AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene052655


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene052655.t1 MTR_5g071410 30.469 256 142 3 21 243 19 271 1.32e-30 114
MS.gene052655.t1 MTR_3g082920 49.057 106 38 2 30 133 327 418 1.05e-20 90.5
MS.gene052655.t1 MTR_6g477950 49.412 85 42 1 156 240 61 144 2.44e-19 85.5
MS.gene052655.t1 MTR_7g117585 37.736 106 66 0 138 243 43 148 1.04e-18 80.1
MS.gene052655.t1 MTR_8g069780 41.250 80 47 0 161 240 76 155 9.92e-15 69.7
MS.gene052655.t1 MTR_2g012700 30.508 118 76 2 125 240 6 119 3.29e-13 64.7
MS.gene052655.t1 MTR_3g117130 42.683 82 47 0 159 240 197 278 3.88e-13 67.8
MS.gene052655.t1 MTR_2g062330 35.366 82 52 1 159 240 58 138 1.22e-12 63.9
MS.gene052655.t1 MTR_0010s0310 25.424 236 137 6 20 231 20 240 9.38e-12 63.5
MS.gene052655.t1 MTR_2g437520 39.759 83 47 1 161 240 121 203 9.74e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 55 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACCAGAAGTCGTGAAATTT+TGG 0.193946 3.3:+43362287 None:intergenic
GCAAACTTATCACTTCAAAT+AGG 0.238418 3.3:-43361829 MS.gene052655:CDS
AGCCAAAATTTCACGACTTC+TGG 0.271151 3.3:-43362289 MS.gene052655:CDS
TCACCTAAGTATTTCTCATT+TGG 0.308885 3.3:+43361803 None:intergenic
AAACTGCAAAAGTATGATTA+TGG 0.310821 3.3:-43362367 MS.gene052655:CDS
CAAACTTATCACTTCAAATA+GGG 0.313955 3.3:-43361828 MS.gene052655:CDS
ACCTGTGTACGAGTTAAGTT+TGG 0.331180 3.3:-43362322 MS.gene052655:CDS
GCAGTTGATAGATATCTTAT+TGG 0.337824 3.3:+43361913 None:intergenic
CAGGTTCAAGATGATGGTTT+TGG 0.363392 3.3:-43362194 MS.gene052655:CDS
AGTATGATTATGGATGGATT+AGG 0.381484 3.3:-43362357 MS.gene052655:CDS
CAGTTGATAGATATCTTATT+GGG 0.382252 3.3:+43361914 None:intergenic
TCTACTATCCTTCACGAACT+TGG 0.384344 3.3:+43361772 None:intergenic
CGCTTTCCAATGGAATCAAC+CGG 0.384860 3.3:-43363070 None:intergenic
ACAGGAGAGCATTACTTTGC+AGG 0.396717 3.3:-43361879 MS.gene052655:CDS
ACGTCGCAGCTAAATTCAAC+TGG 0.409112 3.3:-43362261 MS.gene052655:CDS
ACTCGTACACAGGTGCCATT+TGG 0.409607 3.3:+43362331 None:intergenic
TAAGTTTGCACTCATATTCT+CGG 0.417716 3.3:+43361843 None:intergenic
AACTATCATTTATCCACAAC+AGG 0.425989 3.3:-43362548 MS.gene052655:intron
GTATGATTATGGATGGATTA+GGG 0.435600 3.3:-43362356 MS.gene052655:CDS
GGTTGTCCGACGTCGTCGTT+AGG 0.436504 3.3:-43361687 None:intergenic
ACCTCCACAAAGAGACGATT+GGG 0.451863 3.3:+43361707 None:intergenic
