AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0409840

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0409840 MtrunA17_Chr3g0101031 96.544 434 13 2 12 445 1 432 0.0 853
Msa0409840 MtrunA17_Chr5g0445221 71.659 434 104 7 14 445 1 417 0.0 605
Msa0409840 MtrunA17_Chr5g0441911 36.905 420 212 10 65 445 32 437 1.09e-79 253
Msa0409840 MtrunA17_Chr3g0094501 37.560 418 215 10 65 445 35 443 2.91e-79 252
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0409840 AT5G55530.2 56.193 436 156 9 14 445 1 405 9.36e-156 447
Msa0409840 AT5G55530.1 56.193 436 156 9 14 445 1 405 9.36e-156 447
Msa0409840 AT5G55530.3 56.193 436 156 9 14 445 1 405 9.36e-156 447
Msa0409840 AT1G50570.2 53.652 397 151 9 52 445 22 388 1.34e-125 370
Msa0409840 AT1G50570.1 53.652 397 151 9 52 445 22 388 1.34e-125 370
Msa0409840 AT5G12300.1 44.872 78 28 2 383 445 297 374 5.49e-12 67.4

Find 127 sgRNAs with CRISPR-Local

Find 2 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATTGTGAAATTGAACTTTA+TGG 0.192348 3_2:+50999222 Msa0409840:three_prime_UTR
TGTATTTCTTCTGATGTTGT+AGG 0.215421 3_2:+50999090 Msa0409840:three_prime_UTR
CAATCTTCGTCTCAATGTTT+TGG 0.227735 3_2:+50997797 Msa0409840:CDS
CTTCTGATGTTGTAGGTTAC+AGG 0.233561 3_2:+50999097 Msa0409840:three_prime_UTR
CTTTCTCTAGTTTACCATTC+TGG 0.234179 3_2:-50997929 None:intergenic
TTAATGGTTTCGGAATATTT+TGG 0.254413 3_2:+50998173 Msa0409840:CDS
GATCTGTTTCATTCTCCTTC+AGG 0.261707 3_2:+50997972 Msa0409840:CDS
TGGTCTTCGTTTGCAATCTT+AGG 0.278614 3_2:-50998149 None:intergenic
GTCTCTACTAAGACCATTAA+TGG 0.281756 3_2:+50997747 Msa0409840:CDS
GTTCCTTCCACCACCATTAA+TGG 0.282080 3_2:-50997760 None:intergenic
TGCAAACGAAGACCACTTAA+TGG 0.284606 3_2:+50998157 Msa0409840:CDS
CCAAGTCATGAAGAAGTTTC+AGG 0.290335 3_2:+50998437 Msa0409840:CDS
TGAGTCATTGGCCAGAGATT+TGG 0.310125 3_2:+50998106 Msa0409840:CDS
ATTGACTTCAATGTCCTTAG+AGG 0.310219 3_2:-50997574 None:intergenic
TTTGTTGAGCGTAGGGAATT+CGG 0.312645 3_2:+50999004 Msa0409840:three_prime_UTR
CATTGACATTTAGATCAAAA+AGG 0.329626 3_2:-50999200 None:intergenic
TGCTGAACCATCTGCGGCTC+TGG 0.358153 3_2:-50998566 None:intergenic
AATCTGTTGTATCACCCTTT+AGG 0.360952 3_2:+50997487 Msa0409840:CDS
CCTGAAACTTCTTCATGACT+TGG 0.362546 3_2:-50998437 None:intergenic
ACCCTTTAGGACCTCAGTCT+TGG 0.363648 3_2:+50997500 Msa0409840:CDS
CGGTGCTACACCTGATGTTA+TGG 0.365739 3_2:+50998022 Msa0409840:CDS
CGAAGACCACTTAATGGTTT+CGG 0.367450 3_2:+50998163 Msa0409840:CDS
