AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54938

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54938.t1 MTR_4g036615 64.463 121 32 2 78 198 1 110 4.24e-45 147
MS.gene54938.t1 MTR_3g408420 28.159 277 139 6 7 236 6 269 3.62e-22 92.8
MS.gene54938.t1 MTR_3g408380 29.615 260 149 8 6 234 5 261 4.44e-21 89.7
MS.gene54938.t1 MTR_3g008310 29.278 263 152 8 6 234 5 267 9.63e-19 83.6
MS.gene54938.t1 MTR_4g100860 24.422 303 164 8 9 252 6 302 5.58e-16 76.3
MS.gene54938.t1 MTR_0160s0030 41.000 100 34 4 177 252 240 338 1.40e-12 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54938.t1 AT1G02030 28.090 267 152 7 9 252 7 256 2.84e-20 87.4
MS.gene54938.t1 AT3G60580 28.763 299 131 10 9 252 6 277 8.33e-16 75.5
MS.gene54938.t1 AT2G45120 32.812 128 54 3 157 252 174 301 2.24e-12 66.2
MS.gene54938.t1 AT5G43170 30.769 117 63 2 139 237 28 144 4.87e-11 60.8

Find 61 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTGGATCGTTTGCGGGTT+GGG 0.196951 4.3:-63276485 None:intergenic
TTCTGTGTCTGTTGTTCTTC+AGG 0.213608 4.3:-63276381 None:intergenic
GATTGTTAGTCTCAAGCTTT+GGG 0.255553 4.3:-63276290 None:intergenic
TTGAACTCTCTGTTGCAATA+TGG 0.277005 4.3:-63276822 None:intergenic
AGTTGCTAGCCTCTTCATTT+AGG 0.305435 4.3:-63276936 None:intergenic
TGATTGTTAGTCTCAAGCTT+TGG 0.307297 4.3:-63276291 None:intergenic
ATCCAGATGTTATGATGTTA+TGG 0.316124 4.3:+63276556 MS.gene54938:CDS
ATTAAGTTTGCGGTGGCATT+TGG 0.323114 4.3:-63276502 None:intergenic
ATCATAACATCTGGATCTAT+TGG 0.340367 4.3:-63276549 None:intergenic
AGTGAGGAAGCAGTTTGATT+TGG 0.345105 4.3:-63276348 None:intergenic
CATTTGGATCGTTTGCGGGT+TGG 0.363193 4.3:-63276486 None:intergenic
GCCTCCAATGGCTTTCCAAC+TGG 0.372433 4.3:-63276232 None:intergenic
CGATCTTATCAAGCTCTTTG+TGG 0.375754 4.3:+63276741 MS.gene54938:CDS
GTGGCATTTGGATCGTTTGC+GGG 0.380859 4.3:-63276490 None:intergenic
GCACCTCTGGCACTTGAAGC+TGG 0.387662 4.3:-63276706 None:intergenic
GATCAAGAAACAAAATATAA+AGG 0.388263 4.3:+63276611 MS.gene54938:CDS
TGAACTCTCTGTTGCAATAT+GGG 0.395083 4.3:-63276821 None:intergenic
AGAAGTTGCGTTTCATAAAT+CGG 0.400917 4.3:-63276407 None:intergenic
AAGCAGTTTGATTTGGATGC+TGG 0.401835 4.3:-63276341 None:intergenic
TTTGGATCGTTTGCGGGTTG+GGG 0.405217 4.3:-63276484 None:intergenic
