AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0100420

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0100420 MtrunA17_Chr3g0137181 100.000 51 0 0 36 86 1 51 9.40e-33 107
Msa0100420 MtrunA17_Chr1g0149761 100.000 51 0 0 36 86 1 51 9.40e-33 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0100420 AT4G31985.1 90.196 51 5 0 36 86 1 51 1.39e-29 100
Msa0100420 AT3G02190.1 88.235 51 6 0 36 86 1 51 3.59e-28 96.7
Msa0100420 AT2G25210.1 90.909 44 4 0 43 86 1 44 4.89e-24 85.9

Find 33 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCGATTTGATTTACCATTT+TGG 0.219156 1_3:+6893494 None:intergenic
TCTCCCATTTGAGCTGATTT+TGG 0.268648 1_3:-6892854 Msa0100420:three_prime_UTR
CCTTCTTCTTCGGCTGCGTC+TGG 0.331724 1_3:+6893535 None:intergenic
TTCACCAAAATCAGCTCAAA+TGG 0.361802 1_3:+6892850 None:intergenic
ACGGCGATACCAAACCCTAA+TGG 0.370707 1_3:+6893576 None:intergenic
AGAGGTCGAGTAACCCATTA+GGG 0.375345 1_3:-6893590 Msa0100420:CDS
TCTTCTTCTTCCTTCTTCTT+CGG 0.378925 1_3:+6893525 None:intergenic
CGGCGATACCAAACCCTAAT+GGG 0.392508 1_3:+6893577 None:intergenic
AATAAGTTGTTTACCTAGAC+AGG 0.400764 1_3:+6892809 None:intergenic
AGAAGAAGAAGCTGCCAAAA+TGG 0.401440 1_3:-6893508 Msa0100420:intron
GTTCTCATACGGATCCAATA+AGG 0.402869 1_3:+6893309 None:intergenic
AAGAGGTCGAGTAACCCATT+AGG 0.404554 1_3:-6893591 Msa0100420:CDS
AGAACAGACCCATCCCTTAT+TGG 0.418161 1_3:-6893323 Msa0100420:CDS
TCGAGTAACCCATTAGGGTT+TGG 0.465477 1_3:-6893585 Msa0100420:CDS
TTCTCATACGGATCCAATAA+GGG 0.468482 1_3:+6893310 None:intergenic
AATTAACCTGATGGTGTTGT+CGG 0.485237 1_3:+6893287 None:intergenic
TTAGGGTTTGGTATCGCCGT+TGG 0.497744 1_3:-6893573 Msa0100420:CDS
CACTGGCGTCGTACCAAGCT+CGG 0.498772 1_3:-6893154 Msa0100420:CDS
TTTGTTATAATAGCCTGTCT+AGG 0.502323 1_3:-6892822 Msa0100420:three_prime_UTR
TGAGAACCGACAACACCATC+AGG 0.505441 1_3:-6893293 Msa0100420:intron
TCACCAAAATCAGCTCAAAT+GGG 0.537404 1_3:+6892851 None:intergenic
AACACCTCAGAATCCGAGCT+TGG 0.538065 1_3:+6893141 None:intergenic
TGGTGTTGTCGGTTCTCATA+CGG 0.540409 1_3:+6893298 None:intergenic
ACAATGCTAAGCGTCGTCAC+TGG 0.548403 1_3:-6893171 Msa0100420:CDS
CCAGACGCAGCCGAAGAAGA+AGG 0.553197 1_3:-6893535 Msa0100420:CDS
CGTACCAAGCTCGGATTCTG+AGG 0.575484 1_3:-6893145 Msa0100420:exon
AGAAGCTCGCGAAGAAGATG+AGG 0.578712 1_3:-6893347 Msa0100420:CDS
