AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0371420


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0371420 MtrunA17_Chr3g0118181 100.000 90 0 0 1 90 1 90 2.03e-63 186
Msa0371420 MtrunA17_Chr3g0122981 69.318 88 27 0 1 88 1 88 1.31e-43 136
Msa0371420 MtrunA17_Chr7g0219981 51.220 82 40 0 5 86 3 84 2.74e-29 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0371420 AT3G48140.1 74.118 85 22 0 4 88 3 87 1.32e-44 139
Msa0371420 AT3G29970.1 51.220 82 40 0 5 86 3 84 8.38e-30 101
Msa0371420 AT3G29970.2 47.059 68 36 0 18 85 1 68 2.33e-20 77.4
Msa0371420 AT3G29970.3 47.059 68 36 0 18 85 1 68 2.33e-20 77.4

Find 49 sgRNAs with CRISPR-Local

Find 107 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTATTATTGTCATGCATTT+AGG 0.207950 3_1:-69568178 Msa0371420:three_prime_UTR
AAGTCGCAACTAAGTTGTTT+TGG 0.340325 3_1:-69568258 Msa0371420:exon
AAACATCAGTACCTGACTTC+AGG 0.347160 3_1:+69569291 None:intergenic
CCACAGCATACACGCTGTTC+AGG 0.369876 3_1:+69568129 None:intergenic
AAAGTTACTTCTAGGGAAAC+TGG 0.375628 3_1:-69567993 Msa0371420:three_prime_UTR
CAACAATTAACGCAACAAAC+AGG 0.381334 3_1:+69568090 None:intergenic
CTCTTCAACCTTGATGATCT+AGG 0.393617 3_1:+69568028 None:intergenic
TACCCTCTGTTTGCTGCGGT+TGG 0.396092 3_1:-69569366 Msa0371420:CDS
CTGCGGTTGGAGCTGCTGTT+GGG 0.406881 3_1:-69569353 Msa0371420:CDS
GCTGCGGTTGGAGCTGCTGT+TGG 0.426937 3_1:-69569354 Msa0371420:CDS
TATAAATTTGTTCGGTGTGC+CGG 0.440486 3_1:-69568058 Msa0371420:three_prime_UTR
GCAGACATGCTTGTTAAAAC+TGG 0.453798 3_1:-69567934 Msa0371420:three_prime_UTR
GTTGAGGCCGGGCATAATCT+CGG 0.455438 3_1:+69568298 None:intergenic
AACATCAGTACCTGACTTCA+GGG 0.462667 3_1:+69569292 None:intergenic
AACAAGCAGTCTCGAGCTGC+AGG 0.464020 3_1:-69568395 Msa0371420:CDS
AGTGAAGAAGCTGTTGAGGC+CGG 0.469984 3_1:+69568286 None:intergenic
ATAAATTTGTGATGTTGTCT+AGG 0.477019 3_1:-69567962 Msa0371420:three_prime_UTR
TTTCAACAAAGTTACTTCTA+GGG 0.478418 3_1:-69568000 Msa0371420:three_prime_UTR
TTGAGGCCGGGCATAATCTC+GGG 0.481836 3_1:+69568299 None:intergenic
GTCTCGAGCTGCAGGAGTGT+TGG 0.483795 3_1:-69568387 Msa0371420:CDS
GATTGCAATTTGCAATGGAA+TGG 0.501934 3_1:+69569553 None:intergenic
AATTTGCAATGGAATGGAAA+TGG 0.511319 3_1:+69569559 None:intergenic
GGGTCTGATCCAGCGATTGG+TGG 0.513757 3_1:+69569480 None:intergenic
TTCTGTGTACTTCTCTCCCT+CGG 0.519035 3_1:+69568355 None:intergenic
CTCGGGTCTGATCCAGCGAT+TGG 0.519677 3_1:+69569477 None:intergenic
GTGAAGAAGCTGTTGAGGCC+GGG 0.521542 3_1:+69568287 None:intergenic
TATCCATGGCCACCAATCGC+TGG 0.522115 3_1:-69569489 Msa0371420:exon
AAAACAACTTAGTTGCGACT+TGG 0.523588 3_1:+69568260 None:intergenic
TCTGCATCAACCCTGAAGTC+AGG 0.524860 3_1:-69569302 Msa0371420:intron
AAACAACTTAGTTGCGACTT+GGG 0.529015 3_1:+69568261 None:intergenic
AAGATGATTGCAATTTGCAA+TGG 0.529414 3_1:+69569548 None:intergenic