TTGTTGAGCGTAGGGAATTC+GGG 0.373496 3_2:+50999005 Msa0409840:three_prime_UTR
TCCTTGGTTTAAGGGAATAC+AGG 0.374155 3_2:+50998782 Msa0409840:three_prime_UTR
TCGTTTGCAATCTTAGGATC+TGG 0.377435 3_2:-50998143 None:intergenic
CCCTTTAGGACCTCAGTCTT+GGG 0.378600 3_2:+50997501 Msa0409840:CDS
AAGCAATGGTCCTTCCTCTA+AGG 0.384615 3_2:+50997560 Msa0409840:CDS
GAAAGTGAACCAACTACTTC+AGG 0.397702 3_2:+50998668 Msa0409840:CDS
ATGACCAAACAACAGTATTT+CGG 0.402513 3_2:-50997453 None:intergenic
CCAAGCAGTGTGTCGACAAA+TGG 0.402778 3_2:+50998347 Msa0409840:CDS
CTTGAATTTCCTGAAGTAGT+TGG 0.407339 3_2:-50998677 None:intergenic
CTCGGTCATTAGATGAAGAT+TGG 0.425115 3_2:+50998871 Msa0409840:three_prime_UTR
TTAGTAGAGACACTGTTCTC+TGG 0.427254 3_2:-50997735 None:intergenic
TTCACAGTCACAACAGGCTT+AGG 0.428362 3_2:-50998536 None:intergenic
CTGAAACTTCTTCATGACTT+GGG 0.428515 3_2:-50998436 None:intergenic
CAAGCAGTGTGTCGACAAAT+GGG 0.428739 3_2:+50998348 Msa0409840:CDS
GAAATACTGTTGTTTGGTCA+TGG 0.437325 3_2:+50997455 Msa0409840:CDS
CATGTGTTCTAGTGATAATA+TGG 0.437417 3_2:+50999263 Msa0409840:three_prime_UTR
GGTTCCGAAATACTGTTGTT+TGG 0.439339 3_2:+50997449 Msa0409840:intron
GTGAGTTATGGATGCTTAGC+AGG 0.442760 3_2:+50997841 Msa0409840:CDS
CTCGGAAACATGTGAGTCAT+TGG 0.443554 3_2:+50998094 Msa0409840:CDS
CATCTCTCAAATGTGAGTTA+TGG 0.448295 3_2:+50997829 Msa0409840:CDS
CCCAAGACTGAGGTCCTAAA+GGG 0.448538 3_2:-50997501 None:intergenic
TGTTCTCTGGATTACTTGTC+AGG 0.449342 3_2:-50997722 None:intergenic
ATTCATGACTGCGTGACTAC+AGG 0.454594 3_2:-50998848 None:intergenic
CACACATGGGATCTGATCAT+TGG 0.456050 3_2:-50998967 None:intergenic
GACTCAGTGCTCTGATAGCT+TGG 0.460570 3_2:+50998211 Msa0409840:CDS
GGGTTAGTGTTCTTAGTTTG+CGG 0.461854 3_2:-50998716 None:intergenic
TATCTTGAAGATCAGTTGCT+TGG 0.461888 3_2:+50997873 Msa0409840:CDS
ATCTGCTATGCCGGGGAAAG+TGG 0.466245 3_2:+50998049 Msa0409840:CDS
TCAATATTCACAGTCACAAC+AGG 0.469854 3_2:-50998542 None:intergenic
ACCCAAGACTGAGGTCCTAA+AGG 0.474095 3_2:-50997502 None:intergenic
CGATGCTGAAAATCATAGTT+CGG 0.476825 3_2:+50998241 Msa0409840:CDS
GGAAGCTGGTGTTCGTCTTG+TGG 0.480983 3_2:+50998262 Msa0409840:CDS
TATGGCAATATCTGCTATGC+CGG 0.490303 3_2:+50998040 Msa0409840:CDS
TGCGCAAGTGGAACCTCCTA+AGG 0.490411 3_2:+50998313 Msa0409840:CDS
CTTGGTGGAGACTCAACCTT+AGG 0.499060 3_2:-50998329 None:intergenic
GCAGATATTGCCATAACATC+AGG 0.499230 3_2:-50998032 None:intergenic
ATGGCAATATCTGCTATGCC+GGG 0.503138 3_2:+50998041 Msa0409840:CDS
TCACAGTCACAACAGGCTTA+GGG 0.508245 3_2:-50998535 None:intergenic
