AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG040380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG040380 MtrunA17_Chr4g0039751 70.468 342 69 6 1 315 1 337 2.09e-159 454
MsaG040380 MtrunA17_Chr7g0269651 93.421 228 15 0 237 464 1 228 4.95e-147 444
MsaG040380 MtrunA17_Chr4g0039741 64.140 343 87 7 1 315 1 335 2.52e-142 411
MsaG040380 MtrunA17_Chr7g0269641 89.637 193 18 2 1 192 1 192 1.16e-116 340
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG040380 AT5G03415.1 64.493 276 83 5 1 267 27 296 4.01e-111 333
MsaG040380 AT5G03415.2 62.681 276 82 6 1 267 27 290 1.08e-105 319
MsaG040380 AT5G02470.3 43.478 230 104 8 40 262 32 242 3.51e-53 181
MsaG040380 AT5G02470.1 43.478 230 104 8 40 262 32 242 3.51e-53 181
MsaG040380 AT5G02470.2 43.478 230 104 8 40 262 32 242 3.51e-53 181

Find 96 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGGCATCACCTCCGCTTTC+TGG 0.140961 7:+99659150 MsaT040380.1:CDS
TCAATTTCCACATGACATTT+TGG 0.179498 7:-99660000 None:intergenic
AAAACCTTTCATGCTAATTT+GGG 0.213087 7:-99656886 None:intergenic
ACATAGCTACCAGGTGAAAT+AGG 0.227025 7:-99661882 None:intergenic
GTCAGGCTTGCATCAGTTGC+AGG 0.260541 7:+99659092 MsaT040380.1:CDS
TATTATTTCCAAGGATAAAA+AGG 0.267147 7:+99657585 MsaT040380.1:CDS
TATTATTGCATCAAGTTTGT+AGG 0.312560 7:+99658000 MsaT040380.1:intron
AGACCATCAATTTCCACATT+TGG 0.319213 7:-99662882 None:intergenic
CAGTTTCAAGCGTGTCAATT+AGG 0.323437 7:+99659124 MsaT040380.1:CDS
CTAAACAAAGCAACCGTAAC+CGG 0.330991 7:+99661939 MsaT040380.1:CDS
CTTGTTCCTCAAGCTCCTTT+AGG 0.331825 7:-99657827 None:intergenic
CATAGCTACCAGGTGAAATA+GGG 0.349787 7:-99661881 None:intergenic
GTTGGAGAAGGTAGAAAGTA+AGG 0.363432 7:+99657002 MsaT040380.1:CDS
TCCGCTTTCTGGAATACTTA+AGG 0.378685 7:+99659161 MsaT040380.1:CDS
CGGTTACGGTTGCTTTGTTT+AGG 0.378746 7:-99661938 None:intergenic
GTCGGCTTGCTCCGGCTAGA+TGG 0.379241 7:-99656252 None:intergenic
GGGGAAGGTTCTAGCTTGTC+AGG 0.408012 7:+99659075 MsaT040380.1:CDS
TGACGTTCCTGACAATGAAT+TGG 0.410222 7:+99662016 MsaT040380.1:CDS
AACGTTTCAGCTGCTGCAAC+GGG 0.415747 7:+99662948 MsaT040380.1:CDS
GGGGACAAAACACTATTCAT+TGG 0.417434 7:-99657379 None:intergenic
AACTTACCCAATTCATTGTC+AGG 0.420608 7:-99662023 None:intergenic
TCACCGCAATGCAAATTTCC+AGG 0.421335 7:-99661915 None:intergenic
TGTTTGTTAGGAAAGCTAAC+TGG 0.430033 7:+99659850 MsaT040380.1:intron
GCTGCTGCAACGGGTGCAAC+TGG 0.430950 7:+99662957 MsaT040380.1:CDS
ATTCTCATTTGACCCGGTTA+CGG 0.436888 7:-99661952 None:intergenic
AAAGATAAATCTCCGCTTGA+AGG 0.440338 7:-99658072 None:intergenic
AATTGTGTGTCATTCACCTT+AGG 0.455505 7:-99662906 None:intergenic
AATGAGCAATTATATAGATC+AGG 0.460541 7:+99658045 MsaT040380.1:CDS
AAGCGTGTCAATTAGGCCTC+AGG 0.469004 7:+99659131 MsaT040380.1:CDS
CTTTCTTGTCACATTTCTGT+TGG 0.471125 7:-99661853 None:intergenic
TATCTAGAGTGTGACGAGAA+TGG 0.480614 7:+99661984 MsaT040380.1:CDS