AGATCACCCGAGATTATGCC+CGG 0.535231 3_1:-69568305 Msa0371420:CDS
GATGTTACGAACAAGTGAAA+AGG 0.535731 3_1:+69569323 None:intergenic
TCTCTGAGAGAGAAAGAGAA+TGG 0.541987 3_1:+69569582 None:intergenic
TCTTCTTCAACTGCTATCCA+TGG 0.546319 3_1:-69569503 Msa0371420:exon
TGATGATCTAGGTTCGATAC+CGG 0.576141 3_1:+69568039 None:intergenic
GATCCAGCGATTGGTGGCCA+TGG 0.584846 3_1:+69569486 None:intergenic
CTGAGAGAGAAAGAGAATGG+AGG 0.609358 3_1:+69569585 None:intergenic
CTCCAACCGCAGCAAACAGA+GGG 0.612181 3_1:+69569364 None:intergenic
GTGTTGGAGAACTTTGCCGA+GGG 0.614956 3_1:-69568371 Msa0371420:CDS
AACAATTAACGCAACAAACA+GGG 0.625184 3_1:+69568091 None:intergenic
GGTATACCCTCTGTTTGCTG+CGG 0.632424 3_1:-69569370 Msa0371420:CDS
CCTGAACAGCGTGTATGCTG+TGG 0.641592 3_1:-69568129 Msa0371420:three_prime_UTR
AGTGTTGGAGAACTTTGCCG+AGG 0.642190 3_1:-69568372 Msa0371420:CDS
GGTCAGTGAAGAAGCTGTTG+AGG 0.648101 3_1:+69568282 None:intergenic
GCTCCAACCGCAGCAAACAG+AGG 0.651727 3_1:+69569363 None:intergenic
GTATCGAACCTAGATCATCA+AGG 0.676860 3_1:-69568036 Msa0371420:three_prime_UTR
CAATCGCTGGATCAGACCCG+AGG 0.698764 3_1:-69569476 Msa0371420:intron
AGTACACAGAACATTTGCTG+AGG 0.706764 3_1:-69568343 Msa0371420:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAGATATTAACAAAATTTAA+TGG - chr3_1:69568391-69568410 Msa0371420:CDS 10.0%
!! AGATATTAACAAAATTTAAT+GGG - chr3_1:69568392-69568411 Msa0371420:CDS 10.0%
!!! ATAAAAATTTTCATTTTCAA+TGG + chr3_1:69568922-69568941 None:intergenic 10.0%
!!! GAATATTCCTTTTTTATTTT+TGG - chr3_1:69568312-69568331 Msa0371420:CDS 15.0%
!! TTAATCTCTAATATCAAATA+GGG + chr3_1:69568645-69568664 None:intergenic 15.0%
!! ATTAATCTCTAATATCAAAT+AGG + chr3_1:69568646-69568665 None:intergenic 15.0%
!!! AGAGATTAATTTTTATTCAT+TGG - chr3_1:69568656-69568675 Msa0371420:intron 15.0%
!!! GAAAATGAAAATTTTTATCT+CGG - chr3_1:69568924-69568943 Msa0371420:intron 15.0%
!!! TGTAGTTTTATAAATTTGTT+CGG - chr3_1:69569379-69569398 Msa0371420:intron 15.0%
!! AAGAAGATAACAAAAACAAA+GGG + chr3_1:69567926-69567945 None:intergenic 20.0%
!! TATACCTATAACAAAAAAGA+TGG + chr3_1:69568061-69568080 None:intergenic 20.0%
!! CTAATCGGATAATTAATTAA+TGG + chr3_1:69568281-69568300 None:intergenic 20.0%
!! AGGAAAACCAAAAATAAAAA+AGG + chr3_1:69568322-69568341 None:intergenic 20.0%
!! ACAAATTGTGAAAATTTAAG+CGG + chr3_1:69568368-69568387 None:intergenic 20.0%
!! GATACATGAGTTATTTAATT+TGG + chr3_1:69568467-69568486 None:intergenic 20.0%
!! AATTAAATAACTCATGTATC+TGG - chr3_1:69568467-69568486 Msa0371420:intron 20.0%
!!! TCCTAAAAATCACTTTTTTA+AGG + chr3_1:69568515-69568534 None:intergenic 20.0%
!!! GATTAATTTTTATTCATTGG+AGG - chr3_1:69568659-69568678 Msa0371420:intron 20.0%
!!! TTGTTGTTTAATTTTTAGCT+AGG - chr3_1:69568968-69568987 Msa0371420:intron 20.0%
