AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1229560

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1229560 MtrunA17_Chr8g0336681 68.421 114 6 1 4 87 232 345 9.27e-46 149
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 138 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGATATTGTGATCAGATTAA+TGG 0.236799 8_2:-5285287 Msa1229560:intron
AACCCTAGGTAGTTCCTTCT+TGG 0.253397 8_2:+5285366 None:intergenic
CCTTCTTGGAATAATATCTA+TGG 0.307248 8_2:+5285380 None:intergenic
AAACCGACATAAACAAGAAT+TGG 0.346505 8_2:+5284082 None:intergenic
AGCGTGAATGATCTAGTTAA+TGG 0.406466 8_2:-5284174 Msa1229560:CDS
ATATCTATGGTCATCATTAT+CGG 0.421868 8_2:+5285393 None:intergenic
ATAATGATAATATTTCTTAG+AGG 0.424597 8_2:-5284119 Msa1229560:exon
ATGTATAAAGCTATGTATGA+TGG 0.433061 8_2:-5284017 Msa1229560:three_prime_UTR
TTTGTTTGTTTGTAATGAAA+GGG 0.455439 8_2:-5283991 Msa1229560:three_prime_UTR
ATTTGTTTGTTTGTAATGAA+AGG 0.467962 8_2:-5283992 Msa1229560:three_prime_UTR
ATAGACAAGGAAATTCTCAT+TGG 0.487223 8_2:-5285331 Msa1229560:CDS
ATGACTCTTGCTTCAACCCT+AGG 0.499751 8_2:+5285352 None:intergenic
CCTCCAATTCTTGTTTATGT+CGG 0.514798 8_2:-5284085 Msa1229560:three_prime_UTR
TGGCCTGCGGCAAAATCTCA+TGG 0.524286 8_2:-5284154 Msa1229560:CDS
CCGACATAAACAAGAATTGG+AGG 0.531310 8_2:+5284085 None:intergenic
AATCCATTGTGAGAAACAAA+AGG 0.531350 8_2:-5285308 Msa1229560:CDS
TGTATAAAGCTATGTATGAT+GGG 0.542335 8_2:-5284016 Msa1229560:three_prime_UTR
TAATGATAATATTTCTTAGA+GGG 0.544633 8_2:-5284118 Msa1229560:exon
TTCCAAGAAGGAACTACCTA+GGG 0.547352 8_2:-5285368 Msa1229560:CDS
ATTCCAAGAAGGAACTACCT+AGG 0.568835 8_2:-5285369 Msa1229560:CDS
CCATAGATATTATTCCAAGA+AGG 0.603704 8_2:-5285380 Msa1229560:CDS
ATGATCTAGTTAATGGCCTG+CGG 0.675515 8_2:-5284167 Msa1229560:CDS
TGAAGCAAGAGTCATAGACA+AGG 0.722379 8_2:-5285344 Msa1229560:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTAATATTAAAATGATTTTT+TGG - chr8_2:5284463-5284482 Msa1229560:intron 10.0%
!!! TTTTTTGATGATTTTTTTTA+AGG - chr8_2:5284714-5284733 Msa1229560:intron 10.0%
!!! GTAATATTAAAATGATTTTT+TGG - chr8_2:5284463-5284482 Msa1229560:intron 10.0%
!!! TTTTTTGATGATTTTTTTTA+AGG - chr8_2:5284714-5284733 Msa1229560:intron 10.0%
!! AAATGTTTATGTATTGTTTA+AGG + chr8_2:5284409-5284428 None:intergenic 15.0%