TAGTGCTATTGAGAAGCTAA+AGG 0.482438 7:+99657633 MsaT040380.1:CDS
AAACGTTTCAGCTGCTGCAA+CGG 0.496994 7:+99662947 MsaT040380.1:CDS
TGTACCTGAACCAGAACAAA+AGG 0.501925 7:-99658096 None:intergenic
GGCAATGGATATTATTTCCA+AGG 0.507516 7:+99657576 MsaT040380.1:CDS
ATTCAACAGATCGAATGTCT+AGG 0.511456 7:+99657771 MsaT040380.1:intron
TCTGCGTCGTCGGCTTGCTC+CGG 0.512862 7:-99656260 None:intergenic
TGCAACTGTTGAACTTGAAG+TGG 0.513525 7:+99658643 MsaT040380.1:CDS
AGCTATGTTCTAAAGCGTCC+TGG 0.518991 7:+99661897 MsaT040380.1:CDS
TTCAACAGATCGAATGTCTA+GGG 0.521141 7:+99657772 MsaT040380.1:intron
CATCATCATGTATGTCAAGA+TGG 0.522280 7:-99656305 None:intergenic
GACGTTCCTGACAATGAATT+GGG 0.527489 7:+99662017 MsaT040380.1:CDS
GATCCAAATGTGGAAATTGA+TGG 0.529723 7:+99662879 MsaT040380.1:intron
GAATGACACACAGTTTCCCT+TGG 0.532011 7:+99660038 MsaT040380.1:CDS
ACTTACCATTGCTGTAATGA+TGG 0.533611 7:-99659885 None:intergenic
ACACTCAATGTTACGGAAGG+AGG 0.535766 7:+99659054 MsaT040380.1:CDS
TATTGCTACACTCAATGTTA+CGG 0.535816 7:+99659047 MsaT040380.1:CDS
AAGCAAAGTATCCTACCTAA+AGG 0.541642 7:+99657812 MsaT040380.1:CDS
CACTCAATGTTACGGAAGGA+GGG 0.556476 7:+99659055 MsaT040380.1:CDS
ATCCTACCTAAAGGAGCTTG+AGG 0.557921 7:+99657821 MsaT040380.1:CDS
TTGGAGAAGGTAGAAAGTAA+GGG 0.559901 7:+99657003 MsaT040380.1:CDS
CGCTTTAGAACATAGCTACC+AGG 0.561886 7:-99661891 None:intergenic
ATTGCTCATTTCGTTGAACA+AGG 0.562679 7:-99658032 None:intergenic
ACCTTAAGTATTCCAGAAAG+CGG 0.563806 7:-99659162 None:intergenic
AAACCTTTCATGCTAATTTG+GGG 0.565405 7:-99656885 None:intergenic
AATCATGTGTAGATGAAAGC+AGG 0.569304 7:+99656217 MsaT040380.1:CDS
TTTAGCTTCTCAATAGCACT+AGG 0.575236 7:-99657631 None:intergenic
GCAGCGGCTCTCTGCGTCGT+CGG 0.575942 7:-99656270 None:intergenic
TAAACAAAGCAACCGTAACC+GGG 0.576188 7:+99661940 MsaT040380.1:CDS
GACATACATGATGATGATGC+AGG 0.583166 7:+99656312 MsaT040380.1:CDS
AACCTTTCATGCTAATTTGG+GGG 0.587021 7:-99656884 None:intergenic
TTCAGATCCAAAATGTCATG+TGG 0.587452 7:+99659993 MsaT040380.1:intron
CTACTATGTGCTCAAAGCAA+TGG 0.590968 7:+99658999 MsaT040380.1:CDS
GATGATGATGCAGGATCACA+AGG 0.593414 7:+99656321 MsaT040380.1:CDS
GTTGGTAAATTGTGATAAGT+CGG 0.595561 7:-99661835 None:intergenic
AAGCTTACCCCTATTTCACC+TGG 0.596386 7:+99661873 MsaT040380.1:CDS
AACGTATTCAGAATTCTCCA+AGG 0.597884 7:-99660055 None:intergenic
TACAACCATCATTACAGCAA+TGG 0.598226 7:+99659880 MsaT040380.1:CDS
GTAGATGAAAGCAGGAGTGC+TGG 0.600296 7:+99656225 MsaT040380.1:CDS
GTTGTATGCAGTGTTGGAGA+AGG 0.602504 7:+99656990 MsaT040380.1:intron
AATGTTACGGAAGGAGGGGA+AGG 0.604293 7:+99659060 MsaT040380.1:CDS
TGATGTTCTGAATGTTCTCA+TGG 0.604294 7:+99657555 MsaT040380.1:CDS
TCTGAATGTTCTCATGGCAA+TGG 0.604838 7:+99657561 MsaT040380.1:CDS
TCTGTTTGCAGATCCAAATG+TGG 0.606015 7:+99662869 MsaT040380.1:intron
GCTTTGATTCTCATTTGACC+CGG 0.611038 7:-99661958 None:intergenic
