4_1:-70237948 None:intergenic
CCCAAATACACGTATAGTAG+AGG 0.592182 4_1:+70237790 Msa0568610:five_prime_UTR
TGGATTACACTCCAGCAAGA+AGG 0.596499 4_1:+70238484 Msa0568610:CDS
GCAAAAGAAGAACATAATGT+GGG 0.604097 4_1:+70238444 Msa0568610:CDS
GGGTAGATATGAAACAGAGA+AGG 0.633587 4_1:-70238193 None:intergenic
TTCATATCTACCCAAGCTAG+AGG 0.668712 4_1:+70238203 Msa0568610:CDS
TGCACAATAAGAGAGAGTAA+TGG 0.674857 4_1:-70237920 None:intergenic
ATACATATTGATATGATACA+CGG 0.690316 4_1:+70238656 Msa0568610:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACAAATATTTTTCTATATA+AGG + chr4_1:70238016-70238035 Msa0568610:five_prime_UTR 10.0%
!!! ACAAATATTTTTCTATATAA+GGG + chr4_1:70238017-70238036 Msa0568610:five_prime_UTR 10.0%
!!! GATTATGATTTTATTAAAAA+AGG - chr4_1:70238294-70238313 None:intergenic 10.0%
!!! TACAAATATTTTTCTATATA+AGG + chr4_1:70238016-70238035 Msa0568610:five_prime_UTR 10.0%
!!! ACAAATATTTTTCTATATAA+GGG + chr4_1:70238017-70238036 Msa0568610:five_prime_UTR 10.0%
!!! GATTATGATTTTATTAAAAA+AGG - chr4_1:70238294-70238313 None:intergenic 10.0%
!! GATTATGTTCTTAATTATAT+TGG + chr4_1:70238242-70238261 Msa0568610:intron 15.0%
!! TCTAACATGATTTATATATA+TGG + chr4_1:70238345-70238364 Msa0568610:intron 15.0%
!! GATTATGTTCTTAATTATAT+TGG + chr4_1:70238242-70238261 Msa0568610:intron 15.0%
!! TCTAACATGATTTATATATA+TGG + chr4_1:70238345-70238364 Msa0568610:intron 15.0%
!! AAAAGTCGAATTATTTAAGA+TGG + chr4_1:70238130-70238149 Msa0568610:exon 20.0%
!! AATGAGTAATACTCATAATA+AGG + chr4_1:70238404-70238423 Msa0568610:CDS 20.0%
!! ACAATATTTCAATTGTGAAT+CGG - chr4_1:70238516-70238535 None:intergenic 20.0%
!! ATACATATTGATATGATACA+CGG + chr4_1:70238656-70238675 Msa0568610:three_prime_UTR 20.0%
!! AAAAGTCGAATTATTTAAGA+TGG + chr4_1:70238130-70238149 Msa0568610:exon 20.0%
!! AATGAGTAATACTCATAATA+AGG + chr4_1:70238404-70238423 Msa0568610:CDS 20.0%
!! ACAATATTTCAATTGTGAAT+CGG - chr4_1:70238516-70238535 None:intergenic 20.0%
!! ATACATATTGATATGATACA+CGG + chr4_1:70238656-70238675 Msa0568610:three_prime_UTR 20.0%
! TAAGGTAGATCATATGTTTA+AGG + chr4_1:70238422-70238441 Msa0568610:CDS 25.0%
! TAAGGTAGATCATATGTTTA+AGG + chr4_1:70238422-70238441 Msa0568610:CDS 25.0%
! AAATATGGGTATGTGCTATT+GGG - chr4_1:70237857-70237876 None:intergenic 30.0%
AAAATATGGGTATGTGCTAT+TGG - chr4_1:70237858-70237877 None:intergenic 30.0%
TGCATAATACCACAATCATA+TGG + chr4_1:70237939-70237958 Msa0568610:five_prime_UTR 30.0%
TTAATGCAACCATATGATTG+TGG - chr4_1:70237951-70237970 None:intergenic 30.0%
! CTAGTAATTTTCAACCTAGA+AGG + chr4_1:70237990-70238009 Msa0568610:five_prime_UTR 30.0%
AAATATTTGTAGCTCCTTCT+AGG - chr4_1:70238007-70238026 None:intergenic 30.0%
! TAACTTAATACCTCTAGCTT+GGG - chr4_1:70238216-70238235 None:intergenic 30.0%
ATAACTTAATACCTCTAGCT+TGG - chr4_1:70238217-70238236 None:intergenic 30.0%
GCAAAAGAAGAACATAATGT+GGG + chr4_1:70238444-70238463 Msa0568610:CDS 30.0%