CCATTTGTCGACACACTGCT+TGG 0.508473 3_2:-50998347 None:intergenic
TCTAAGGACATTGAAGTCAA+TGG 0.508878 3_2:+50997576 Msa0409840:CDS
GAGCGTAGGGAATTCGGGTC+CGG 0.509470 3_2:+50999010 Msa0409840:three_prime_UTR
AGAGCCGCAGATGGTTCAGC+AGG 0.512099 3_2:+50998568 Msa0409840:CDS
AATATTCCGAAACCATTAAG+TGG 0.512567 3_2:-50998169 None:intergenic
GAAAATCATAGTTCGGAAGC+TGG 0.519872 3_2:+50998248 Msa0409840:CDS
AGCGAAAATGAAGCTTCCTA+TGG 0.519913 3_2:+50998640 Msa0409840:CDS
AGGGTGATACAACAGATTGT+GGG 0.523722 3_2:-50997482 None:intergenic
AAGGGTGATACAACAGATTG+TGG 0.527553 3_2:-50997483 None:intergenic
ACTAAGACCATTAATGGTGG+TGG 0.529485 3_2:+50997753 Msa0409840:CDS
TTCTGATGTTGTAGGTTACA+GGG 0.533539 3_2:+50999098 Msa0409840:three_prime_UTR
GGACATTGAAGTCAATGGTA+AGG 0.536615 3_2:+50997581 Msa0409840:CDS
TGAAACTTCTTCATGACTTG+GGG 0.539050 3_2:-50998435 None:intergenic
TTCATGACTGCGTGACTACA+GGG 0.539476 3_2:-50998847 None:intergenic
CTCTGCTTCCATAATAGACA+CGG 0.542849 3_2:-50998739 None:intergenic
GGTGGAGACTCAACCTTAGG+AGG 0.548492 3_2:-50998326 None:intergenic
TGGTTTAAGGGAATACAGGC+AGG 0.549356 3_2:+50998786 Msa0409840:three_prime_UTR
TTTGTCGACACACTGCTTGG+TGG 0.552483 3_2:-50998344 None:intergenic
AGCACACGGTCACACACACA+TGG 0.553151 3_2:-50998981 None:intergenic
GGTTCACTTTCAATGTCCAT+AGG 0.554954 3_2:-50998656 None:intergenic
AGGACCTCAGTCTTGGGTGA+AGG 0.559353 3_2:+50997507 Msa0409840:CDS
GGATACACATGTCACTCAGC+AGG 0.561617 3_2:+50998070 Msa0409840:CDS
CGAAGATTGTCGTTAAACAC+AGG 0.561622 3_2:-50997783 None:intergenic
CAGTGGTGAGTCTGCGCAAG+TGG 0.564989 3_2:+50998301 Msa0409840:CDS
ACATGTGTATCCACTTTCCC+CGG 0.566139 3_2:-50998059 None:intergenic
TAGCATAAACATCTTGCTTG+TGG 0.568663 3_2:-50997692 None:intergenic
GCCTGTATTCCCTTAAACCA+AGG 0.572851 3_2:-50998783 None:intergenic
GAGCACTCCAACGCATTCCT+CGG 0.573851 3_2:-50997622 None:intergenic
ACTTCAATGTCCTTAGAGGA+AGG 0.576019 3_2:-50997570 None:intergenic
TCGTGTTCACCATGTGAACG+TGG 0.578860 3_2:-50999288 None:intergenic
TGTAGCACCGGTGTAAGCAA+TGG 0.580116 3_2:-50998009 None:intergenic
CAATTGTCCATTGCTTACAC+CGG 0.580933 3_2:+50998002 Msa0409840:CDS
TCTGCGCTTTCATGAGCAGA+AGG 0.581314 3_2:-50998380 None:intergenic
AACTATCATGTCAAATGCCG+AGG 0.594132 3_2:+50997605 Msa0409840:CDS
TCAAATGCCGAGGAATGCGT+TGG 0.596916 3_2:+50997615 Msa0409840:CDS
CATAACATCAGGTGTAGCAC+CGG 0.601546 3_2:-50998021 None:intergenic
TCTGCTTCCATAATAGACAC+GGG 0.601885 3_2:-50998738 None:intergenic
GACAATTGAACAAAACCTGA+AGG 0.605270 3_2:-50997987 None:intergenic