!!! TATTTCTAAGAGAAATTAAA+TGG + chr8_2:5284789-5284808 None:intergenic 15.0%
!! ATAATGATAATATTTCTTAG+AGG - chr8_2:5285274-5285293 Msa1229560:intron 15.0%
!! TAATGATAATATTTCTTAGA+GGG - chr8_2:5285275-5285294 Msa1229560:intron 15.0%
!! AAATCTAAATACAAAAAAAG+AGG - chr8_2:5285436-5285455 Msa1229560:intron 15.0%
!! AAATGTTTATGTATTGTTTA+AGG + chr8_2:5284409-5284428 None:intergenic 15.0%
!!! TATTTCTAAGAGAAATTAAA+TGG + chr8_2:5284789-5284808 None:intergenic 15.0%
!! ATAATGATAATATTTCTTAG+AGG - chr8_2:5285274-5285293 Msa1229560:intron 15.0%
!! TAATGATAATATTTCTTAGA+GGG - chr8_2:5285275-5285294 Msa1229560:intron 15.0%
!! AAATCTAAATACAAAAAAAG+AGG - chr8_2:5285436-5285455 Msa1229560:intron 15.0%
!! TCAGGTAATAATTAAACAAT+GGG - chr8_2:5284212-5284231 Msa1229560:intron 20.0%
!!! AATGCAAAATTTCTCATTTT+AGG + chr8_2:5284276-5284295 None:intergenic 20.0%
!!! TAAAATGAGAAATTTTGCAT+TGG - chr8_2:5284275-5284294 Msa1229560:intron 20.0%
!!! TCATTTTCCAAAATAATTAG+AGG - chr8_2:5284428-5284447 Msa1229560:intron 20.0%
!!! ATATTGACCTCTAATTATTT+TGG + chr8_2:5284438-5284457 None:intergenic 20.0%
!! ATGATTATTGAACGAATAAT+AGG - chr8_2:5284762-5284781 Msa1229560:intron 20.0%
!! ATCAAAATATAACAACCTTT+AGG - chr8_2:5284828-5284847 Msa1229560:intron 20.0%
!!! AAGTTTTTTTGACAATTATG+AGG + chr8_2:5285064-5285083 None:intergenic 20.0%
!!! AAGTTTGTAGAAATTTTGTT+TGG - chr8_2:5285336-5285355 Msa1229560:CDS 20.0%
!! ATTTGTTTGTTTGTAATGAA+AGG - chr8_2:5285401-5285420 Msa1229560:CDS 20.0%
!! TTTGTTTGTTTGTAATGAAA+GGG - chr8_2:5285402-5285421 Msa1229560:CDS 20.0%
!! TCAGGTAATAATTAAACAAT+GGG - chr8_2:5284212-5284231 Msa1229560:intron 20.0%
!!! AATGCAAAATTTCTCATTTT+AGG + chr8_2:5284276-5284295 None:intergenic 20.0%
!!! TAAAATGAGAAATTTTGCAT+TGG - chr8_2:5284275-5284294 Msa1229560:intron 20.0%
!!! TCATTTTCCAAAATAATTAG+AGG - chr8_2:5284428-5284447 Msa1229560:intron 20.0%
!!! ATATTGACCTCTAATTATTT+TGG + chr8_2:5284438-5284457 None:intergenic 20.0%
!! ATGATTATTGAACGAATAAT+AGG - chr8_2:5284762-5284781 Msa1229560:intron 20.0%
!! ATCAAAATATAACAACCTTT+AGG - chr8_2:5284828-5284847 Msa1229560:intron 20.0%
!!! AAGTTTTTTTGACAATTATG+AGG + chr8_2:5285064-5285083 None:intergenic 20.0%
!!! AAGTTTGTAGAAATTTTGTT+TGG - chr8_2:5285336-5285355 Msa1229560:CDS 20.0%
!! ATTTGTTTGTTTGTAATGAA+AGG - chr8_2:5285401-5285420 Msa1229560:CDS 20.0%
