AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0466340


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0466340 MtrunA17_Chr3g0119011 92.969 128 8 1 1 127 1 128 1.02e-82 238
Msa0466340 MtrunA17_Chr3g0118991 73.770 61 13 2 68 127 1 59 8.43e-23 84.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0466340 AT5G20935.1 79.012 81 17 0 45 125 37 117 4.46e-41 132
Msa0466340 AT5G20935.2 77.083 48 11 0 45 92 37 84 1.89e-19 77.4

Find 42 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAATGACACTGAAATATT+TGG 0.193807 3_3:+66903816 None:intergenic
CCTTGCCTCAGAGTTAATTC+TGG 0.251411 3_3:-66903669 Msa0466340:CDS
GATTTGTGGTTTCAATGTTT+TGG 0.261828 3_3:+66903946 None:intergenic
CGTACTGCCCACACATCTTT+TGG 0.272835 3_3:+66903212 None:intergenic
ACTATACTCAACCAGATCTA+AGG 0.289522 3_3:+66903145 None:intergenic
TGGAGCTTCGATGATAATAA+TGG 0.291436 3_3:+66903719 None:intergenic
AAACGTTCAAAGTTGGATAA+AGG 0.314200 3_3:-66903747 Msa0466340:CDS
ATTGGAACTTATCTTATTGA+TGG 0.358224 3_3:-66903182 Msa0466340:CDS
CCCAACCAGCAGGTGGCTCT+TGG 0.375234 3_3:-66903066 Msa0466340:three_prime_UTR
GTTGCAATGTTTCTGATTTG+TGG 0.375721 3_3:+66903932 None:intergenic
CCAAGAGCCACCTGCTGGTT+GGG 0.395859 3_3:+66903066 None:intergenic
TATGTGTGAGGAAGGATATT+AGG 0.413182 3_3:+66904022 None:intergenic
GGAGCTTCGATGATAATAAT+GGG 0.430762 3_3:+66903720 None:intergenic
AACGTTCAAAGTTGGATAAA+GGG 0.431347 3_3:-66903746 Msa0466340:CDS
ATATTTCAAGCCCTTAGATC+TGG 0.435238 3_3:-66903156 Msa0466340:CDS
ACACATACACTGCAAATGAT+TGG 0.445934 3_3:-66904006 Msa0466340:five_prime_UTR
ATATTTCAGTGTCATTAGTA+AGG 0.457947 3_3:-66903812 Msa0466340:CDS
CTGTTGTTGAACTTTAGAAA+TGG 0.461418 3_3:+66903861 None:intergenic
GCCAAGAGCCACCTGCTGGT+TGG 0.499573 3_3:+66903065 None:intergenic
ATGTCTTTGTCCCTTTCTTG+TGG 0.510900 3_3:-66903894 Msa0466340:CDS
CTTTGTGATACCACAAGAAA+GGG 0.530774 3_3:+66903884 None:intergenic
GCTTTGTGATACCACAAGAA+AGG 0.545899 3_3:+66903883 None:intergenic
CAAAAGATGTGTGGGCAGTA+CGG 0.550493 3_3:-66903211 Msa0466340:CDS
AATTCTGGCTTAGTCAAACC+TGG 0.553371 3_3:-66903654 Msa0466340:CDS
AGTCAAGCAAAATATTACAT+TGG 0.554810 3_3:-66903008 Msa0466340:three_prime_UTR
CAGAATTAACTCTGAGGCAA+GGG 0.557005 3_3:+66903670 None:intergenic
CTATACTCAACCAGATCTAA+GGG 0.566149 3_3:+66903146 None:intergenic
TGGGCAGTACGGCTCAACAT+TGG 0.579445 3_3:-66903200 Msa0466340:CDS