AGAAATACTTAGGTGAAGAT+TGG 0.462766 3.3:-43361796 MS.gene052655:CDS
TCCTCCCAATCGTCTCTTTG+TGG 0.465471 3.3:-43361711 MS.gene052655:CDS
GTAATGCTCTCCTGTGTGTC+GGG 0.473972 3.3:+43361887 None:intergenic
CAATGGAATCAACCGGGAAA+AGG 0.480353 3.3:-43363063 MS.gene052655:intron
TGGATGAAGTTGGAAGTTCA+AGG 0.497813 3.3:-43362171 MS.gene052655:CDS
CGTGTTAGACTTGAATATAC+TGG 0.498920 3.3:-43362226 MS.gene052655:CDS
CCTGTGTACGAGTTAAGTTT+GGG 0.512909 3.3:-43362321 MS.gene052655:CDS
GGTCCAAATGAGAAATACTT+AGG 0.515401 3.3:-43361806 MS.gene052655:CDS
TGCAAAAGTATGATTATGGA+TGG 0.520237 3.3:-43362363 MS.gene052655:CDS
TGGATAAATGATAGTTTCGA+AGG 0.529484 3.3:+43362555 None:intergenic
CTACTATCCTTCACGAACTT+GGG 0.542504 3.3:+43361773 None:intergenic
AACCTCCACAAAGAGACGAT+TGG 0.547571 3.3:+43361706 None:intergenic
TATTCAAGTCTAACACGTGT+TGG 0.547805 3.3:+43362232 None:intergenic
AAATTTCACGACTTCTGGTA+GGG 0.551367 3.3:-43362284 MS.gene052655:CDS
CAACAAGAGATGTCAAGTAA+TGG 0.551729 3.3:-43362041 MS.gene052655:intron
TTCAAGGGGAAATACAATCA+AGG 0.560197 3.3:-43362155 MS.gene052655:CDS
TCCCAATCGTCTCTTTGTGG+AGG 0.560244 3.3:-43361708 MS.gene052655:CDS
GGATGAAGTTGGAAGTTCAA+GGG 0.560255 3.3:-43362170 MS.gene052655:CDS
AGTAATGCTCTCCTGTGTGT+CGG 0.561176 3.3:+43361886 None:intergenic
TCGTGAAGGATAGTAGACTA+AGG 0.562838 3.3:-43361766 MS.gene052655:CDS
GGATGGATTAGGGATCCAAA+TGG 0.577469 3.3:-43362346 MS.gene052655:CDS
CCCAAACTTAACTCGTACAC+AGG 0.584015 3.3:+43362321 None:intergenic
AAAATTTCACGACTTCTGGT+AGG 0.588749 3.3:-43362285 MS.gene052655:CDS
AAACTTATCACTTCAAATAG+GGG 0.599416 3.3:-43361827 MS.gene052655:CDS
GATGAAGTTGGAAGTTCAAG+GGG 0.628048 3.3:-43362169 MS.gene052655:CDS
CGTCGCAGCTAAATTCAACT+GGG 0.629434 3.3:-43362260 MS.gene052655:CDS
AAGGATAGTAGACTAAGGAA+AGG 0.649294 3.3:-43361761 MS.gene052655:CDS
CAACTGCTTACCCGACACAC+AGG 0.661269 3.3:-43361897 MS.gene052655:CDS
TCCACAAAGAGACGATTGGG+AGG 0.661851 3.3:+43361710 None:intergenic
GCTTTCCAATGGAATCAACC+GGG 0.669471 3.3:-43363069 None:intergenic
TAATATCCTAACGACGACGT+CGG 0.679159 3.3:+43361681 None:intergenic
AGATTGGCCCAAGTTCGTGA+AGG 0.685876 3.3:-43361780 MS.gene052655:CDS
TAGTTTCGAAGGAATTCACG+AGG 0.693574 3.3:+43362566 None:intergenic
AGTTTCGAAGGAATTCACGA+GGG 0.715405 3.3:+43362567 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTCATAAATAATATTAATT+TGG + chr3.3:43362743-43362762 None:intergenic 10.0%