TAGCCTCTTCATTTAGGATC+TGG 0.419554 4.3:-63276930 None:intergenic
CCCCATAACATCATAACATC+TGG 0.429675 4.3:-63276558 None:intergenic
GATCTTATCAAGCTCTTTGT+GGG 0.431442 4.3:+63276742 MS.gene54938:CDS
GTGTCTGTTGTTCTTCAGGA+TGG 0.448149 4.3:-63276377 None:intergenic
TCCAGATGTTATGATGTTAT+GGG 0.452652 4.3:+63276557 MS.gene54938:CDS
GAAAACCCTGTGGGATTTGT+GGG 0.454964 4.3:+63276199 MS.gene54938:CDS
TTGCAATATGGGCACTGAAA+AGG 0.460303 4.3:-63276810 None:intergenic
ATTTGGATGCTGGGTTAAAT+CGG 0.461815 4.3:-63276331 None:intergenic
CCTGTGGGATTTGTGGGAAA+TGG 0.471689 4.3:+63276205 MS.gene54938:CDS
GGAAAACCCTGTGGGATTTG+TGG 0.474170 4.3:+63276198 MS.gene54938:CDS
CAGCCGCCACATTAAGTTTG+CGG 0.480462 4.3:-63276512 None:intergenic
TTCTCCAGTTGGAAAGCCAT+TGG 0.491423 4.3:+63276228 MS.gene54938:CDS
GTGGGAAATGGTTCTCCAGT+TGG 0.502760 4.3:+63276217 MS.gene54938:CDS
AGATCTCATGTGGCCTCCAA+TGG 0.503462 4.3:-63276244 None:intergenic
AGCAGTTTGATTTGGATGCT+GGG 0.520346 4.3:-63276340 None:intergenic
GGTGGCATTTGGATCGTTTG+CGG 0.534803 4.3:-63276491 None:intergenic
AAAGGAAACTAACAAAATGA+AGG 0.534850 4.3:+63276629 MS.gene54938:CDS
TTCAAGACTGCTCAAGCACT+CGG 0.534991 4.3:+63276840 MS.gene54938:CDS
TCCAGTTGGAAAGCCATTGG+AGG 0.544889 4.3:+63276231 MS.gene54938:CDS
CCAGATGTTATGATGTTATG+GGG 0.550013 4.3:+63276558 MS.gene54938:CDS
CACAAAGAGCTTGATAAGAT+CGG 0.560648 4.3:-63276740 None:intergenic
GCAACAATGGAGAGGAGCAT+CGG 0.563031 4.3:+63276177 None:intergenic
CCATTTCCCACAAATCCCAC+AGG 0.578192 4.3:-63276205 None:intergenic
TGAATTTCGAAGTGTGTCAG+TGG 0.600629 4.3:+63276896 MS.gene54938:CDS
AGGCCACATGAGATCTCACT+TGG 0.604186 4.3:+63276251 MS.gene54938:CDS
TTGTTAGTCTCAAGCTTTGG+GGG 0.604653 4.3:-63276288 None:intergenic
AAGCACTCGGTGGACACAAG+AGG 0.606213 4.3:+63276853 MS.gene54938:CDS
CATTTCCCACAAATCCCACA+GGG 0.615076 4.3:-63276204 None:intergenic
ATGCCACCGCAAACTTAATG+TGG 0.617211 4.3:+63276506 MS.gene54938:CDS
CAGATGTTATGATGTTATGG+GGG 0.618129 4.3:+63276559 MS.gene54938:CDS
CCGCCACATTAAGTTTGCGG+TGG 0.618280 4.3:-63276509 None:intergenic
ATTGTTAGTCTCAAGCTTTG+GGG 0.629340 4.3:-63276289 None:intergenic
AGCACTCGGTGGACACAAGA+GGG 0.633704 4.3:+63276854 MS.gene54938:CDS
CCACCGCAAACTTAATGTGG+CGG 0.643129 4.3:+63276509 MS.gene54938:CDS
AAGCCAGCTTCAAGTGCCAG+AGG 0.652459 4.3:+63276703 MS.gene54938:CDS