ACATGTCACTCAGCAGGACT+CGG 0.609387 3_2:+50998076 Msa0409840:CDS
AATATGGTCCCACGTTCACA+TGG 0.611624 3_2:+50999279 Msa0409840:three_prime_UTR
TATTGAGCCAGAGCCGCAGA+TGG 0.613301 3_2:+50998559 Msa0409840:CDS
GGAAGGACCATTGCTTTGTG+TGG 0.614662 3_2:-50997553 None:intergenic
ATATCCTGCTGAACCATCTG+CGG 0.615970 3_2:-50998572 None:intergenic
AGACCATTAATGGTGGTGGA+AGG 0.619791 3_2:+50997757 Msa0409840:CDS
AACATCAGAAGAAATACAGA+AGG 0.623513 3_2:-50999085 None:intergenic
AGTCACGCAGTCATGAATCT+CGG 0.624964 3_2:+50998853 Msa0409840:three_prime_UTR
ATCACTCGGAACAACACTTG+AGG 0.627514 3_2:-50998507 None:intergenic
CTGCTTCCATAATAGACACG+GGG 0.629788 3_2:-50998737 None:intergenic
GGGTGATACAACAGATTGTG+GGG 0.631149 3_2:-50997481 None:intergenic
GGCTTAGGGAATAAATCACT+CGG 0.633496 3_2:-50998521 None:intergenic
TCGGAAGTACTAGTCCAGAA+TGG 0.639492 3_2:+50997915 Msa0409840:CDS
CGTGTTCACCATGTGAACGT+GGG 0.640245 3_2:-50999287 None:intergenic
TGGACTAGTACTTCCGACAA+CGG 0.662125 3_2:-50997909 None:intergenic
GATGTTACCACACAAAGCAA+TGG 0.662541 3_2:+50997546 Msa0409840:CDS
TGGCAATATCTGCTATGCCG+GGG 0.667680 3_2:+50998042 Msa0409840:CDS
CTACGCTCAACAAAAGCACA+CGG 0.671598 3_2:-50998995 None:intergenic
TACAGAAGGAGAAACCACAC+TGG 0.675767 3_2:-50999071 None:intergenic
CTCACCTTCACCCAAGACTG+AGG 0.679650 3_2:-50997511 None:intergenic
GCACACGGTCACACACACAT+GGG 0.680521 3_2:-50998980 None:intergenic
GAAGATTGTCGTTAAACACA+GGG 0.680691 3_2:-50997782 None:intergenic
AGAAGTTTCAGGAACCAAAG+AGG 0.681573 3_2:+50998448 Msa0409840:CDS
AAGCAGTGTGTCGACAAATG+GGG 0.683408 3_2:+50998349 Msa0409840:CDS
TCTACTAAGACCATTAATGG+TGG 0.695392 3_2:+50997750 Msa0409840:CDS
GAAAGCTTCTCAGCATGCAG+TGG 0.698296 3_2:+50998284 Msa0409840:CDS
TGAGTTATGGATGCTTAGCA+GGG 0.699595 3_2:+50997842 Msa0409840:CDS
AAATAATGTAGTATCCAGTG+TGG 0.711608 3_2:+50999057 Msa0409840:three_prime_UTR
TGCTTCCATAATAGACACGG+GGG 0.772529 3_2:-50998736 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTACATTTATAACCTTAAA+AGG - chr3_2:50994801-50994820 None:intergenic 15.0%
!! CAATTAGCTAAAACCTTTTA+AGG + chr3_2:50994785-50994804 Msa0409840:intron 25.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 50994711 50999308 50994711 ID=Msa0409840;Name=Msa0409840
chr3_2 mRNA 50994711 50999308 50994711 ID=Msa0409840-mRNA-1;Parent=Msa0409840;Name=Msa0409840-mRNA-1;_AED=0.09;_eAED=0.09;_QI=0|0|0.33|0.33|1|1|3|536|445
chr3_2 exon 50994711 50994717 50994711 ID=Msa0409840-mRNA-1:exon:10076;Parent=Msa0409840-mRNA-1