CATACGGATCCAATAAGGGA+TGG 0.584103 1_3:+6893314 None:intergenic
ATGACGAATGTCTTGTGTGA+AGG 0.588940 1_3:+6893375 None:intergenic
ATACGGATCCAATAAGGGAT+GGG 0.595390 1_3:+6893315 None:intergenic
TCACTTAATAAAATAAAATG+TGG 0.623318 1_3:+6892985 None:intergenic
GAGATGAAATGCTGAACCAA+CGG 0.639403 1_3:+6893557 None:intergenic
TTGTTATGTAATGAAGTATG+CGG 0.687582 1_3:-6893017 Msa0100420:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGTTATTTCATTTGATTTT+AGG - chr1_3:6893240-6893259 Msa0100420:intron 15.0%
!! TCACTTAATAAAATAAAATG+TGG + chr1_3:6893453-6893472 None:intergenic 15.0%
!!! TTGTTATTTCATTTGATTTT+AGG - chr1_3:6893240-6893259 Msa0100420:intron 15.0%
!! TCACTTAATAAAATAAAATG+TGG + chr1_3:6893453-6893472 None:intergenic 15.0%
!!! TTCGATTTGATTTACCATTT+TGG + chr1_3:6892944-6892963 None:intergenic 25.0%
! ATAGAAAGAAATTAACCTGA+TGG + chr1_3:6893160-6893179 None:intergenic 25.0%
! TAATCGTGTTAAATCATGTT+TGG - chr1_3:6893205-6893224 Msa0100420:intron 25.0%
! TTGTTATGTAATGAAGTATG+CGG - chr1_3:6893418-6893437 Msa0100420:intron 25.0%
!! ATTTTGTTAGGTAGAATGAT+TGG - chr1_3:6893499-6893518 Msa0100420:intron 25.0%
!!! TTCGATTTGATTTACCATTT+TGG + chr1_3:6892944-6892963 None:intergenic 25.0%
! ATAGAAAGAAATTAACCTGA+TGG + chr1_3:6893160-6893179 None:intergenic 25.0%
! TAATCGTGTTAAATCATGTT+TGG - chr1_3:6893205-6893224 Msa0100420:intron 25.0%
! TTGTTATGTAATGAAGTATG+CGG - chr1_3:6893418-6893437 Msa0100420:intron 25.0%
!! ATTTTGTTAGGTAGAATGAT+TGG - chr1_3:6893499-6893518 Msa0100420:intron 25.0%
ATAACGAGAGCTATAAAAAG+AGG - chr1_3:6892827-6892846 Msa0100420:three_prime_UTR 30.0%
GAATTAGGAATAGGAATTAG+AGG + chr1_3:6892985-6893004 None:intergenic 30.0%
AGAATACTGGAATTAGGAAT+AGG + chr1_3:6892994-6893013 None:intergenic 30.0%
AGAAATTGAATCGAGAATAC+TGG + chr1_3:6893007-6893026 None:intergenic 30.0%
!!! TTCTGAGGTGTTTTAGTTTA+TGG - chr1_3:6893305-6893324 Msa0100420:CDS 30.0%
!!! TCTGAGGTGTTTTAGTTTAT+GGG - chr1_3:6893306-6893325 Msa0100420:CDS 30.0%
!!! GACAGTGAATTTTGTTGTTT+TGG - chr1_3:6893350-6893369 Msa0100420:CDS 30.0%
!!! CTCGTGATTTTGATTTTGTT+AGG - chr1_3:6893487-6893506 Msa0100420:intron 30.0%
! TTTGTTATAATAGCCTGTCT+AGG - chr1_3:6893613-6893632 Msa0100420:intron 30.0%
AATAAGTTGTTTACCTAGAC+AGG + chr1_3:6893629-6893648 None:intergenic 30.0%
ATAACGAGAGCTATAAAAAG+AGG - chr1_3:6892827-6892846 Msa0100420:three_prime_UTR 30.0%