TGACCAAGTGAGATCTCATG+TGG 0.656828 4.3:-63276254 None:intergenic
TACTGCAAAAGTGACAGCGA+TGG 0.663269 4.3:+63276774 MS.gene54938:CDS
GGAGCATCGGAAAACCCTGT+GGG 0.672394 4.3:+63276190 MS.gene54938:CDS
AAGACTGCTCAAGCACTCGG+TGG 0.680534 4.3:+63276843 MS.gene54938:CDS
AGGAGCATCGGAAAACCCTG+TGG 0.684970 4.3:+63276189 MS.gene54938:CDS
TTCAGGATGGAAAGTCAGTG+AGG 0.717603 4.3:-63276364 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATCAAGAAACAAAATATAA+AGG + chr4.3:63276611-63276630 MS.gene54938:CDS 20.0%
! AAAGGAAACTAACAAAATGA+AGG + chr4.3:63276629-63276648 MS.gene54938:CDS 25.0%
! TTACAAAGATGCACAAAAAA+GGG + chr4.3:63276584-63276603 MS.gene54938:CDS 25.0%
! TTTACAAAGATGCACAAAAA+AGG + chr4.3:63276583-63276602 MS.gene54938:CDS 25.0%
AGAAGTTGCGTTTCATAAAT+CGG - chr4.3:63276410-63276429 None:intergenic 30.0%
ATCATAACATCTGGATCTAT+TGG - chr4.3:63276552-63276571 None:intergenic 30.0%
ATCCAGATGTTATGATGTTA+TGG + chr4.3:63276556-63276575 MS.gene54938:CDS 30.0%
TCCAGATGTTATGATGTTAT+GGG + chr4.3:63276557-63276576 MS.gene54938:CDS 30.0%
ATTTGGATGCTGGGTTAAAT+CGG - chr4.3:63276334-63276353 None:intergenic 35.0%
CACAAAGAGCTTGATAAGAT+CGG - chr4.3:63276743-63276762 None:intergenic 35.0%
CAGATGTTATGATGTTATGG+GGG + chr4.3:63276559-63276578 MS.gene54938:CDS 35.0%
CCAGATGTTATGATGTTATG+GGG + chr4.3:63276558-63276577 MS.gene54938:CDS 35.0%
GATCTTATCAAGCTCTTTGT+GGG + chr4.3:63276742-63276761 MS.gene54938:CDS 35.0%
TGAACTCTCTGTTGCAATAT+GGG - chr4.3:63276824-63276843 None:intergenic 35.0%
TTGAACTCTCTGTTGCAATA+TGG - chr4.3:63276825-63276844 None:intergenic 35.0%
! ATTGTTAGTCTCAAGCTTTG+GGG - chr4.3:63276292-63276311 None:intergenic 35.0%
! GATTGTTAGTCTCAAGCTTT+GGG - chr4.3:63276293-63276312 None:intergenic 35.0%
! TGATTGTTAGTCTCAAGCTT+TGG - chr4.3:63276294-63276313 None:intergenic 35.0%
AGTGAGGAAGCAGTTTGATT+TGG - chr4.3:63276351-63276370 None:intergenic 40.0%
ATTAAGTTTGCGGTGGCATT+TGG - chr4.3:63276505-63276524 None:intergenic 40.0%
CCCCATAACATCATAACATC+TGG - chr4.3:63276561-63276580 None:intergenic 40.0%
CGATCTTATCAAGCTCTTTG+TGG + chr4.3:63276741-63276760 MS.gene54938:CDS 40.0%
TGAATTTCGAAGTGTGTCAG+TGG + chr4.3:63276896-63276915 MS.gene54938:CDS 40.0%
TTCTGTGTCTGTTGTTCTTC+AGG - chr4.3:63276384-63276403 None:intergenic 40.0%