!! TTTGTTTGTTTGTAATGAAA+GGG - chr8_2:5285402-5285421 Msa1229560:CDS 20.0%
! ATATCTATGGTCATCATTAT+CGG + chr8_2:5284003-5284022 None:intergenic 25.0%
!!! ATGATTGTAACTTTTAAGAG+TGG + chr8_2:5284189-5284208 None:intergenic 25.0%
! CTCAGGTAATAATTAAACAA+TGG - chr8_2:5284211-5284230 Msa1229560:intron 25.0%
! AAATTATTTCAAGATGACCA+TGG + chr8_2:5284682-5284701 None:intergenic 25.0%
! TTCTCTTAGAAATAAAAGAG+TGG - chr8_2:5284795-5284814 Msa1229560:intron 25.0%
! AAGGAAGAGAAAAAGAAAAA+AGG + chr8_2:5285040-5285059 None:intergenic 25.0%
!! TTTTTGACAATTATGAGGAA+AGG + chr8_2:5285059-5285078 None:intergenic 25.0%
! ATGTATAAAGCTATGTATGA+TGG - chr8_2:5285376-5285395 Msa1229560:CDS 25.0%
! TGTATAAAGCTATGTATGAT+GGG - chr8_2:5285377-5285396 Msa1229560:CDS 25.0%
! ATATCTATGGTCATCATTAT+CGG + chr8_2:5284003-5284022 None:intergenic 25.0%
!!! ATGATTGTAACTTTTAAGAG+TGG + chr8_2:5284189-5284208 None:intergenic 25.0%
! CTCAGGTAATAATTAAACAA+TGG - chr8_2:5284211-5284230 Msa1229560:intron 25.0%
! AAATTATTTCAAGATGACCA+TGG + chr8_2:5284682-5284701 None:intergenic 25.0%
! TTCTCTTAGAAATAAAAGAG+TGG - chr8_2:5284795-5284814 Msa1229560:intron 25.0%
! AAGGAAGAGAAAAAGAAAAA+AGG + chr8_2:5285040-5285059 None:intergenic 25.0%
!! TTTTTGACAATTATGAGGAA+AGG + chr8_2:5285059-5285078 None:intergenic 25.0%
! ATGTATAAAGCTATGTATGA+TGG - chr8_2:5285376-5285395 Msa1229560:CDS 25.0%
! TGTATAAAGCTATGTATGAT+GGG - chr8_2:5285377-5285396 Msa1229560:CDS 25.0%
CCTTCTTGGAATAATATCTA+TGG + chr8_2:5284016-5284035 None:intergenic 30.0%
CCATAGATATTATTCCAAGA+AGG - chr8_2:5284013-5284032 Msa1229560:three_prime_UTR 30.0%
ATAGACAAGGAAATTCTCAT+TGG - chr8_2:5284062-5284081 Msa1229560:three_prime_UTR 30.0%
AATCCATTGTGAGAAACAAA+AGG - chr8_2:5284085-5284104 Msa1229560:three_prime_UTR 30.0%
!! TATCCTTTTGTTTCTCACAA+TGG + chr8_2:5284091-5284110 None:intergenic 30.0%
GGATATTGTGATCAGATTAA+TGG - chr8_2:5284106-5284125 Msa1229560:exon 30.0%
AAAAGTTACAATCATTGCTC+AGG - chr8_2:5284194-5284213 Msa1229560:CDS 30.0%
TTGGCAACAGTATACAAATA+TGG - chr8_2:5284958-5284977 Msa1229560:intron 30.0%
!!! CAAGAATTGGAGGTTTTATT+TGG + chr8_2:5285301-5285320 None:intergenic 30.0%
AAACCGACATAAACAAGAAT+TGG + chr8_2:5285314-5285333 None:intergenic 30.0%
CCTTCTTGGAATAATATCTA+TGG + chr8_2:5284016-5284035 None:intergenic 30.0%