GAATTAGGAATAGGAATTAG+AGG + chr1_3:6892985-6893004 None:intergenic 30.0%
AGAATACTGGAATTAGGAAT+AGG + chr1_3:6892994-6893013 None:intergenic 30.0%
AGAAATTGAATCGAGAATAC+TGG + chr1_3:6893007-6893026 None:intergenic 30.0%
!!! TTCTGAGGTGTTTTAGTTTA+TGG - chr1_3:6893305-6893324 Msa0100420:CDS 30.0%
!!! TCTGAGGTGTTTTAGTTTAT+GGG - chr1_3:6893306-6893325 Msa0100420:CDS 30.0%
!!! GACAGTGAATTTTGTTGTTT+TGG - chr1_3:6893350-6893369 Msa0100420:CDS 30.0%
!!! CTCGTGATTTTGATTTTGTT+AGG - chr1_3:6893487-6893506 Msa0100420:intron 30.0%
! TTTGTTATAATAGCCTGTCT+AGG - chr1_3:6893613-6893632 Msa0100420:intron 30.0%
AATAAGTTGTTTACCTAGAC+AGG + chr1_3:6893629-6893648 None:intergenic 30.0%
TCTTCTTCTTCCTTCTTCTT+CGG + chr1_3:6892913-6892932 None:intergenic 35.0%
GAATCGAGAATACTGGAATT+AGG + chr1_3:6893000-6893019 None:intergenic 35.0%
TTCTCATACGGATCCAATAA+GGG + chr1_3:6893128-6893147 None:intergenic 35.0%
!! AATTAACCTGATGGTGTTGT+CGG + chr1_3:6893151-6893170 None:intergenic 35.0%
TTAACAGTACAACGTTGTTG+TGG + chr1_3:6893188-6893207 None:intergenic 35.0%
TCACCAAAATCAGCTCAAAT+GGG + chr1_3:6893587-6893606 None:intergenic 35.0%
TTCACCAAAATCAGCTCAAA+TGG + chr1_3:6893588-6893607 None:intergenic 35.0%
TCTTCTTCTTCCTTCTTCTT+CGG + chr1_3:6892913-6892932 None:intergenic 35.0%
GAATCGAGAATACTGGAATT+AGG + chr1_3:6893000-6893019 None:intergenic 35.0%
TTCTCATACGGATCCAATAA+GGG + chr1_3:6893128-6893147 None:intergenic 35.0%
!! AATTAACCTGATGGTGTTGT+CGG + chr1_3:6893151-6893170 None:intergenic 35.0%
TTAACAGTACAACGTTGTTG+TGG + chr1_3:6893188-6893207 None:intergenic 35.0%
TCACCAAAATCAGCTCAAAT+GGG + chr1_3:6893587-6893606 None:intergenic 35.0%
TTCACCAAAATCAGCTCAAA+TGG + chr1_3:6893588-6893607 None:intergenic 35.0%
GAGATGAAATGCTGAACCAA+CGG + chr1_3:6892881-6892900 None:intergenic 40.0%
AGAAGAAGAAGCTGCCAAAA+TGG - chr1_3:6892927-6892946 Msa0100420:three_prime_UTR 40.0%
ATGACGAATGTCTTGTGTGA+AGG + chr1_3:6893063-6893082 None:intergenic 40.0%
ATACGGATCCAATAAGGGAT+GGG + chr1_3:6893123-6893142 None:intergenic 40.0%
GTTCTCATACGGATCCAATA+AGG + chr1_3:6893129-6893148 None:intergenic 40.0%
!! TCTCCCATTTGAGCTGATTT+TGG - chr1_3:6893581-6893600 Msa0100420:CDS 40.0%
GAGATGAAATGCTGAACCAA+CGG + chr1_3:6892881-6892900 None:intergenic 40.0%
AGAAGAAGAAGCTGCCAAAA+TGG - chr1_3:6892927-6892946 Msa0100420:three_prime_UTR 40.0%