! TTGTTAGTCTCAAGCTTTGG+GGG - chr4.3:63276291-63276310 None:intergenic 40.0%
!! AAGCAGTTTGATTTGGATGC+TGG - chr4.3:63276344-63276363 None:intergenic 40.0%
!! AGCAGTTTGATTTGGATGCT+GGG - chr4.3:63276343-63276362 None:intergenic 40.0%
!! TTGCAATATGGGCACTGAAA+AGG - chr4.3:63276813-63276832 None:intergenic 40.0%
ATGCCACCGCAAACTTAATG+TGG + chr4.3:63276506-63276525 MS.gene54938:CDS 45.0%
ATTTGGATCGTTTGCGGGTT+GGG - chr4.3:63276488-63276507 None:intergenic 45.0%
CATTTCCCACAAATCCCACA+GGG - chr4.3:63276207-63276226 None:intergenic 45.0%
GAAAACCCTGTGGGATTTGT+GGG + chr4.3:63276199-63276218 MS.gene54938:CDS 45.0%
GTGTCTGTTGTTCTTCAGGA+TGG - chr4.3:63276380-63276399 None:intergenic 45.0%
TACTGCAAAAGTGACAGCGA+TGG + chr4.3:63276774-63276793 MS.gene54938:CDS 45.0%
TGACCAAGTGAGATCTCATG+TGG - chr4.3:63276257-63276276 None:intergenic 45.0%
TTCAAGACTGCTCAAGCACT+CGG + chr4.3:63276840-63276859 MS.gene54938:CDS 45.0%
TTCAGGATGGAAAGTCAGTG+AGG - chr4.3:63276367-63276386 None:intergenic 45.0%
TTCTCCAGTTGGAAAGCCAT+TGG + chr4.3:63276228-63276247 MS.gene54938:CDS 45.0%
! GGAACATTTTTCTGCACCTC+TGG - chr4.3:63276722-63276741 None:intergenic 45.0%
AGATCTCATGTGGCCTCCAA+TGG - chr4.3:63276247-63276266 None:intergenic 50.0%
AGGCCACATGAGATCTCACT+TGG + chr4.3:63276251-63276270 MS.gene54938:CDS 50.0%
CAGCCGCCACATTAAGTTTG+CGG - chr4.3:63276515-63276534 None:intergenic 50.0%
CATTTGGATCGTTTGCGGGT+TGG - chr4.3:63276489-63276508 None:intergenic 50.0%
CCACCGCAAACTTAATGTGG+CGG + chr4.3:63276509-63276528 MS.gene54938:CDS 50.0%
CCATTTCCCACAAATCCCAC+AGG - chr4.3:63276208-63276227 None:intergenic 50.0%
CCTGTGGGATTTGTGGGAAA+TGG + chr4.3:63276205-63276224 MS.gene54938:CDS 50.0%
GGAAAACCCTGTGGGATTTG+TGG + chr4.3:63276198-63276217 MS.gene54938:CDS 50.0%
GGTGGCATTTGGATCGTTTG+CGG - chr4.3:63276494-63276513 None:intergenic 50.0%
GTGGCATTTGGATCGTTTGC+GGG - chr4.3:63276493-63276512 None:intergenic 50.0%
GTGGGAAATGGTTCTCCAGT+TGG + chr4.3:63276217-63276236 MS.gene54938:CDS 50.0%
TCCAGTTGGAAAGCCATTGG+AGG + chr4.3:63276231-63276250 MS.gene54938:CDS 50.0%
! TTTGGATCGTTTGCGGGTTG+GGG - chr4.3:63276487-63276506 None:intergenic 50.0%
!! GTCTCAAGCTTTGGGGGAAT+CGG - chr4.3:63276285-63276304 None:intergenic 50.0%
AAGACTGCTCAAGCACTCGG+TGG + chr4.3:63276843-63276862 MS.gene54938:CDS 55.0%