!!! TTTTTATTATATTCTTTCTA+TGG + chr3.3:43362069-43362088 None:intergenic 10.0%
!! ATACATATTTATGATTTAAC+AGG - chr3.3:43361992-43362011 MS.gene052655:intron 15.0%
!! TTTCAGTAACAAAAAAAATT+TGG + chr3.3:43361895-43361914 None:intergenic 15.0%
!!! ATATTTTATCAAATTTCGTA+TGG - chr3.3:43362268-43362287 MS.gene052655:CDS 15.0%
!! TAAAACATAGAAGGTAATAT+GGG - chr3.3:43361808-43361827 MS.gene052655:CDS 20.0%
! AAACTTATCACTTCAAATAG+GGG - chr3.3:43362922-43362941 MS.gene052655:intron 25.0%
! ACATATAAGATGTATAAGTC+AGG + chr3.3:43362296-43362315 None:intergenic 25.0%
! AGGTATTACAAAATATTGCT+TGG - chr3.3:43362221-43362240 MS.gene052655:CDS 25.0%
! ATATAAGATGTATAAGTCAG+GGG + chr3.3:43362294-43362313 None:intergenic 25.0%
! CAAACTTATCACTTCAAATA+GGG - chr3.3:43362921-43362940 MS.gene052655:intron 25.0%
! CACTATTACTATATTTACGA+TGG + chr3.3:43361761-43361780 None:intergenic 25.0%
! CATATAAGATGTATAAGTCA+GGG + chr3.3:43362295-43362314 None:intergenic 25.0%
! CATCGTAAATATAGTAATAG+TGG - chr3.3:43361759-43361778 MS.gene052655:CDS 25.0%
! CTAAAACATAGAAGGTAATA+TGG - chr3.3:43361807-43361826 MS.gene052655:CDS 25.0%
!! AAACTGCAAAAGTATGATTA+TGG - chr3.3:43362382-43362401 MS.gene052655:CDS 25.0%
!! ATATTTTGTAATACCTGTTG+TGG + chr3.3:43362217-43362236 None:intergenic 25.0%
!! TTTTTACATATCCCATGTTA+TGG - chr3.3:43362030-43362049 MS.gene052655:intron 25.0%
!!! CAGTTGATAGATATCTTATT+GGG + chr3.3:43362838-43362857 None:intergenic 25.0%
AACTATCATTTATCCACAAC+AGG - chr3.3:43362201-43362220 MS.gene052655:CDS 30.0%
AGAAATACTTAGGTGAAGAT+TGG - chr3.3:43362953-43362972 MS.gene052655:intron 30.0%
ATATCCCATGTTATGGAATT+CGG - chr3.3:43362037-43362056 MS.gene052655:intron 30.0%
CACATATCCTTATCAAGTTT+AGG - chr3.3:43361917-43361936 MS.gene052655:CDS 30.0%
CTAAACTTGATAAGGATATG+TGG + chr3.3:43361919-43361938 None:intergenic 30.0%
GCAAACTTATCACTTCAAAT+AGG - chr3.3:43362920-43362939 MS.gene052655:intron 30.0%
TAAGTTTGCACTCATATTCT+CGG + chr3.3:43362909-43362928 None:intergenic 30.0%
TCACCTAAGTATTTCTCATT+TGG + chr3.3:43362949-43362968 None:intergenic 30.0%
TGGATAAATGATAGTTTCGA+AGG + chr3.3:43362197-43362216 None:intergenic 30.0%
! ACATGCAATTTTGTAATGAG+TGG - chr3.3:43361952-43361971 MS.gene052655:intron 30.0%
! AGAGTAAAATTACCTTTTCC+CGG + chr3.3:43361701-43361720 None:intergenic 30.0%
! AGTATGATTATGGATGGATT+AGG - chr3.3:43362392-43362411 MS.gene052655:CDS 30.0%