ATGACGAATGTCTTGTGTGA+AGG + chr1_3:6893063-6893082 None:intergenic 40.0%
ATACGGATCCAATAAGGGAT+GGG + chr1_3:6893123-6893142 None:intergenic 40.0%
GTTCTCATACGGATCCAATA+AGG + chr1_3:6893129-6893148 None:intergenic 40.0%
!! TCTCCCATTTGAGCTGATTT+TGG - chr1_3:6893581-6893600 Msa0100420:CDS 40.0%
AAGAGGTCGAGTAACCCATT+AGG - chr1_3:6892844-6892863 Msa0100420:three_prime_UTR 45.0%
AGAGGTCGAGTAACCCATTA+GGG - chr1_3:6892845-6892864 Msa0100420:three_prime_UTR 45.0%
TCGAGTAACCCATTAGGGTT+TGG - chr1_3:6892850-6892869 Msa0100420:three_prime_UTR 45.0%
AGAACAGACCCATCCCTTAT+TGG - chr1_3:6893112-6893131 Msa0100420:three_prime_UTR 45.0%
CATACGGATCCAATAAGGGA+TGG + chr1_3:6893124-6893143 None:intergenic 45.0%
!! TGGTGTTGTCGGTTCTCATA+CGG + chr1_3:6893140-6893159 None:intergenic 45.0%
AAGAGGTCGAGTAACCCATT+AGG - chr1_3:6892844-6892863 Msa0100420:three_prime_UTR 45.0%
AGAGGTCGAGTAACCCATTA+GGG - chr1_3:6892845-6892864 Msa0100420:three_prime_UTR 45.0%
TCGAGTAACCCATTAGGGTT+TGG - chr1_3:6892850-6892869 Msa0100420:three_prime_UTR 45.0%
AGAACAGACCCATCCCTTAT+TGG - chr1_3:6893112-6893131 Msa0100420:three_prime_UTR 45.0%
CATACGGATCCAATAAGGGA+TGG + chr1_3:6893124-6893143 None:intergenic 45.0%
!! TGGTGTTGTCGGTTCTCATA+CGG + chr1_3:6893140-6893159 None:intergenic 45.0%
!!! TTTATTTTATTTTATTTTTG+AGG + chr1_3:6892802-6892821 None:intergenic 5.0%
!!! TTTATTTTATTTTATTTTTG+AGG + chr1_3:6892802-6892821 None:intergenic 5.0%
CGGCGATACCAAACCCTAAT+GGG + chr1_3:6892861-6892880 None:intergenic 50.0%
ACGGCGATACCAAACCCTAA+TGG + chr1_3:6892862-6892881 None:intergenic 50.0%
! TTAGGGTTTGGTATCGCCGT+TGG - chr1_3:6892862-6892881 Msa0100420:three_prime_UTR 50.0%
AGAAGCTCGCGAAGAAGATG+AGG - chr1_3:6893088-6893107 Msa0100420:three_prime_UTR 50.0%
TGAGAACCGACAACACCATC+AGG - chr1_3:6893142-6893161 Msa0100420:exon 50.0%
! ACAATGCTAAGCGTCGTCAC+TGG - chr1_3:6893264-6893283 Msa0100420:intron 50.0%
AACACCTCAGAATCCGAGCT+TGG + chr1_3:6893297-6893316 None:intergenic 50.0%
CGGCGATACCAAACCCTAAT+GGG + chr1_3:6892861-6892880 None:intergenic 50.0%
ACGGCGATACCAAACCCTAA+TGG + chr1_3:6892862-6892881 None:intergenic 50.0%
! TTAGGGTTTGGTATCGCCGT+TGG - chr1_3:6892862-6892881 Msa0100420:three_prime_UTR 50.0%
AGAAGCTCGCGAAGAAGATG+AGG - chr1_3:6893088-6893107 Msa0100420:three_prime_UTR 50.0%
TGAGAACCGACAACACCATC+AGG - chr1_3:6893142-6893161 Msa0100420:exon 50.0%