TTCCTCAAGCTCCTTTAGGT+AGG 0.612657 7:-99657823 None:intergenic
GAACATCATATGCCCTTCGA+CGG 0.612919 7:-99657540 None:intergenic
AGCTTCTCAATAGCACTAGG+AGG 0.614094 7:-99657628 None:intergenic
ATGGTTTAATTTGAGAGCAG+CGG 0.615471 7:-99656286 None:intergenic
CTAGGTGGCAGATGAACTTG+TGG 0.615812 7:+99657342 MsaT040380.1:intron
ACTCAATGTTACGGAAGGAG+GGG 0.616617 7:+99659056 MsaT040380.1:CDS
GGGAAGAACAACTTTCAATG+AGG 0.618421 7:+99657023 MsaT040380.1:CDS
ACGTATTCAGAATTCTCCAA+GGG 0.620753 7:-99660054 None:intergenic
GGAAATTGATGGTCTTCCTA+AGG 0.631711 7:+99662890 MsaT040380.1:CDS
ATAGCTACCAGGTGAAATAG+GGG 0.632130 7:-99661880 None:intergenic
GGAAGATGGGAACGCGACTG+CGG 0.633565 7:+99656193 None:intergenic
ATTGACACGCTTGAAACTGA+AGG 0.637612 7:-99659120 None:intergenic
AGATCAGGAAATCCTTCAAG+CGG 0.637885 7:+99658060 MsaT040380.1:CDS
GCTACACTCAATGTTACGGA+AGG 0.641637 7:+99659051 MsaT040380.1:CDS
GGAAATTGATAGTCTTGCTA+AGG 0.641726 7:+99660014 MsaT040380.1:CDS
TCAAGTTCAACAGTTGCATG+AGG 0.655545 7:-99658638 None:intergenic
GAAAGCGGAGGTGATGCCTG+AGG 0.658645 7:-99659147 None:intergenic
CGTCCTGGAAATTTGCATTG+CGG 0.662002 7:+99661912 MsaT040380.1:CDS
GACACGCTTGAAACTGAAGG+AGG 0.686824 7:-99659117 None:intergenic
TTAAGTATTCCAGAAAGCGG+AGG 0.697488 7:-99659159 None:intergenic
AGTGTAGCAATATCTCTCCG+AGG 0.743133 7:-99659036 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr7 gene 99656198 99663627 99656198 ID=MsaG040380
Chr7 mRNA 99656198 99663627 99656198 ID=MsaT040380.1;Parent=MsaG040380
Chr7 exon 99656198 99656352 99656198 ID=MsaT040380.1.exon1;Parent=MsaT040380.1
Chr7 CDS 99656198 99656352 99656198 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99656821 99656903 99656821 ID=MsaT040380.1.exon2;Parent=MsaT040380.1
Chr7 CDS 99656821 99656903 99656821 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99657001 99657044 99657001 ID=MsaT040380.1.exon3;Parent=MsaT040380.1
Chr7 CDS 99657001 99657044 99657001 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99657346 99657408 99657346 ID=MsaT040380.1.exon4;Parent=MsaT040380.1
Chr7 CDS 99657346 99657408 99657346 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99657517 99657654 99657517 ID=MsaT040380.1.exon5;Parent=MsaT040380.1
Chr7 CDS 99657517 99657654 99657517 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99657780 99657848 99657780 ID=MsaT040380.1.exon6;Parent=MsaT040380.1
Chr7 CDS 99657780 99657848 99657780 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99658015 99658113 99658015 ID=MsaT040380.1.exon7;Parent=MsaT040380.1
Chr7 CDS 99658015 99658113 99658015 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99658632 99658717 99658632 ID=MsaT040380.1.exon8;Parent=MsaT040380.1
Chr7 CDS 99658632 99658717 99658632 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99658975 99659182 99658975 ID=MsaT040380.1.exon9;Parent=MsaT040380.1