!!! TTTAATTTTTAGCTAGGATT+TGG - chr3_1:69568974-69568993 Msa0371420:intron 20.0%
! AGAAGATAACAAAAACAAAG+GGG + chr3_1:69567925-69567944 None:intergenic 25.0%
! GAAGAAGATAACAAAAACAA+AGG + chr3_1:69567927-69567946 None:intergenic 25.0%
!!! TTCACCATCTTTTTTGTTAT+AGG - chr3_1:69568054-69568073 Msa0371420:three_prime_UTR 25.0%
!!! TGATTGATTTTTCTCTTCTT+TGG - chr3_1:69568207-69568226 Msa0371420:three_prime_UTR 25.0%
! ATTCCATCATGTTTACTAAT+CGG + chr3_1:69568296-69568315 None:intergenic 25.0%
!! GCCTTAAAAAAGTGATTTTT+AGG - chr3_1:69568511-69568530 Msa0371420:intron 25.0%
!!! AATGGTGATTTTAAAGTTGT+TGG - chr3_1:69568616-69568635 Msa0371420:intron 25.0%
!! ATGTTTGTTTGTTCTTTTGA+TGG - chr3_1:69569017-69569036 Msa0371420:intron 25.0%
!! TGTTTGTTTGTTCTTTTGAT+GGG - chr3_1:69569018-69569037 Msa0371420:intron 25.0%
!!! TTGTTTTGGATTAATAACAG+TGG - chr3_1:69569201-69569220 Msa0371420:intron 25.0%
! AGTATTATTGTCATGCATTT+AGG - chr3_1:69569267-69569286 Msa0371420:intron 25.0%
!! TTTTCAACAAAGTTACTTCT+AGG - chr3_1:69569444-69569463 Msa0371420:intron 25.0%
! TTTCAACAAAGTTACTTCTA+GGG - chr3_1:69569445-69569464 Msa0371420:intron 25.0%
! ATAAATTTGTGATGTTGTCT+AGG - chr3_1:69569483-69569502 Msa0371420:CDS 25.0%
AATTTGCAATGGAATGGAAA+TGG + chr3_1:69567889-69567908 None:intergenic 30.0%
AAGATGATTGCAATTTGCAA+TGG + chr3_1:69567900-69567919 None:intergenic 30.0%
AAATGCAAAGTAGTAAATGG+CGG + chr3_1:69568017-69568036 None:intergenic 30.0%
ACGAAATGCAAAGTAGTAAA+TGG + chr3_1:69568020-69568039 None:intergenic 30.0%
TATCCGATTAGTAAACATGA+TGG - chr3_1:69568290-69568309 Msa0371420:CDS 30.0%
CATCATATCATTTCTCAGAT+AGG + chr3_1:69568342-69568361 None:intergenic 30.0%
TGAGATATAACTCAAAAGAG+TGG - chr3_1:69568735-69568754 Msa0371420:intron 30.0%
! TTTTTATCTCGGTTTTACAC+AGG - chr3_1:69568935-69568954 Msa0371420:intron 30.0%
! TTTTATCTCGGTTTTACACA+GGG - chr3_1:69568936-69568955 Msa0371420:intron 30.0%
!!! TTTGTTCTTTTGATGGGTTT+AGG - chr3_1:69569024-69569043 Msa0371420:intron 30.0%
!!! TTGTTCTTTTGATGGGTTTA+GGG - chr3_1:69569025-69569044 Msa0371420:intron 30.0%
AACAATTAACGCAACAAACA+GGG + chr3_1:69569357-69569376 None:intergenic 30.0%
GATTGCAATTTGCAATGGAA+TGG + chr3_1:69567895-69567914 None:intergenic 35.0%
TTGCATTTCGTAAGAGAGTT+AGG - chr3_1:69568029-69568048 Msa0371420:three_prime_UTR 35.0%
TGCATTTCGTAAGAGAGTTA+GGG - chr3_1:69568030-69568049 Msa0371420:three_prime_UTR 35.0%
GATGTTACGAACAAGTGAAA+AGG + chr3_1:69568125-69568144 None:intergenic 35.0%
! GAGTTTGACTTATCTCAGAT+CGG - chr3_1:69568229-69568248 Msa0371420:three_prime_UTR 35.0%
ACTCATGTATCTGGACTAAA+TGG - chr3_1:69568476-69568495 Msa0371420:intron 35.0%
GACAAATCAGCTTCAATCAT+CGG + chr3_1:69568560-69568579 None:intergenic 35.0%
! CGAATTTTGCACAAATAACG+TGG - chr3_1:69568593-69568612 Msa0371420:intron 35.0%