! ACAATGCTAAGCGTCGTCAC+TGG - chr1_3:6893264-6893283 Msa0100420:intron 50.0%
AACACCTCAGAATCCGAGCT+TGG + chr1_3:6893297-6893316 None:intergenic 50.0%
CGTACCAAGCTCGGATTCTG+AGG - chr1_3:6893290-6893309 Msa0100420:intron 55.0%
CGTACCAAGCTCGGATTCTG+AGG - chr1_3:6893290-6893309 Msa0100420:intron 55.0%
CCTTCTTCTTCGGCTGCGTC+TGG + chr1_3:6892903-6892922 None:intergenic 60.0%
CCAGACGCAGCCGAAGAAGA+AGG - chr1_3:6892900-6892919 Msa0100420:three_prime_UTR 60.0%
CACTGGCGTCGTACCAAGCT+CGG - chr1_3:6893281-6893300 Msa0100420:intron 60.0%
CCTTCTTCTTCGGCTGCGTC+TGG + chr1_3:6892903-6892922 None:intergenic 60.0%
CCAGACGCAGCCGAAGAAGA+AGG - chr1_3:6892900-6892919 Msa0100420:three_prime_UTR 60.0%
CACTGGCGTCGTACCAAGCT+CGG - chr1_3:6893281-6893300 Msa0100420:intron 60.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 6892787 6893670 6892787 ID=Msa0100420;Name=Msa0100420
chr1_3 mRNA 6892787 6893670 6892787 ID=Msa0100420-mRNA-1;Parent=Msa0100420;Name=Msa0100420-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0.66|0.5|0.75|1|0.75|4|360|86
chr1_3 exon 6892787 6893195 6892787 ID=Msa0100420-mRNA-1:exon:2639;Parent=Msa0100420-mRNA-1
chr1_3 exon 6893294 6893397 6893294 ID=Msa0100420-mRNA-1:exon:2638;Parent=Msa0100420-mRNA-1
chr1_3 exon 6893509 6893610 6893509 ID=Msa0100420-mRNA-1:exon:2637;Parent=Msa0100420-mRNA-1
chr1_3 exon 6893665 6893670 6893665 ID=Msa0100420-mRNA-1:exon:2636;Parent=Msa0100420-mRNA-1
chr1_3 CDS 6893665 6893670 6893665 ID=Msa0100420-mRNA-1:cds;Parent=Msa0100420-mRNA-1
chr1_3 CDS 6893509 6893610 6893509 ID=Msa0100420-mRNA-1:cds;Parent=Msa0100420-mRNA-1
chr1_3 CDS 6893294 6893397 6893294 ID=Msa0100420-mRNA-1:cds;Parent=Msa0100420-mRNA-1
chr1_3 CDS 6893147 6893195 6893147 ID=Msa0100420-mRNA-1:cds;Parent=Msa0100420-mRNA-1
chr1_3 three_prime_UTR 6892787 6893146 6892787 ID=Msa0100420-mRNA-1:three_prime_utr;Parent=Msa0100420-mRNA-1
Gene Sequence

>Msa0100420

ATGAGAAGGTCGAGTAACCCATTAGGGTTTGGTATCGCCGTTGGTTCAGCATTTCATCTCCAGACGCAGCCGAAGAAGAAGGAAGAAGAAGAAGAAGCTGCCAAAATGCCTTCACACAAGACATTCGTCATCAAGAAGAAGCTCGCGAAGAAGATGAGGCAGAACAGACCCATCCCTTATTGGATCCGTATGAGAACCGACAACACCATCAGGTACAATGCTAAGCGTCGTCACTGGCGTCGTACCAAGCTCGGATTCTGA
Protein sequence

>Msa0100420

MRRSSNPLGFGIAVGSAFHLQTQPKKKEEEEEAAKMPSHKTFVIKKKLAKKMRQNRPIPYWIRMRTDNTIRYNAKRRHWRRTKLGF*