CCATAGATATTATTCCAAGA+AGG - chr8_2:5284013-5284032 Msa1229560:three_prime_UTR 30.0%
ATAGACAAGGAAATTCTCAT+TGG - chr8_2:5284062-5284081 Msa1229560:three_prime_UTR 30.0%
AATCCATTGTGAGAAACAAA+AGG - chr8_2:5284085-5284104 Msa1229560:three_prime_UTR 30.0%
!! TATCCTTTTGTTTCTCACAA+TGG + chr8_2:5284091-5284110 None:intergenic 30.0%
GGATATTGTGATCAGATTAA+TGG - chr8_2:5284106-5284125 Msa1229560:exon 30.0%
AAAAGTTACAATCATTGCTC+AGG - chr8_2:5284194-5284213 Msa1229560:CDS 30.0%
TTGGCAACAGTATACAAATA+TGG - chr8_2:5284958-5284977 Msa1229560:intron 30.0%
!!! CAAGAATTGGAGGTTTTATT+TGG + chr8_2:5285301-5285320 None:intergenic 30.0%
AAACCGACATAAACAAGAAT+TGG + chr8_2:5285314-5285333 None:intergenic 30.0%
!! CTTTTAAGAGTGGAAGTTCA+AGG + chr8_2:5284179-5284198 None:intergenic 35.0%
AAACAAGATAGGAGAAAAGC+TGG - chr8_2:5284614-5284633 Msa1229560:intron 35.0%
ATAGGAGAAAAGCTGGAAAA+GGG - chr8_2:5284621-5284640 Msa1229560:intron 35.0%
TTAGAAAAAGAGAGCTTCCA+TGG - chr8_2:5284662-5284681 Msa1229560:intron 35.0%
TCTTCATTCGAATGTCCTAA+AGG + chr8_2:5284846-5284865 None:intergenic 35.0%
!! CTTTTGCTATATCATGCAGA+TGG - chr8_2:5285179-5285198 Msa1229560:intron 35.0%
AGCGTGAATGATCTAGTTAA+TGG - chr8_2:5285219-5285238 Msa1229560:intron 35.0%
! CCTCCAATTCTTGTTTATGT+CGG - chr8_2:5285308-5285327 Msa1229560:CDS 35.0%
!! CTTTTAAGAGTGGAAGTTCA+AGG + chr8_2:5284179-5284198 None:intergenic 35.0%
AAACAAGATAGGAGAAAAGC+TGG - chr8_2:5284614-5284633 Msa1229560:intron 35.0%
ATAGGAGAAAAGCTGGAAAA+GGG - chr8_2:5284621-5284640 Msa1229560:intron 35.0%
TTAGAAAAAGAGAGCTTCCA+TGG - chr8_2:5284662-5284681 Msa1229560:intron 35.0%
TCTTCATTCGAATGTCCTAA+AGG + chr8_2:5284846-5284865 None:intergenic 35.0%
!! CTTTTGCTATATCATGCAGA+TGG - chr8_2:5285179-5285198 Msa1229560:intron 35.0%
AGCGTGAATGATCTAGTTAA+TGG - chr8_2:5285219-5285238 Msa1229560:intron 35.0%
! CCTCCAATTCTTGTTTATGT+CGG - chr8_2:5285308-5285327 Msa1229560:CDS 35.0%
ATTCCAAGAAGGAACTACCT+AGG - chr8_2:5284024-5284043 Msa1229560:three_prime_UTR 40.0%
TTCCAAGAAGGAACTACCTA+GGG - chr8_2:5284025-5284044 Msa1229560:three_prime_UTR 40.0%
TGAAGCAAGAGTCATAGACA+AGG - chr8_2:5284049-5284068 Msa1229560:three_prime_UTR 40.0%
! TCATGTTAAGTTGTGCCCTA+AGG - chr8_2:5284235-5284254 Msa1229560:intron 40.0%
! CATGTTAAGTTGTGCCCTAA+GGG - chr8_2:5284236-5284255 Msa1229560:intron 40.0%