TCAAACCTGGTGATGTTGGA+AGG 0.583959 3_3:-66903641 Msa0466340:intron
AAGAAAGCCAAAAGATGTGT+GGG 0.587735 3_3:-66903219 Msa0466340:CDS
CCAGAATTAACTCTGAGGCA+AGG 0.590927 3_3:+66903669 None:intergenic
CAAGAAAGCCAAAAGATGTG+TGG 0.602135 3_3:-66903220 Msa0466340:CDS
TTAGTCAAACCTGGTGATGT+TGG 0.604419 3_3:-66903645 Msa0466340:CDS
AAATACCTTCCAACATCACC+AGG 0.606725 3_3:+66903636 None:intergenic
TTTGTTTCCCAACCAGCAGG+TGG 0.609564 3_3:-66903073 Msa0466340:three_prime_UTR
GTATGCCAAGAGCCACCTGC+TGG 0.623688 3_3:+66903061 None:intergenic
TTGCAGTGTATGTGTGAGGA+AGG 0.631311 3_3:+66904014 None:intergenic
TGAATCAAAAGAGTCATCAG+AGG 0.675313 3_3:-66903787 Msa0466340:CDS
CTAAGCCAGAATTAACTCTG+AGG 0.700737 3_3:+66903664 None:intergenic
ACAGCTTGAAGTATCAACAA+CGG 0.721755 3_3:-66903842 Msa0466340:CDS
TCATTTGCAGTGTATGTGTG+AGG 0.727329 3_3:+66904010 None:intergenic
GCTTGAAGTATCAACAACGG+AGG 0.739120 3_3:-66903839 Msa0466340:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGTATAAATGATTTAATT+TGG - chr3_3:66903600-66903619 Msa0466340:intron 10.0%
!! AATTAATATCATGTATAAAA+TGG - chr3_3:66903753-66903772 Msa0466340:CDS 10.0%
!! AATGTATAAATGATTTAATT+TGG - chr3_3:66903600-66903619 Msa0466340:intron 10.0%
!! AATTAATATCATGTATAAAA+TGG - chr3_3:66903753-66903772 Msa0466340:CDS 10.0%
!! GTAAATAATTATATATCACT+TGG - chr3_3:66903783-66903802 Msa0466340:CDS 15.0%
!! GTAAATAATTATATATCACT+TGG - chr3_3:66903783-66903802 Msa0466340:CDS 15.0%
!! AATGAAAAACTTAAAAGATG+AGG + chr3_3:66903431-66903450 None:intergenic 20.0%
!! GATTAGATACATAGTAAAAA+AGG + chr3_3:66903631-66903650 None:intergenic 20.0%
!! AATGAAAAACTTAAAAGATG+AGG + chr3_3:66903431-66903450 None:intergenic 20.0%
!! GATTAGATACATAGTAAAAA+AGG + chr3_3:66903631-66903650 None:intergenic 20.0%
!!! TTCAATGTTTTGGAATTTGT+TGG + chr3_3:66903086-66903105 None:intergenic 25.0%
! ACTAATGACACTGAAATATT+TGG + chr3_3:66903226-66903245 None:intergenic 25.0%
!! ATATTTCAGTGTCATTAGTA+AGG - chr3_3:66903227-66903246 Msa0466340:CDS 25.0%
!! TTACGTGTAGAAATTTTGTA+AGG - chr3_3:66903722-66903741 Msa0466340:CDS 25.0%
! TATCATGTATAAAATGGCAA+TGG - chr3_3:66903759-66903778 Msa0466340:CDS 25.0%
! ATTGGAACTTATCTTATTGA+TGG - chr3_3:66903857-66903876 Msa0466340:CDS 25.0%
! AGTCAAGCAAAATATTACAT+TGG - chr3_3:66904031-66904050 Msa0466340:five_prime_UTR 25.0%
