AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54939

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54939.t1 MTR_4g036615 80.769 104 20 0 78 181 1 104 1.96e-56 176
MS.gene54939.t1 MTR_3g408380 27.547 265 148 7 3 229 2 260 8.69e-20 85.9
MS.gene54939.t1 MTR_4g100860 27.820 266 144 8 9 229 6 268 1.15e-17 80.9
MS.gene54939.t1 MTR_3g408420 25.806 279 139 7 7 232 6 269 1.82e-16 77.0
MS.gene54939.t1 MTR_3g008310 26.038 265 158 7 3 229 2 266 7.38e-16 75.1
MS.gene54939.t1 MTR_0160s0030 41.975 81 37 1 170 240 239 319 4.46e-14 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54939.t1 AT3G60580 30.566 265 116 6 9 229 6 246 4.93e-19 84.3
MS.gene54939.t1 AT1G02030 45.570 79 30 2 171 236 160 238 3.02e-13 67.8
MS.gene54939.t1 AT5G61470 41.096 73 31 2 168 229 225 296 4.15e-12 65.1

Find 60 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAACACTTTGTTGCAATT+TGG 0.166386 4.3:-63387451 None:intergenic
TTCTGTGTTTGTTGTATTTC+GGG 0.187551 4.3:-63387022 None:intergenic
ATTCTGTGTTTGTTGTATTT+CGG 0.237824 4.3:-63387023 None:intergenic
TACTCAAGCTGTAGACAATT+TGG 0.312612 4.3:+63386949 MS.gene54939:CDS
AATTGGATCTCTTGCGGGTT+GGG 0.313326 4.3:-63387126 None:intergenic
TGAACACTTTGTTGCAATTT+GGG 0.315013 4.3:-63387450 None:intergenic
TGAGTATTAGTTTCAAGCTT+TGG 0.337317 4.3:-63386932 None:intergenic
GCCGCAATTGGATCTCTTGC+GGG 0.342035 4.3:-63387131 None:intergenic
CAATTGGATCTCTTGCGGGT+TGG 0.402481 4.3:-63387127 None:intergenic
ATTAAGTTCGCGGCCGCAAT+TGG 0.437633 4.3:-63387143 None:intergenic
ATTTGTGGGAAGTGGTTCTC+CGG 0.453707 4.3:+63386854 MS.gene54939:CDS
GTTTCAAGCTTTGGAGCAAT+CGG 0.454553 4.3:-63386923 None:intergenic
TTCCGATCTTATCAGGCTCT+TGG 0.457389 4.3:+63387361 MS.gene54939:CDS
TACAGAATCACAAATCAATA+CGG 0.462697 4.3:-63387547 None:intergenic
TTCTCCGGTGGGAAAGCCCT+TGG 0.463478 4.3:+63386869 MS.gene54939:CDS
TTGCAATTTGGGCAGTGAAA+AGG 0.463868 4.3:-63387439 None:intergenic
GGAAAGCCTGTGGGATTTGT+GGG 0.467351 4.3:+63386840 MS.gene54939:CDS
GGGAAAGCCTGTGGGATTTG+TGG 0.468727 4.3:+63386839 MS.gene54939:CDS
CGATCTTATCAGGCTCTTGG+TGG 0.468794 4.3:+63387364 MS.gene54939:CDS
GCCTCCAAGGGCTTTCCCAC+CGG 0.472807 4.3:-63386873 None:intergenic
AGATCTCATGTGGCCTCCAA+GGG 0.485485 4.3:-63386885 None:intergenic
TCCGGTGGGAAAGCCCTTGG+AGG 0.494800 4.3:+63386872 MS.gene54939:CDS
TTCAAGTCTGCTCAGGCACT+CGG 0.500253 4.3:+63387469 MS.gene54939:CDS