ATATTTCAATTGTGAATCGG+TGG - chr4_1:70238513-70238532 None:intergenic 30.0%
! AAATATGGGTATGTGCTATT+GGG - chr4_1:70237857-70237876 None:intergenic 30.0%
AAAATATGGGTATGTGCTAT+TGG - chr4_1:70237858-70237877 None:intergenic 30.0%
TGCATAATACCACAATCATA+TGG + chr4_1:70237939-70237958 Msa0568610:five_prime_UTR 30.0%
TTAATGCAACCATATGATTG+TGG - chr4_1:70237951-70237970 None:intergenic 30.0%
! CTAGTAATTTTCAACCTAGA+AGG + chr4_1:70237990-70238009 Msa0568610:five_prime_UTR 30.0%
AAATATTTGTAGCTCCTTCT+AGG - chr4_1:70238007-70238026 None:intergenic 30.0%
! TAACTTAATACCTCTAGCTT+GGG - chr4_1:70238216-70238235 None:intergenic 30.0%
ATAACTTAATACCTCTAGCT+TGG - chr4_1:70238217-70238236 None:intergenic 30.0%
GCAAAAGAAGAACATAATGT+GGG + chr4_1:70238444-70238463 Msa0568610:CDS 30.0%
ATATTTCAATTGTGAATCGG+TGG - chr4_1:70238513-70238532 None:intergenic 30.0%
CCTCTACTATACGTGTATTT+GGG - chr4_1:70237793-70237812 None:intergenic 35.0%
ACCTCTACTATACGTGTATT+TGG - chr4_1:70237794-70237813 None:intergenic 35.0%
ATAGTAGAGGTTGACATTCA+TGG + chr4_1:70237803-70237822 Msa0568610:five_prime_UTR 35.0%
! AATATGGGTATGTGCTATTG+GGG - chr4_1:70237856-70237875 None:intergenic 35.0%
! AGCACATACCCATATTTTCT+AGG + chr4_1:70237860-70237879 Msa0568610:five_prime_UTR 35.0%
CTTGTCTGCCTAGAAAATAT+GGG - chr4_1:70237871-70237890 None:intergenic 35.0%
ACTTGTCTGCCTAGAAAATA+TGG - chr4_1:70237872-70237891 None:intergenic 35.0%
! TATTTTCTAGGCAGACAAGT+AGG + chr4_1:70237872-70237891 Msa0568610:five_prime_UTR 35.0%
TGCACAATAAGAGAGAGTAA+TGG - chr4_1:70237923-70237942 None:intergenic 35.0%
TATGGTTGCATTAAACTTCG+TGG + chr4_1:70237957-70237976 Msa0568610:five_prime_UTR 35.0%
AAACAAACGTTTCCTAGTAG+TGG + chr4_1:70238163-70238182 Msa0568610:CDS 35.0%
GGCAAAAGAAGAACATAATG+TGG + chr4_1:70238443-70238462 Msa0568610:CDS 35.0%
!! GGGAGATGAAGTATTTTCAA+TGG + chr4_1:70238464-70238483 Msa0568610:CDS 35.0%
CCTCTACTATACGTGTATTT+GGG - chr4_1:70237793-70237812 None:intergenic 35.0%
ACCTCTACTATACGTGTATT+TGG - chr4_1:70237794-70237813 None:intergenic 35.0%
ATAGTAGAGGTTGACATTCA+TGG + chr4_1:70237803-70237822 Msa0568610:five_prime_UTR 35.0%
! AATATGGGTATGTGCTATTG+GGG - chr4_1:70237856-70237875 None:intergenic 35.0%
! AGCACATACCCATATTTTCT+AGG + chr4_1:70237860-70237879 Msa0568610:five_prime_UTR 35.0%
CTTGTCTGCCTAGAAAATAT+GGG - chr4_1:70237871-70237890 None:intergenic 35.0%
ACTTGTCTGCCTAGAAAATA+TGG - chr4_1:70237872-70237891 None:intergenic 35.0%
! TATTTTCTAGGCAGACAAGT+AGG + chr4_1:70237872-70237891 Msa0568610:five_prime_UTR 35.0%
TGCACAATAAGAGAGAGTAA+TGG - chr4_1:70237923-70237942 None:intergenic 35.0%
TATGGTTGCATTAAACTTCG+TGG + chr4_1:70237957-70237976 Msa0568610:five_prime_UTR 35.0%
AAACAAACGTTTCCTAGTAG+TGG + chr4_1:70238163-70238182 Msa0568610:CDS 35.0%
GGCAAAAGAAGAACATAATG+TGG + chr4_1:70238443-70238462 Msa0568610:CDS 35.0%