! CTGATTATGATCATTTTGAG+AGG - chr3.3:43362662-43362681 MS.gene052655:intron 30.0%
! GTAATATGGGTTCTTTTCTA+GGG - chr3.3:43361821-43361840 MS.gene052655:CDS 30.0%
! TGCAAAAGTATGATTATGGA+TGG - chr3.3:43362386-43362405 MS.gene052655:CDS 30.0%
! TTTTAACAGGTTCAAGATGA+TGG - chr3.3:43362549-43362568 MS.gene052655:CDS 30.0%
!! GCAGTTGATAGATATCTTAT+TGG + chr3.3:43362839-43362858 None:intergenic 30.0%
!! GTATGATTATGGATGGATTA+GGG - chr3.3:43362393-43362412 MS.gene052655:CDS 30.0%
AAAATTTCACGACTTCTGGT+AGG - chr3.3:43362464-43362483 MS.gene052655:intron 35.0%
AAATTTCACGACTTCTGGTA+GGG - chr3.3:43362465-43362484 MS.gene052655:intron 35.0%
AAGGATAGTAGACTAAGGAA+AGG - chr3.3:43362988-43363007 MS.gene052655:intron 35.0%
CAACAAGAGATGTCAAGTAA+TGG - chr3.3:43362708-43362727 MS.gene052655:intron 35.0%
CGTGTTAGACTTGAATATAC+TGG - chr3.3:43362523-43362542 MS.gene052655:intron 35.0%
GGTCCAAATGAGAAATACTT+AGG - chr3.3:43362943-43362962 MS.gene052655:intron 35.0%
TAAGGTGGCTAAAACATAGA+AGG - chr3.3:43361799-43361818 MS.gene052655:CDS 35.0%
TATTCAAGTCTAACACGTGT+TGG + chr3.3:43362520-43362539 None:intergenic 35.0%
TTCAAGGGGAAATACAATCA+AGG - chr3.3:43362594-43362613 MS.gene052655:CDS 35.0%
! AATATACTGGCGCTTTTAAC+AGG - chr3.3:43362536-43362555 MS.gene052655:intron 35.0%
! GGTAATATGGGTTCTTTTCT+AGG - chr3.3:43361820-43361839 MS.gene052655:CDS 35.0%
! TACCAGAAGTCGTGAAATTT+TGG + chr3.3:43362465-43362484 None:intergenic 35.0%
ACCTGTGTACGAGTTAAGTT+TGG - chr3.3:43362427-43362446 MS.gene052655:intron 40.0%
AGCCAAAATTTCACGACTTC+TGG - chr3.3:43362460-43362479 MS.gene052655:intron 40.0%
AGTTTCGAAGGAATTCACGA+GGG + chr3.3:43362185-43362204 None:intergenic 40.0%
CCTGTGTACGAGTTAAGTTT+GGG - chr3.3:43362428-43362447 MS.gene052655:intron 40.0%
CCTTATCAAGTTTAGGCTGA+CGG - chr3.3:43361924-43361943 MS.gene052655:intron 40.0%
CTACTATCCTTCACGAACTT+GGG + chr3.3:43362979-43362998 None:intergenic 40.0%
GATGAAGTTGGAAGTTCAAG+GGG - chr3.3:43362580-43362599 MS.gene052655:CDS 40.0%
GGATGAAGTTGGAAGTTCAA+GGG - chr3.3:43362579-43362598 MS.gene052655:CDS 40.0%
TAGTTTCGAAGGAATTCACG+AGG + chr3.3:43362186-43362205 None:intergenic 40.0%
TCCACCGAATTCCATAACAT+GGG + chr3.3:43362044-43362063 None:intergenic 40.0%
TCGTGAAGGATAGTAGACTA+AGG - chr3.3:43362983-43363002 MS.gene052655:intron 40.0%
TCTACTATCCTTCACGAACT+TGG + chr3.3:43362980-43362999 None:intergenic 40.0%
TGGATGAAGTTGGAAGTTCA+AGG - chr3.3:43362578-43362597 MS.gene052655:CDS 40.0%