Chr7 CDS 99658975 99659182 99658975 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99659865 99659901 99659865 ID=MsaT040380.1.exon10;Parent=MsaT040380.1
Chr7 CDS 99659865 99659901 99659865 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99659998 99660093 99659998 ID=MsaT040380.1.exon11;Parent=MsaT040380.1
Chr7 CDS 99659998 99660093 99659998 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99661823 99662038 99661823 ID=MsaT040380.1.exon12;Parent=MsaT040380.1
Chr7 CDS 99661823 99662038 99661823 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99662880 99662978 99662880 ID=MsaT040380.1.exon13;Parent=MsaT040380.1
Chr7 CDS 99662880 99662978 99662880 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Chr7 exon 99663623 99663627 99663623 ID=MsaT040380.1.exon14;Parent=MsaT040380.1
Chr7 CDS 99663623 99663627 99663623 ID=cds.MsaT040380.1;Parent=MsaT040380.1
Gene Sequence

>MsaT040380.1

ATGGGAACGCGACTGCGGAAATCATGTGTAGATGAAAGCAGGAGTGCTGGTTTTCCATCTAGCCGGAGCAAGCCGACGACGCAGAGAGCCGCTGCTCTCAAATTAAACCATCTTGACATACATGATGATGATGCAGGATCACAAGGAGCAGTTGTTAGCAAGAAGAAAAAGAGGGGCCAACAACGGGATGCTAGAAAAAATAAGAGTAGAAGAGGGCTCCCCCAAATTAGCATGAAAGTGTTGGAGAAGGTAGAAAGTAAGGGAAGAACAACTTTCAATGAGGTGGCAGATGAACTTGTGGCTGAACTTGCTGATCCAATGAATAGTGTTTTGTCCCCTAATAAGCAACAATATGATGAGAAAAACGTCCGTCGAAGGGCATATGATGTTCTGAATGTTCTCATGGCAATGGATATTATTTCCAAGGATAAAAAGGAAATACAATGGAAGGGTCTTCCTCCTAGTGCTATTGAGAAGCTAAAGATCGAATGTCTAGGGATCAAGAATAGAATTGAAAGCAAAGTATCCTACCTAAAGGAGCTTGAGGAACAATTTGTAGGTCTTAAGAACCTTGTTCAACGAAATGAGCAATTATATAGATCAGGAAATCCTTCAAGCGGAGATTTATCTTTACCTTTTGTTCTGGTTCAGACATGTCCTCATGCAACTGTTGAACTTGAAGTGGAAATATCAGAAGAAAATCAAAACATGCAGCTTGTTCATTTTGATTTCAATAGTACTCTTTTTGAACTGCATGACGACTACTATGTGCTCAAAGCAATGGAATTTTGTGATAGACCTCGGAGAGATATTGCTACACTCAATGTTACGGAAGGAGGGGAAGGTTCTAGCTTGTCAGGCTTGCATCAGTTGCAGGTTCCTCCTTCAGTTTCAAGCGTGTCAATTAGGCCTCAGGCATCACCTCCGCTTTCTGGAATACTTAAGCTAACTGGACATCATTACAACCATCATTACAGCAATGATCCAAAATGTCATGTGGAAATTGATAGTCTTGCTAAGGTGAATGACACACAGTTTCCCTTGGAGAATTCTGAATACGTTTTAACTGCTGCAACTGTTGCTTCATCATCCGACTTATCACAATTTACCAACAGAAATGTGACAAGAAAGCTTACCCCTATTTCACCTGGTAGCTATGTTCTAAAGCGTCCTGGAAATTTGCATTGCGGTGACCTAAACAAAGCAACCGTAACCGGGTCAAATGAGAATCAAAGCTTTTATCTAGAGTGTGACGAGAATGGTGAAGATTGTGACGTTCCTGACAATGAATTGGATCCAAATGTGGAAATTGATGGTCTTCCTAAGGTGAATGACACACAATTTCCCTCAGAGAATTCTGAAAACGTTTCAGCTGCTGCAACGGGTGCAACTGGATGA

Protein sequence

>MsaT040380.1

MGTRLRKSCVDESRSAGFPSSRSKPTTQRAAALKLNHLDIHDDDAGSQGAVVSKKKKRGQQRDARKNKSRRGLPQISMKVLEKVESKGRTTFNEVADELVAELADPMNSVLSPNKQQYDEKNVRRRAYDVLNVLMAMDIISKDKKEIQWKGLPPSAIEKLKIECLGIKNRIESKVSYLKELEEQFVGLKNLVQRNEQLYRSGNPSSGDLSLPFVLVQTCPHATVELEVEISEENQNMQLVHFDFNSTLFELHDDYYVLKAMEFCDRPRRDIATLNVTEGGEGSSLSGLHQLQVPPSVSSVSIRPQASPPLSGILKLTGHHYNHHYSNDPKCHVEIDSLAKVNDTQFPLENSEYVLTAATVASSSDLSQFTNRNVTRKLTPISPGSYVLKRPGNLHCGDLNKATVTGSNENQSFYLECDENGEDCDVPDNELDPNVEIDGLPKVNDTQFPSENSENVSAAATGATG*