!! GGGAGATGAAGTATTTTCAA+TGG + chr4_1:70238464-70238483 Msa0568610:CDS 35.0%
CCCAAATACACGTATAGTAG+AGG + chr4_1:70237790-70237809 Msa0568610:five_prime_UTR 40.0%
GCATTAAACTTCGTGGCAAT+TGG + chr4_1:70237964-70237983 Msa0568610:five_prime_UTR 40.0%
GAAGGAATAGAACCACTACT+AGG - chr4_1:70238178-70238197 None:intergenic 40.0%
GGGTAGATATGAAACAGAGA+AGG - chr4_1:70238196-70238215 None:intergenic 40.0%
TTCATATCTACCCAAGCTAG+AGG + chr4_1:70238203-70238222 Msa0568610:CDS 40.0%
CCCAAATACACGTATAGTAG+AGG + chr4_1:70237790-70237809 Msa0568610:five_prime_UTR 40.0%
GCATTAAACTTCGTGGCAAT+TGG + chr4_1:70237964-70237983 Msa0568610:five_prime_UTR 40.0%
GAAGGAATAGAACCACTACT+AGG - chr4_1:70238178-70238197 None:intergenic 40.0%
GGGTAGATATGAAACAGAGA+AGG - chr4_1:70238196-70238215 None:intergenic 40.0%
TTCATATCTACCCAAGCTAG+AGG + chr4_1:70238203-70238222 Msa0568610:CDS 40.0%
TGGATTACACTCCAGCAAGA+AGG + chr4_1:70238484-70238503 Msa0568610:CDS 45.0%
TGGATTACACTCCAGCAAGA+AGG + chr4_1:70238484-70238503 Msa0568610:CDS 45.0%
! GGGTATGTGCTATTGGGGAA+GGG - chr4_1:70237851-70237870 None:intergenic 50.0%
! TGGGTATGTGCTATTGGGGA+AGG - chr4_1:70237852-70237871 None:intergenic 50.0%
! GGGTATGTGCTATTGGGGAA+GGG - chr4_1:70237851-70237870 None:intergenic 50.0%
! TGGGTATGTGCTATTGGGGA+AGG - chr4_1:70237852-70237871 None:intergenic 50.0%
TGGTGCAGCACGAACTCTGA+AGG + chr4_1:70238365-70238384 Msa0568610:intron 55.0%
ATCGGTGGCTTCCTTCTTGC+TGG - chr4_1:70238498-70238517 None:intergenic 55.0%
TGGTGCAGCACGAACTCTGA+AGG + chr4_1:70238365-70238384 Msa0568610:intron 55.0%
ATCGGTGGCTTCCTTCTTGC+TGG - chr4_1:70238498-70238517 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 70237771 70238711 70237771 ID=Msa0568610;Name=Msa0568610
chr4_1 mRNA 70237771 70238711 70237771 ID=Msa0568610-mRNA-1;Parent=Msa0568610;Name=Msa0568610-mRNA-1;_AED=0.03;_eAED=0.03;_QI=378|1|1|1|1|1|2|184|76
chr4_1 exon 70237771 70238224 70237771 ID=Msa0568610-mRNA-1:exon:23623;Parent=Msa0568610-mRNA-1
chr4_1 exon 70238373 70238711 70238373 ID=Msa0568610-mRNA-1:exon:23624;Parent=Msa0568610-mRNA-1
chr4_1 five_prime_UTR 70237771 70238148 70237771 ID=Msa0568610-mRNA-1:five_prime_utr;Parent=Msa0568610-mRNA-1
chr4_1 CDS 70238149 70238224 70238149 ID=Msa0568610-mRNA-1:cds;Parent=Msa0568610-mRNA-1
chr4_1 CDS 70238373 70238527 70238373 ID=Msa0568610-mRNA-1:cds;Parent=Msa0568610-mRNA-1
chr4_1 three_prime_UTR 70238528 70238711 70238528 ID=Msa0568610-mRNA-1:three_prime_utr;Parent=Msa0568610-mRNA-1
Gene Sequence

>Msa0568610

ATGGCTATTGCACAAAACAAACGTTTCCTAGTAGTGGTTCTATTCCTTCTCTGTTTCATATCTACCCAAGCTAGAGCACGAACTCTGAAGGAAAAAAGCAATGATGTAATGAGTAATACTCATAATAAGGTAGATCATATGTTTAAGGCAAAAGAAGAACATAATGTGGGAGATGAAGTATTTTCAATGGATTACACTCCAGCAAGAAGGAAGCCACCGATTCACAATTGA

Protein sequence

>Msa0568610

MAIAQNKRFLVVVLFLLCFISTQARARTLKEKSNDVMSNTHNKVDHMFKAKEEHNVGDEVFSMDYTPARRKPPIHN*