TTCCTTAACATGTGCCCTTA+GGG + chr8_2:5284253-5284272 None:intergenic 40.0%
!! ATGTTAACTTGTGCCCTCAA+GGG + chr8_2:5284383-5284402 None:intergenic 40.0%
!! AATGTTAACTTGTGCCCTCA+AGG + chr8_2:5284384-5284403 None:intergenic 40.0%
AATGAGTGTGACAAGAGAGA+GGG - chr8_2:5284589-5284608 Msa1229560:intron 40.0%
GAGAGAGGGAAAAACAAGAT+AGG - chr8_2:5284603-5284622 Msa1229560:intron 40.0%
GATAGGAGAAAAGCTGGAAA+AGG - chr8_2:5284620-5284639 Msa1229560:intron 40.0%
ATGATCTAGTTAATGGCCTG+CGG - chr8_2:5285226-5285245 Msa1229560:intron 40.0%
CCGACATAAACAAGAATTGG+AGG + chr8_2:5285311-5285330 None:intergenic 40.0%
ATTCCAAGAAGGAACTACCT+AGG - chr8_2:5284024-5284043 Msa1229560:three_prime_UTR 40.0%
TTCCAAGAAGGAACTACCTA+GGG - chr8_2:5284025-5284044 Msa1229560:three_prime_UTR 40.0%
TGAAGCAAGAGTCATAGACA+AGG - chr8_2:5284049-5284068 Msa1229560:three_prime_UTR 40.0%
! TCATGTTAAGTTGTGCCCTA+AGG - chr8_2:5284235-5284254 Msa1229560:intron 40.0%
! CATGTTAAGTTGTGCCCTAA+GGG - chr8_2:5284236-5284255 Msa1229560:intron 40.0%
TTCCTTAACATGTGCCCTTA+GGG + chr8_2:5284253-5284272 None:intergenic 40.0%
!! ATGTTAACTTGTGCCCTCAA+GGG + chr8_2:5284383-5284402 None:intergenic 40.0%
!! AATGTTAACTTGTGCCCTCA+AGG + chr8_2:5284384-5284403 None:intergenic 40.0%
AATGAGTGTGACAAGAGAGA+GGG - chr8_2:5284589-5284608 Msa1229560:intron 40.0%
GAGAGAGGGAAAAACAAGAT+AGG - chr8_2:5284603-5284622 Msa1229560:intron 40.0%
GATAGGAGAAAAGCTGGAAA+AGG - chr8_2:5284620-5284639 Msa1229560:intron 40.0%
ATGATCTAGTTAATGGCCTG+CGG - chr8_2:5285226-5285245 Msa1229560:intron 40.0%
CCGACATAAACAAGAATTGG+AGG + chr8_2:5285311-5285330 None:intergenic 40.0%
AACCCTAGGTAGTTCCTTCT+TGG + chr8_2:5284030-5284049 None:intergenic 45.0%
ATGACTCTTGCTTCAACCCT+AGG + chr8_2:5284044-5284063 None:intergenic 45.0%
GTTCCTTAACATGTGCCCTT+AGG + chr8_2:5284365-5284384 None:intergenic 45.0%
TTCCTTAACATGTGCCCTTG+AGG - chr8_2:5284366-5284385 Msa1229560:intron 45.0%
TCCTTAACATGTGCCCTTGA+GGG - chr8_2:5284367-5284386 Msa1229560:intron 45.0%
GAATGAGTGTGACAAGAGAG+AGG - chr8_2:5284588-5284607 Msa1229560:intron 45.0%
! ATTCCATGAGATTTTGCCGC+AGG + chr8_2:5285245-5285264 None:intergenic 45.0%
AACCCTAGGTAGTTCCTTCT+TGG + chr8_2:5284030-5284049 None:intergenic 45.0%
ATGACTCTTGCTTCAACCCT+AGG + chr8_2:5284044-5284063 None:intergenic 45.0%