AAGCCAGCTTCAAGTGCCAG+AGG + chr4.3:63276703-63276722 MS.gene54938:CDS 55.0%
CCGCCACATTAAGTTTGCGG+TGG - chr4.3:63276512-63276531 None:intergenic 55.0%
GCCTCCAATGGCTTTCCAAC+TGG - chr4.3:63276235-63276254 None:intergenic 55.0%
! AAGCACTCGGTGGACACAAG+AGG + chr4.3:63276853-63276872 MS.gene54938:CDS 55.0%
! AGCACTCGGTGGACACAAGA+GGG + chr4.3:63276854-63276873 MS.gene54938:CDS 55.0%
!! AGGAGCATCGGAAAACCCTG+TGG + chr4.3:63276189-63276208 MS.gene54938:CDS 55.0%
!! GGAGCATCGGAAAACCCTGT+GGG + chr4.3:63276190-63276209 MS.gene54938:CDS 55.0%
!!! CGTTTGCGGGTTGGGGTTTT+CGG - chr4.3:63276480-63276499 None:intergenic 55.0%
!!! GGGGTTTTCGGGTAAGACAC+AGG - chr4.3:63276468-63276487 None:intergenic 55.0%
!!! GTTTGCGGGTTGGGGTTTTC+GGG - chr4.3:63276479-63276498 None:intergenic 55.0%
GCACCTCTGGCACTTGAAGC+TGG - chr4.3:63276709-63276728 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 63276183 63276944 63276183 ID=MS.gene54938
chr4.3 mRNA 63276183 63276944 63276183 ID=MS.gene54938.t1;Parent=MS.gene54938
chr4.3 exon 63276183 63276944 63276183 ID=MS.gene54938.t1.exon1;Parent=MS.gene54938.t1
chr4.3 CDS 63276183 63276944 63276183 ID=cds.MS.gene54938.t1;Parent=MS.gene54938.t1
Gene Sequence

>MS.gene54938

ATGGAGAGGAGCATCGGAAAACCCTGTGGGATTTGTGGGAAATGGTTCTCCAGTTGGAAAGCCATTGGAGGCCACATGAGATCTCACTTGGTCAAATTGCCGATTCCCCCAAAGCTTGAGACTAACAATCAAGCTCAAGATAATTCAGCCGATTTAACCCAGCATCCAAATCAAACTGCTTCCTCACTGACTTTCCATCCTGAAGAACAACAGACACAGAACTTCCGATTTATGAAACGCAACTTCTCTGCTTTCTCTGCAGACTCAAACAGAGAAAACGAACCTGTGTCTTACCCGAAAACCCCAACCCGCAAACGATCCAAATGCCACCGCAAACTTAATGTGGCGGCTGATACAAAAGATCTGCCAATAGATCCAGATGTTATGATGTTATGGGGGTTTTACAAAGATGCACAAAAAAGGGAAGAGATCAAGAAACAAAATATAAAGGAAACTAACAAAATGAAGGAAAAAGACACTGAAGACAGTAGAGATGACTCGATTATTCAAGCTCACACTCAAGCCAGCTTCAAGTGCCAGAGGTGCAGAAAAATGTTCCGATCTTATCAAGCTCTTTGTGGGCACAAAGCATACTGCAAAAGTGACAGCGATGGTGAAGATCAGAAACCTTTTCAGTGCCCATATTGCAACAGAGAGTTCAAGACTGCTCAAGCACTCGGTGGACACAAGAGGGTACACTTTTCAAGTGCTAATGAATTTCGAAGTGTGTCAGTGGATCTCAATTTTCCAGATCCTAAATGA
Protein sequence

>MS.gene54938.t1

MERSIGKPCGICGKWFSSWKAIGGHMRSHLVKLPIPPKLETNNQAQDNSADLTQHPNQTASSLTFHPEEQQTQNFRFMKRNFSAFSADSNRENEPVSYPKTPTRKRSKCHRKLNVAADTKDLPIDPDVMMLWGFYKDAQKREEIKKQNIKETNKMKEKDTEDSRDDSIIQAHTQASFKCQRCRKMFRSYQALCGHKAYCKSDSDGEDQKPFQCPYCNREFKTAQALGGHKRVHFSSANEFRSVSVDLNFPDPK