TTTGCACAAATAACGTGGAA+TGG - chr3_1:69568598-69568617 Msa0371420:intron 35.0%
AAATCCATGATATGTTTGCC+TGG - chr3_1:69568825-69568844 Msa0371420:intron 35.0%
! TGGTGTTTGAAGGAGTATAA+TGG - chr3_1:69568994-69569013 Msa0371420:intron 35.0%
AAACAACTTAGTTGCGACTT+GGG + chr3_1:69569187-69569206 None:intergenic 35.0%
AAAACAACTTAGTTGCGACT+TGG + chr3_1:69569188-69569207 None:intergenic 35.0%
! AAGTCGCAACTAAGTTGTTT+TGG - chr3_1:69569187-69569206 Msa0371420:intron 35.0%
CAACAATTAACGCAACAAAC+AGG + chr3_1:69569358-69569377 None:intergenic 35.0%
!! TATAAATTTGTTCGGTGTGC+CGG - chr3_1:69569387-69569406 Msa0371420:intron 35.0%
! AAAGTTACTTCTAGGGAAAC+TGG - chr3_1:69569452-69569471 Msa0371420:intron 35.0%
! TCTCTGAGAGAGAAAGAGAA+TGG + chr3_1:69567866-69567885 None:intergenic 40.0%
TCTTCTTCAACTGCTATCCA+TGG - chr3_1:69567942-69567961 Msa0371420:three_prime_UTR 40.0%
AACATCAGTACCTGACTTCA+GGG + chr3_1:69568156-69568175 None:intergenic 40.0%
AAACATCAGTACCTGACTTC+AGG + chr3_1:69568157-69568176 None:intergenic 40.0%
AACTCAAAAGAGTGGCATCA+TGG - chr3_1:69568743-69568762 Msa0371420:intron 40.0%
TCAACCAGGCAAACATATCA+TGG + chr3_1:69568832-69568851 None:intergenic 40.0%
CTGGTTGAGTGAAATGAAGT+CGG - chr3_1:69568844-69568863 Msa0371420:intron 40.0%
!! AGCTAGGATTTGGTGTTTGA+AGG - chr3_1:69568984-69569003 Msa0371420:intron 40.0%
! AGTACACAGAACATTTGCTG+AGG - chr3_1:69569102-69569121 Msa0371420:intron 40.0%
TGATGATCTAGGTTCGATAC+CGG + chr3_1:69569409-69569428 None:intergenic 40.0%
GTATCGAACCTAGATCATCA+AGG - chr3_1:69569409-69569428 Msa0371420:intron 40.0%
! CTCTTCAACCTTGATGATCT+AGG + chr3_1:69569420-69569439 None:intergenic 40.0%
! GCAGACATGCTTGTTAAAAC+TGG - chr3_1:69569511-69569530 Msa0371420:five_prime_UTR 40.0%
CTGAGAGAGAAAGAGAATGG+AGG + chr3_1:69567863-69567882 None:intergenic 45.0%
AGATCGAAAAGGACTCACCT+CGG + chr3_1:69567989-69568008 None:intergenic 45.0%
TGGCGGAATACAGATCGAAA+AGG + chr3_1:69568000-69568019 None:intergenic 45.0%
GTCGCTTATAGAGAGAGAGT+AGG + chr3_1:69568433-69568452 None:intergenic 45.0%
CGACTTCATTTCACTCAACC+AGG + chr3_1:69568846-69568865 None:intergenic 45.0%
TTCTGTGTACTTCTCTCCCT+CGG + chr3_1:69569093-69569112 None:intergenic 45.0%
GATCGAAAAGGACTCACCTC+GGG + chr3_1:69567988-69568007 None:intergenic 50.0%
! GGTATACCCTCTGTTTGCTG+CGG - chr3_1:69568075-69568094 Msa0371420:three_prime_UTR 50.0%
TCTGCATCAACCCTGAAGTC+AGG - chr3_1:69568143-69568162 Msa0371420:three_prime_UTR 50.0%
! AGTGTTGGAGAACTTTGCCG+AGG - chr3_1:69569073-69569092 Msa0371420:intron 50.0%
GTGTTGGAGAACTTTGCCGA+GGG - chr3_1:69569074-69569093 Msa0371420:intron 50.0%
AGATCACCCGAGATTATGCC+CGG - chr3_1:69569140-69569159 Msa0371420:intron 50.0%
AGTGAAGAAGCTGTTGAGGC+CGG + chr3_1:69569162-69569181 None:intergenic 50.0%
GGTCAGTGAAGAAGCTGTTG+AGG + chr3_1:69569166-69569185 None:intergenic 50.0%