GTTCCTTAACATGTGCCCTT+AGG + chr8_2:5284365-5284384 None:intergenic 45.0%
TTCCTTAACATGTGCCCTTG+AGG - chr8_2:5284366-5284385 Msa1229560:intron 45.0%
TCCTTAACATGTGCCCTTGA+GGG - chr8_2:5284367-5284386 Msa1229560:intron 45.0%
GAATGAGTGTGACAAGAGAG+AGG - chr8_2:5284588-5284607 Msa1229560:intron 45.0%
! ATTCCATGAGATTTTGCCGC+AGG + chr8_2:5285245-5285264 None:intergenic 45.0%
!!! AAAAAAATATTTTGTTAAAT+TGG - chr8_2:5284939-5284958 Msa1229560:intron 5.0%
!!! AAAAAAATATTTTGTTAAAT+TGG - chr8_2:5284939-5284958 Msa1229560:intron 5.0%
! TGCCCTAAGGGCACATGTTA+AGG - chr8_2:5284248-5284267 Msa1229560:intron 50.0%
! TGCCCTAAGGGCACATGTTA+AGG - chr8_2:5284248-5284267 Msa1229560:intron 50.0%
! GCCCTCAAGGGCACATGTTA+AGG + chr8_2:5284371-5284390 None:intergenic 55.0%
TGGCCTGCGGCAAAATCTCA+TGG - chr8_2:5285239-5285258 Msa1229560:intron 55.0%
! GCCCTCAAGGGCACATGTTA+AGG + chr8_2:5284371-5284390 None:intergenic 55.0%
TGGCCTGCGGCAAAATCTCA+TGG - chr8_2:5285239-5285258 Msa1229560:intron 55.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 5283956 5285459 5283956 ID=Msa1229560;Name=Msa1229560
chr8_2 mRNA 5283956 5285459 5283956 ID=Msa1229560-mRNA-1;Parent=Msa1229560;Name=Msa1229560-mRNA-1;_AED=0.19;_eAED=0.40;_QI=0|0|0.33|0.66|0|0|3|166|87
chr8_2 exon 5283956 5284217 5283956 ID=Msa1229560-mRNA-1:exon:1824;Parent=Msa1229560-mRNA-1
chr8_2 exon 5285288 5285448 5285288 ID=Msa1229560-mRNA-1:exon:1823;Parent=Msa1229560-mRNA-1
chr8_2 exon 5285453 5285459 5285453 ID=Msa1229560-mRNA-1:exon:1822;Parent=Msa1229560-mRNA-1
chr8_2 CDS 5285453 5285459 5285453 ID=Msa1229560-mRNA-1:cds;Parent=Msa1229560-mRNA-1
chr8_2 CDS 5285288 5285448 5285288 ID=Msa1229560-mRNA-1:cds;Parent=Msa1229560-mRNA-1
chr8_2 CDS 5284122 5284217 5284122 ID=Msa1229560-mRNA-1:cds;Parent=Msa1229560-mRNA-1
chr8_2 three_prime_UTR 5283956 5284121 5283956 ID=Msa1229560-mRNA-1:three_prime_utr;Parent=Msa1229560-mRNA-1
Gene Sequence

>Msa1229560

ATGCATAACAAGGAAAAAAGTACTTCATGTGAAGAGAATTCCGATAATGATGACCATAGATATTATTCCAAGAAGGAACTACCTAGGGTTGAAGCAAGAGTCATAGACAAGGAAATTCTCATTGGAATCCATTGTGAGAAACAAAAGGATATTGTGATCAGATTAATGATGGATGATGAATACTGCTTGAGCGTGAATGATCTAGTTAATGGCCTGCGGCAAAATCTCATGGAATCACGTGACAATAATGATAATATTTCTTAG
Protein sequence

>Msa1229560

MHNKEKSTSCEENSDNDDHRYYSKKELPRVEARVIDKEILIGIHCEKQKDIVIRLMMDDEYCLSVNDLVNGLRQNLMESRDNNDNIS*