!!! TTCAATGTTTTGGAATTTGT+TGG + chr3_3:66903086-66903105 None:intergenic 25.0%
! ACTAATGACACTGAAATATT+TGG + chr3_3:66903226-66903245 None:intergenic 25.0%
!! ATATTTCAGTGTCATTAGTA+AGG - chr3_3:66903227-66903246 Msa0466340:CDS 25.0%
!! TTACGTGTAGAAATTTTGTA+AGG - chr3_3:66903722-66903741 Msa0466340:CDS 25.0%
! TATCATGTATAAAATGGCAA+TGG - chr3_3:66903759-66903778 Msa0466340:CDS 25.0%
! ATTGGAACTTATCTTATTGA+TGG - chr3_3:66903857-66903876 Msa0466340:CDS 25.0%
! AGTCAAGCAAAATATTACAT+TGG - chr3_3:66904031-66904050 Msa0466340:five_prime_UTR 25.0%
!!! GTTTTGGAATTTGTTGGTTA+TGG + chr3_3:66903080-66903099 None:intergenic 30.0%
! GATTTGTGGTTTCAATGTTT+TGG + chr3_3:66903096-66903115 None:intergenic 30.0%
! CTGTTGTTGAACTTTAGAAA+TGG + chr3_3:66903181-66903200 None:intergenic 30.0%
AAACGTTCAAAGTTGGATAA+AGG - chr3_3:66903292-66903311 Msa0466340:intron 30.0%
AACGTTCAAAGTTGGATAAA+GGG - chr3_3:66903293-66903312 Msa0466340:intron 30.0%
CTTATCCCATTAAATTGGAT+CGG - chr3_3:66903542-66903561 Msa0466340:intron 30.0%
!!! GTTTTGGAATTTGTTGGTTA+TGG + chr3_3:66903080-66903099 None:intergenic 30.0%
! GATTTGTGGTTTCAATGTTT+TGG + chr3_3:66903096-66903115 None:intergenic 30.0%
! CTGTTGTTGAACTTTAGAAA+TGG + chr3_3:66903181-66903200 None:intergenic 30.0%
AAACGTTCAAAGTTGGATAA+AGG - chr3_3:66903292-66903311 Msa0466340:intron 30.0%
AACGTTCAAAGTTGGATAAA+GGG - chr3_3:66903293-66903312 Msa0466340:intron 30.0%
CTTATCCCATTAAATTGGAT+CGG - chr3_3:66903542-66903561 Msa0466340:intron 30.0%
TATGTGTGAGGAAGGATATT+AGG + chr3_3:66903020-66903039 None:intergenic 35.0%
ACACATACACTGCAAATGAT+TGG - chr3_3:66903033-66903052 Msa0466340:three_prime_UTR 35.0%
! GTTGCAATGTTTCTGATTTG+TGG + chr3_3:66903110-66903129 None:intergenic 35.0%
CTTTGTGATACCACAAGAAA+GGG + chr3_3:66903158-66903177 None:intergenic 35.0%
! ACAGCTTGAAGTATCAACAA+CGG - chr3_3:66903197-66903216 Msa0466340:CDS 35.0%
TGAATCAAAAGAGTCATCAG+AGG - chr3_3:66903252-66903271 Msa0466340:intron 35.0%
GCTTGAAAAACGTTCAAAGT+TGG - chr3_3:66903285-66903304 Msa0466340:intron 35.0%
GGAGCTTCGATGATAATAAT+GGG + chr3_3:66903322-66903341 None:intergenic 35.0%
TGGAGCTTCGATGATAATAA+TGG + chr3_3:66903323-66903342 None:intergenic 35.0%
CAATTTAATGGGATAAGGCT+TGG + chr3_3:66903539-66903558 None:intergenic 35.0%
! CAAGCCTTATCCCATTAAAT+TGG - chr3_3:66903537-66903556 Msa0466340:intron 35.0%
CGATCCAATTTAATGGGATA+AGG + chr3_3:66903544-66903563 None:intergenic 35.0%