chr3_2 exon 50997238 50997245 50997238 ID=Msa0409840-mRNA-1:exon:10077;Parent=Msa0409840-mRNA-1
chr3_2 exon 50997450 50999308 50997450 ID=Msa0409840-mRNA-1:exon:10078;Parent=Msa0409840-mRNA-1
chr3_2 CDS 50994711 50994717 50994711 ID=Msa0409840-mRNA-1:cds;Parent=Msa0409840-mRNA-1
chr3_2 CDS 50997238 50997245 50997238 ID=Msa0409840-mRNA-1:cds;Parent=Msa0409840-mRNA-1
chr3_2 CDS 50997450 50998772 50997450 ID=Msa0409840-mRNA-1:cds;Parent=Msa0409840-mRNA-1
chr3_2 three_prime_UTR 50998773 50999308 50998773 ID=Msa0409840-mRNA-1:three_prime_utr;Parent=Msa0409840-mRNA-1
Gene Sequence

>Msa0409840

ATGTCATTTATGTTAGTTCCGAAATACTGTTGTTTGGTCATGGATTCCCCACAATCTGTTGTATCACCCTTTAGGACCTCAGTCTTGGGTGAAGGTGAGAAGCACAAGTCTGATGTTACCACACAAAGCAATGGTCCTTCCTCTAAGGACATTGAAGTCAATGGTAAGGAAACTATCATGTCAAATGCCGAGGAATGCGTTGGAGTGCTCGATGTTTTTATACATCAAGCTAGAGACATTCAGAATATTTGCATATACCACAAGCAAGATGTTTATGCTAAGATTTACCTGACAAGTAATCCAGAGAACAGTGTCTCTACTAAGACCATTAATGGTGGTGGAAGGAACCCTGTGTTTAACGACAATCTTCGTCTCAATGTTTTGGATGTTGATTCATCTCTCAAATGTGAGTTATGGATGCTTAGCAGGGTGAAGAATTATCTTGAAGATCAGTTGCTTGGTTTTGCTTTGGTGCCGTTGTCGGAAGTACTAGTCCAGAATGGTAAACTAGAGAAAGAGTTTTCTCTTTCTTCAACTGATCTGTTTCATTCTCCTTCAGGTTTTGTTCAATTGTCCATTGCTTACACCGGTGCTACACCTGATGTTATGGCAATATCTGCTATGCCGGGGAAAGTGGATACACATGTCACTCAGCAGGACTCGGAAACATGTGAGTCATTGGCCAGAGATTTGGATAAAATTGAGTTTCCAGATCCTAAGATTGCAAACGAAGACCACTTAATGGTTTCGGAATATTTTGGCATTTCGTGCGAGGAGACTCAGTGCTCTGATAGCTTGGCAACTTCCGATGCTGAAAATCATAGTTCGGAAGCTGGTGTTCGTCTTGTGGAAAGCTTCTCAGCATGCAGTGGTGAGTCTGCGCAAGTGGAACCTCCTAAGGTTGAGTCTCCACCAAGCAGTGTGTCGACAAATGGGGTTTCTTCTCCTTCTGCTCATGAAAGCGCAGAATCATCTGATGCTGCAGCAGCAGCTTCTAAGTCCCCAAGTCATGAAGAAGTTTCAGGAACCAAAGAGGTAAAAAAAGTGGATGTCAAAGACGGTGAGAGTGATTCCTCAAGTGTTGTTCCGAGTGATTTATTCCCTAAGCCTGTTGTGACTGTGAATATTGAGCCAGAGCCGCAGATGGTTCAGCAGGATATAGTTGACATGTACATGAAAAGCATGCAGCAATTTACTGAGTCATTAGCGAAAATGAAGCTTCCTATGGACATTGAAAGTGAACCAACTACTTCAGGAAATTCAAGTACTGAGCAGAAACTACCGCAAACTAAGAACACTAACCCCCGTGTCTATTATGGAAGCAGAGCTTTCTTCTGA
Protein sequence

>Msa0409840

MSFMLVPKYCCLVMDSPQSVVSPFRTSVLGEGEKHKSDVTTQSNGPSSKDIEVNGKETIMSNAEECVGVLDVFIHQARDIQNICIYHKQDVYAKIYLTSNPENSVSTKTINGGGRNPVFNDNLRLNVLDVDSSLKCELWMLSRVKNYLEDQLLGFALVPLSEVLVQNGKLEKEFSLSSTDLFHSPSGFVQLSIAYTGATPDVMAISAMPGKVDTHVTQQDSETCESLARDLDKIEFPDPKIANEDHLMVSEYFGISCEETQCSDSLATSDAENHSSEAGVRLVESFSACSGESAQVEPPKVESPPSSVSTNGVSSPSAHESAESSDAAAAASKSPSHEEVSGTKEVKKVDVKDGESDSSSVVPSDLFPKPVVTVNIEPEPQMVQQDIVDMYMKSMQQFTESLAKMKLPMDIESEPTTSGNSSTEQKLPQTKNTNPRVYYGSRAFF*