TTCCACCGAATTCCATAACA+TGG + chr3.3:43362045-43362064 None:intergenic 40.0%
!! CAGGTTCAAGATGATGGTTT+TGG - chr3.3:43362555-43362574 MS.gene052655:CDS 40.0%
!!! ATGGTTTTGGTGGATGAAGT+TGG - chr3.3:43362568-43362587 MS.gene052655:CDS 40.0%
!!! GTTCAAGATGATGGTTTTGG+TGG - chr3.3:43362558-43362577 MS.gene052655:CDS 40.0%
AACCTCCACAAAGAGACGAT+TGG + chr3.3:43363046-43363065 None:intergenic 45.0%
ACCTCCACAAAGAGACGATT+GGG + chr3.3:43363045-43363064 None:intergenic 45.0%
ACGTCGCAGCTAAATTCAAC+TGG - chr3.3:43362488-43362507 MS.gene052655:intron 45.0%
AGTAATGCTCTCCTGTGTGT+CGG + chr3.3:43362866-43362885 None:intergenic 45.0%
ATAGTGGTCCCCTATAGTCT+TGG - chr3.3:43361775-43361794 MS.gene052655:CDS 45.0%
CACCTTAGCCAAGACTATAG+GGG + chr3.3:43361786-43361805 None:intergenic 45.0%
CCACCTTAGCCAAGACTATA+GGG + chr3.3:43361787-43361806 None:intergenic 45.0%
CCCAAACTTAACTCGTACAC+AGG + chr3.3:43362431-43362450 None:intergenic 45.0%
CCGTCAGCCTAAACTTGATA+AGG + chr3.3:43361927-43361946 None:intergenic 45.0%
CGTCGCAGCTAAATTCAACT+GGG - chr3.3:43362489-43362508 MS.gene052655:intron 45.0%
TCCCATGTTATGGAATTCGG+TGG - chr3.3:43362040-43362059 MS.gene052655:intron 45.0%
!! ACAGGAGAGCATTACTTTGC+AGG - chr3.3:43362870-43362889 MS.gene052655:intron 45.0%
!! GGATGGATTAGGGATCCAAA+TGG - chr3.3:43362403-43362422 MS.gene052655:CDS 45.0%
GCCACCTTAGCCAAGACTAT+AGG + chr3.3:43361788-43361807 None:intergenic 50.0%
GTAATGCTCTCCTGTGTGTC+GGG + chr3.3:43362865-43362884 None:intergenic 50.0%
TCCACAAAGAGACGATTGGG+AGG + chr3.3:43363042-43363061 None:intergenic 50.0%
TCCCAATCGTCTCTTTGTGG+AGG - chr3.3:43363041-43363060 MS.gene052655:intron 50.0%
TCCTCCCAATCGTCTCTTTG+TGG - chr3.3:43363038-43363057 MS.gene052655:intron 50.0%
! AGATTGGCCCAAGTTCGTGA+AGG - chr3.3:43362969-43362988 MS.gene052655:intron 50.0%
! CCCTATAGTCTTGGCTAAGG+TGG - chr3.3:43361784-43361803 MS.gene052655:CDS 50.0%
! GTCCCCTATAGTCTTGGCTA+AGG - chr3.3:43361781-43361800 MS.gene052655:CDS 50.0%
!! ACTCGTACACAGGTGCCATT+TGG + chr3.3:43362421-43362440 None:intergenic 50.0%
CAACTGCTTACCCGACACAC+AGG - chr3.3:43362852-43362871 MS.gene052655:intron 55.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 43361688 43363083 43361688 ID=MS.gene052655
chr3.3 mRNA 43361688 43363083 43361688 ID=MS.gene052655.t1;Parent=MS.gene052655
chr3.3 exon 43363064 43363083 43363064 ID=MS.gene052655.t1.exon1;Parent=MS.gene052655.t1