TGTTGCCGATCCAATTTAAT+GGG + chr3_3:66903550-66903569 None:intergenic 35.0%
ATGTTGCCGATCCAATTTAA+TGG + chr3_3:66903551-66903570 None:intergenic 35.0%
AAGAAAGCCAAAAGATGTGT+GGG - chr3_3:66903820-66903839 Msa0466340:CDS 35.0%
ATATTTCAAGCCCTTAGATC+TGG - chr3_3:66903883-66903902 Msa0466340:CDS 35.0%
CTATACTCAACCAGATCTAA+GGG + chr3_3:66903896-66903915 None:intergenic 35.0%
ACTATACTCAACCAGATCTA+AGG + chr3_3:66903897-66903916 None:intergenic 35.0%
TATGTGTGAGGAAGGATATT+AGG + chr3_3:66903020-66903039 None:intergenic 35.0%
ACACATACACTGCAAATGAT+TGG - chr3_3:66903033-66903052 Msa0466340:three_prime_UTR 35.0%
! GTTGCAATGTTTCTGATTTG+TGG + chr3_3:66903110-66903129 None:intergenic 35.0%
CTTTGTGATACCACAAGAAA+GGG + chr3_3:66903158-66903177 None:intergenic 35.0%
! ACAGCTTGAAGTATCAACAA+CGG - chr3_3:66903197-66903216 Msa0466340:CDS 35.0%
TGAATCAAAAGAGTCATCAG+AGG - chr3_3:66903252-66903271 Msa0466340:intron 35.0%
GCTTGAAAAACGTTCAAAGT+TGG - chr3_3:66903285-66903304 Msa0466340:intron 35.0%
GGAGCTTCGATGATAATAAT+GGG + chr3_3:66903322-66903341 None:intergenic 35.0%
TGGAGCTTCGATGATAATAA+TGG + chr3_3:66903323-66903342 None:intergenic 35.0%
CAATTTAATGGGATAAGGCT+TGG + chr3_3:66903539-66903558 None:intergenic 35.0%
! CAAGCCTTATCCCATTAAAT+TGG - chr3_3:66903537-66903556 Msa0466340:intron 35.0%
CGATCCAATTTAATGGGATA+AGG + chr3_3:66903544-66903563 None:intergenic 35.0%
TGTTGCCGATCCAATTTAAT+GGG + chr3_3:66903550-66903569 None:intergenic 35.0%
ATGTTGCCGATCCAATTTAA+TGG + chr3_3:66903551-66903570 None:intergenic 35.0%
AAGAAAGCCAAAAGATGTGT+GGG - chr3_3:66903820-66903839 Msa0466340:CDS 35.0%
ATATTTCAAGCCCTTAGATC+TGG - chr3_3:66903883-66903902 Msa0466340:CDS 35.0%
CTATACTCAACCAGATCTAA+GGG + chr3_3:66903896-66903915 None:intergenic 35.0%
ACTATACTCAACCAGATCTA+AGG + chr3_3:66903897-66903916 None:intergenic 35.0%
TCATTTGCAGTGTATGTGTG+AGG + chr3_3:66903032-66903051 None:intergenic 40.0%
ATGTCTTTGTCCCTTTCTTG+TGG - chr3_3:66903145-66903164 Msa0466340:CDS 40.0%
GCTTTGTGATACCACAAGAA+AGG + chr3_3:66903159-66903178 None:intergenic 40.0%
!! GCTGCAGTTTTGATCATCTT+TGG + chr3_3:66903343-66903362 None:intergenic 40.0%
!! CAGAATTAACTCTGAGGCAA+GGG + chr3_3:66903372-66903391 None:intergenic 40.0%
CTAAGCCAGAATTAACTCTG+AGG + chr3_3:66903378-66903397 None:intergenic 40.0%