TATCCATGGCCACCAATCGC+TGG - chr3_1:69567956-69567975 Msa0371420:three_prime_UTR 55.0%
! TACCCTCTGTTTGCTGCGGT+TGG - chr3_1:69568079-69568098 Msa0371420:three_prime_UTR 55.0%
CTCCAACCGCAGCAAACAGA+GGG + chr3_1:69568084-69568103 None:intergenic 55.0%
AACAAGCAGTCTCGAGCTGC+AGG - chr3_1:69569050-69569069 Msa0371420:intron 55.0%
TTGAGGCCGGGCATAATCTC+GGG + chr3_1:69569149-69569168 None:intergenic 55.0%
GTTGAGGCCGGGCATAATCT+CGG + chr3_1:69569150-69569169 None:intergenic 55.0%
GTGAAGAAGCTGTTGAGGCC+GGG + chr3_1:69569161-69569180 None:intergenic 55.0%
CCACAGCATACACGCTGTTC+AGG + chr3_1:69569319-69569338 None:intergenic 55.0%
CCTGAACAGCGTGTATGCTG+TGG - chr3_1:69569316-69569335 Msa0371420:CDS 55.0%
! GATCCAGCGATTGGTGGCCA+TGG + chr3_1:69567962-69567981 None:intergenic 60.0%
GGGTCTGATCCAGCGATTGG+TGG + chr3_1:69567968-69567987 None:intergenic 60.0%
CTCGGGTCTGATCCAGCGAT+TGG + chr3_1:69567971-69567990 None:intergenic 60.0%
CAATCGCTGGATCAGACCCG+AGG - chr3_1:69567969-69567988 Msa0371420:three_prime_UTR 60.0%
GCTCCAACCGCAGCAAACAG+AGG + chr3_1:69568085-69568104 None:intergenic 60.0%
CTGCGGTTGGAGCTGCTGTT+GGG - chr3_1:69568092-69568111 Msa0371420:three_prime_UTR 60.0%
! GTCTCGAGCTGCAGGAGTGT+TGG - chr3_1:69569058-69569077 Msa0371420:intron 60.0%
GCTGCGGTTGGAGCTGCTGT+TGG - chr3_1:69568091-69568110 Msa0371420:three_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 69567845 69569622 69567845 ID=Msa0371420;Name=Msa0371420
chr3_1 mRNA 69567845 69569622 69567845 ID=Msa0371420-mRNA-1;Parent=Msa0371420;Name=Msa0371420-mRNA-1;_AED=0.01;_eAED=0.01;_QI=116|1|1|1|1|1|3|423|90
chr3_1 exon 69567845 69568421 69567845 ID=Msa0371420-mRNA-1:exon:14860;Parent=Msa0371420-mRNA-1
chr3_1 exon 69569303 69569391 69569303 ID=Msa0371420-mRNA-1:exon:14859;Parent=Msa0371420-mRNA-1
chr3_1 exon 69569477 69569622 69569477 ID=Msa0371420-mRNA-1:exon:14858;Parent=Msa0371420-mRNA-1
chr3_1 five_prime_UTR 69569507 69569622 69569507 ID=Msa0371420-mRNA-1:five_prime_utr;Parent=Msa0371420-mRNA-1
chr3_1 CDS 69569477 69569506 69569477 ID=Msa0371420-mRNA-1:cds;Parent=Msa0371420-mRNA-1
chr3_1 CDS 69569303 69569391 69569303 ID=Msa0371420-mRNA-1:cds;Parent=Msa0371420-mRNA-1
chr3_1 CDS 69568268 69568421 69568268 ID=Msa0371420-mRNA-1:cds;Parent=Msa0371420-mRNA-1
chr3_1 three_prime_UTR 69567845 69568267 69567845 ID=Msa0371420-mRNA-1:three_prime_utr;Parent=Msa0371420-mRNA-1
Gene Sequence

>Msa0371420

ATGGCCACCAATCGCTGGATCAGACCCGAGGTATACCCTCTGTTTGCTGCGGTTGGAGCTGCTGTTGGGATCTGTGCCTTTTCACTTGTTCGTAACATCTGCATCAACCCTGAAGTCAGGGTGAACAAGCAGTCTCGAGCTGCAGGAGTGTTGGAGAACTTTGCCGAGGGAGAGAAGTACACAGAACATTTGCTGAGGAAGTTTTCACGCAACAGATCACCCGAGATTATGCCCGGCCTCAACAGCTTCTTCACTGACCCAAGTCGCAACTAA

Protein sequence

>Msa0371420

MATNRWIRPEVYPLFAAVGAAVGICAFSLVRNICINPEVRVNKQSRAAGVLENFAEGEKYTEHLLRKFSRNRSPEIMPGLNSFFTDPSRN*