chr3.3 CDS 43363064 43363083 43363064 ID=cds.MS.gene052655.t1;Parent=MS.gene052655.t1
chr3.3 exon 43362549 43362615 43362549 ID=MS.gene052655.t1.exon2;Parent=MS.gene052655.t1
chr3.3 CDS 43362549 43362615 43362549 ID=cds.MS.gene052655.t1;Parent=MS.gene052655.t1
chr3.3 exon 43362042 43362434 43362042 ID=MS.gene052655.t1.exon3;Parent=MS.gene052655.t1
chr3.3 CDS 43362042 43362434 43362042 ID=cds.MS.gene052655.t1;Parent=MS.gene052655.t1
chr3.3 exon 43361688 43361942 43361688 ID=MS.gene052655.t1.exon4;Parent=MS.gene052655.t1
chr3.3 CDS 43361688 43361942 43361688 ID=cds.MS.gene052655.t1;Parent=MS.gene052655.t1
Gene Sequence

>MS.gene052655

ATGGAATCAACCGGGAAAAGGTAATTTTACTCTCTTTTCTTTCATTTTGTCTCTTTCGTCTCTAAGATTTCCATCGTAAATATAGTAATAGTGGTCCCCTATAGTCTTGGCTAAGGTGGCTAAAACATAGAAGGTAATATGGGTTCTTTTCTAGGGTTTGCAAGATATTTTGCATAAATTTGAAGTTAATATGAGTTTTTTCTTCCAAATTTTTTTTGTTACTGAAAACCACATATCCTTATCAAGTTTAGGCTGACGGTTATAACATGCAATTTTGTAATGAGTGGAAATCAATTTTAGTGATATACATATTTATGATTTAACAGGTAGAAGCAATTAGTATTTTTACATATCCCATGTTATGGAATTCGGTGGAAACCATAGAAAGAATATAATAAAAACAGTTTTCTTATAAATATTTAGTTACATGATTTTTGTATGTAATTAACTACAATCAATTGTTTTTAGATTATGCAAAGCAACAAGCTACTATACCCTCGTGAATTCCTTCGAAACTATCATTTATCCACAACAGGTATTACAAAATATTGCTTGGTTGTTATGATATTCTTGTATAATGATATTTTATCAAATTTCGTATGGCCCCTGACTTATACATCTTATATGTGTGTTTTTTTTATCGTTGTAGTCAAAGATACAAGTATGTTCTGTATTCTTCTCATCTTACTTCAAGAAACTGCAAAAGTATGATTATGGATGGATTAGGGATCCAAATGGCACCTGTGTACGAGTTAAGTTTGGGAGAAATTTAAGCCAAAATTTCACGACTTCTGGTAGGGACGTCGCAGCTAAATTCAACTGGGAGAAACCAACACGTGTTAGACTTGAATATACTGGCGCTTTTAACAGGTTCAAGATGATGGTTTTGGTGGATGAAGTTGGAAGTTCAAGGGGAAATACAATCAAGGAAGAAGTTATTGATTCTGATTCTGAAGATGATTGTATAGAAATTGCTGATTATGATCATTTTGAGAGGAATGTCACATATGTCACAGCTAACAACAAGAGATGTCAAGTAATGGTATGTTCAACCAAATTAATATTATTTATGAACATTACAATTATTCATTTAACATTCATTATTTGCATACTAAAGCATGTGAGTTTATAATTTGTTTAGCACTTTCCCAATAAGATATCTATCAACTGCTTACCCGACACACAGGAGAGCATTACTTTGCAGGATGTGCATAATCTCCGAGAATATGAGTGCAAACTTATCACTTCAAATAGGGGTCCAAATGAGAAATACTTAGGTGAAGATTGGCCCAAGTTCGTGAAGGATAGTAGACTAAGGAAAGGTGATAAGTTGATATTTGATCTTTGTGCTCCTCCCAATCGTCTCTTTGTGGAGGTTGTCCGACGTCGTCGTTAG

Protein sequence

>MS.gene052655.t1

MESTGKRLCKATSYYTLVNSFETIIYPQQSKIQVCSVFFSSYFKKLQKYDYGWIRDPNGTCVRVKFGRNLSQNFTTSGRDVAAKFNWEKPTRVRLEYTGAFNRFKMMVLVDEVGSSRGNTIKEEVIDSDSEDDCIEIADYDHFERNVTYVTANNKRCQVMHFPNKISINCLPDTQESITLQDVHNLREYECKLITSNRGPNEKYLGEDWPKFVKDSRLRKGDKLIFDLCAPPNRLFVEVVRRRR