!! AATTCTGGCTTAGTCAAACC+TGG - chr3_3:66903385-66903404 Msa0466340:intron 40.0%
! TTAGTCAAACCTGGTGATGT+TGG - chr3_3:66903394-66903413 Msa0466340:intron 40.0%
AAATACCTTCCAACATCACC+AGG + chr3_3:66903406-66903425 None:intergenic 40.0%
CAAGAAAGCCAAAAGATGTG+TGG - chr3_3:66903819-66903838 Msa0466340:CDS 40.0%
!! ATTTTTGTTTCCCAACCAGC+AGG - chr3_3:66903963-66903982 Msa0466340:five_prime_UTR 40.0%
TCATTTGCAGTGTATGTGTG+AGG + chr3_3:66903032-66903051 None:intergenic 40.0%
ATGTCTTTGTCCCTTTCTTG+TGG - chr3_3:66903145-66903164 Msa0466340:CDS 40.0%
GCTTTGTGATACCACAAGAA+AGG + chr3_3:66903159-66903178 None:intergenic 40.0%
!! GCTGCAGTTTTGATCATCTT+TGG + chr3_3:66903343-66903362 None:intergenic 40.0%
!! CAGAATTAACTCTGAGGCAA+GGG + chr3_3:66903372-66903391 None:intergenic 40.0%
CTAAGCCAGAATTAACTCTG+AGG + chr3_3:66903378-66903397 None:intergenic 40.0%
!! AATTCTGGCTTAGTCAAACC+TGG - chr3_3:66903385-66903404 Msa0466340:intron 40.0%
! TTAGTCAAACCTGGTGATGT+TGG - chr3_3:66903394-66903413 Msa0466340:intron 40.0%
AAATACCTTCCAACATCACC+AGG + chr3_3:66903406-66903425 None:intergenic 40.0%
CAAGAAAGCCAAAAGATGTG+TGG - chr3_3:66903819-66903838 Msa0466340:CDS 40.0%
!! ATTTTTGTTTCCCAACCAGC+AGG - chr3_3:66903963-66903982 Msa0466340:five_prime_UTR 40.0%
TTGCAGTGTATGTGTGAGGA+AGG + chr3_3:66903028-66903047 None:intergenic 45.0%
! GCTTGAAGTATCAACAACGG+AGG - chr3_3:66903200-66903219 Msa0466340:CDS 45.0%
!! CCAGAATTAACTCTGAGGCA+AGG + chr3_3:66903373-66903392 None:intergenic 45.0%
CCTTGCCTCAGAGTTAATTC+TGG - chr3_3:66903370-66903389 Msa0466340:intron 45.0%
! TCAAACCTGGTGATGTTGGA+AGG - chr3_3:66903398-66903417 Msa0466340:intron 45.0%
CAAAAGATGTGTGGGCAGTA+CGG - chr3_3:66903828-66903847 Msa0466340:CDS 45.0%
TTGCAGTGTATGTGTGAGGA+AGG + chr3_3:66903028-66903047 None:intergenic 45.0%
! GCTTGAAGTATCAACAACGG+AGG - chr3_3:66903200-66903219 Msa0466340:CDS 45.0%
!! CCAGAATTAACTCTGAGGCA+AGG + chr3_3:66903373-66903392 None:intergenic 45.0%
CCTTGCCTCAGAGTTAATTC+TGG - chr3_3:66903370-66903389 Msa0466340:intron 45.0%
! TCAAACCTGGTGATGTTGGA+AGG - chr3_3:66903398-66903417 Msa0466340:intron 45.0%
CAAAAGATGTGTGGGCAGTA+CGG - chr3_3:66903828-66903847 Msa0466340:CDS 45.0%
! CGTACTGCCCACACATCTTT+TGG + chr3_3:66903830-66903849 None:intergenic 50.0%
TTTGTTTCCCAACCAGCAGG+TGG - chr3_3:66903966-66903985 Msa0466340:five_prime_UTR 50.0%
! CGTACTGCCCACACATCTTT+TGG + chr3_3:66903830-66903849 None:intergenic 50.0%
TTTGTTTCCCAACCAGCAGG+TGG - chr3_3:66903966-66903985 Msa0466340:five_prime_UTR 50.0%
TGGGCAGTACGGCTCAACAT+TGG - chr3_3:66903839-66903858 Msa0466340:CDS 55.0%
TGGGCAGTACGGCTCAACAT+TGG - chr3_3:66903839-66903858 Msa0466340:CDS 55.0%
! CCAAGAGCCACCTGCTGGTT+GGG + chr3_3:66903976-66903995 None:intergenic 60.0%
GTATGCCAAGAGCCACCTGC+TGG + chr3_3:66903981-66904000 None:intergenic 60.0%
! CCAAGAGCCACCTGCTGGTT+GGG + chr3_3:66903976-66903995 None:intergenic 60.0%
GTATGCCAAGAGCCACCTGC+TGG + chr3_3:66903981-66904000 None:intergenic 60.0%
CCCAACCAGCAGGTGGCTCT+TGG - chr3_3:66903973-66903992 Msa0466340:five_prime_UTR 65.0%
GCCAAGAGCCACCTGCTGGT+TGG + chr3_3:66903977-66903996 None:intergenic 65.0%
CCCAACCAGCAGGTGGCTCT+TGG - chr3_3:66903973-66903992 Msa0466340:five_prime_UTR 65.0%
GCCAAGAGCCACCTGCTGGT+TGG + chr3_3:66903977-66903996 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 66902955 66904106 66902955 ID=Msa0466340;Name=Msa0466340
chr3_3 mRNA 66902955 66904106 66902955 ID=Msa0466340-mRNA-1;Parent=Msa0466340;Name=Msa0466340-mRNA-1;_AED=0.00;_eAED=0.00;_QI=190|1|1|1|1|1|2|187|127
chr3_3 exon 66902955 66903250 66902955 ID=Msa0466340-mRNA-1:exon:15342;Parent=Msa0466340-mRNA-1
chr3_3 exon 66903642 66904106 66903642 ID=Msa0466340-mRNA-1:exon:15341;Parent=Msa0466340-mRNA-1
chr3_3 five_prime_UTR 66903917 66904106 66903917 ID=Msa0466340-mRNA-1:five_prime_utr;Parent=Msa0466340-mRNA-1
chr3_3 CDS 66903642 66903916 66903642 ID=Msa0466340-mRNA-1:cds;Parent=Msa0466340-mRNA-1
chr3_3 CDS 66903142 66903250 66903142 ID=Msa0466340-mRNA-1:cds;Parent=Msa0466340-mRNA-1
chr3_3 three_prime_UTR 66902955 66903141 66902955 ID=Msa0466340-mRNA-1:three_prime_utr;Parent=Msa0466340-mRNA-1
Gene Sequence

>Msa0466340

ATGTCTTTGTCCCTTTCTTGTGGTATCACAAAGCCATTTCTAAAGTTCAACAACAGCTTGAAGTATCAACAACGGAGGCCAAATATTTCAGTGTCATTAGTAAGGTGTGAATCAAAAGAGTCATCAGAGGAGAATGAGTTGCTTGAAAAACGTTCAAAGTTGGATAAAGGGTCTCCCATTATTATCATCGAAGCTCCAAAGATGATCAAAACTGCAGCTTCTGTCCCTTGCCTCAGAGTTAATTCTGGCTTAGTCAAACCTGGTGATGTTGGAAGAATTGTTTCAAGAAAGCCAAAAGATGTGTGGGCAGTACGGCTCAACATTGGAACTTATCTTATTGATGGCAAATATTTCAAGCCCTTAGATCTGGTTGAGTATAGTTAG

Protein sequence

>Msa0466340

MSLSLSCGITKPFLKFNNSLKYQQRRPNISVSLVRCESKESSEENELLEKRSKLDKGSPIIIIEAPKMIKTAASVPCLRVNSGLVKPGDVGRIVSRKPKDVWAVRLNIGTYLIDGKYFKPLDLVEYS*