CCCCATAACATCAAAACACC+TGG 0.500612 4.3:-63387199 None:intergenic
GGCCGCAATTGGATCTCTTG+CGG 0.503301 4.3:-63387132 None:intergenic
TCTGTTTGAGTTTGCAGAGG+AGG 0.504442 4.3:-63387074 None:intergenic
AACGATGGCGAAAGCAGTAC+AGG 0.507873 4.3:+63387277 MS.gene54939:CDS
GCACCTCTCACAGTTGAACC+TGG 0.509618 4.3:-63387329 None:intergenic
CAGCCGCAGCATTAAGTTCG+CGG 0.512384 4.3:-63387153 None:intergenic
TTCTCTGTTTGAGTTTGCAG+AGG 0.512537 4.3:-63387077 None:intergenic
GAGATCTCATGTGGCCTCCA+AGG 0.514030 4.3:-63386886 None:intergenic
GAAGATATGTCAAGAGATCC+AGG 0.516117 4.3:+63387181 MS.gene54939:CDS
TGTGGGAAGTGGTTCTCCGG+TGG 0.517822 4.3:+63386857 MS.gene54939:CDS
ACTTTGAAATTCCTTAGCAC+TGG 0.521740 4.3:-63387515 None:intergenic
CAAAGTGTTCAAGTCTGCTC+AGG 0.524975 4.3:+63387462 MS.gene54939:CDS
CACAAGCAGACTCTGAAGCC+AGG 0.539423 4.3:+63387311 MS.gene54939:CDS
GTGTTTGTTGTATTTCGGGA+AGG 0.552910 4.3:-63387018 None:intergenic
CCTGTGGGATTTGTGGGAAG+TGG 0.558125 4.3:+63386846 MS.gene54939:CDS
GTGGGAAGTGGTTCTCCGGT+GGG 0.561353 4.3:+63386858 MS.gene54939:CDS
GATCTTATCAGGCTCTTGGT+GGG 0.571526 4.3:+63387365 MS.gene54939:CDS
GGTACACTCTTCCAGTGCTA+AGG 0.575791 4.3:+63387504 MS.gene54939:CDS
GCAACTATGGAGAAGAGCGA+TGG 0.579019 4.3:+63386818 None:intergenic
CACCAAGAGCCTGATAAGAT+CGG 0.582662 4.3:-63387363 None:intergenic
AAGAGCGATGGGAAAGCCTG+TGG 0.598960 4.3:+63386830 MS.gene54939:CDS
AGGCACTCGGTGGACACAAG+AGG 0.606213 4.3:+63387482 MS.gene54939:CDS
ACAGAATCACAAATCAATAC+GGG 0.613334 4.3:-63387546 None:intergenic
CAACTATGGAGAAGAGCGAT+GGG 0.616240 4.3:+63386819 None:intergenic
TACTGCAAAAGAGACAATGA+TGG 0.621835 4.3:+63387397 MS.gene54939:CDS
AAGCCAGGTTCAACTGTGAG+AGG 0.622627 4.3:+63387326 MS.gene54939:CDS
ATCACAAATCAATACGGGTG+TGG 0.631203 4.3:-63387541 None:intergenic
GGCACTCGGTGGACACAAGA+GGG 0.632635 4.3:+63387483 MS.gene54939:CDS
CCACTTCCCACAAATCCCAC+AGG 0.647858 4.3:-63386846 None:intergenic
AGAGCGATGGGAAAGCCTGT+GGG 0.654994 4.3:+63386831 MS.gene54939:CDS
CGGCCGCGAACTTAATGCTG+CGG 0.660556 4.3:+63387150 MS.gene54939:CDS
AGGTTCAACTGTGAGAGGTG+CGG 0.663022 4.3:+63387331 MS.gene54939:CDS
TTCGGGAAGGCAAGTCTGTG+AGG 0.669270 4.3:-63387005 None:intergenic
AAGTCTGCTCAGGCACTCGG+TGG 0.670340 4.3:+63387472 MS.gene54939:CDS
AGGCCACATGAGATCTCACA+TGG 0.682156 4.3:+63386892 MS.gene54939:CDS
ACCCGCAAGAGATCCAATTG+CGG 0.686880 4.3:+63387130 MS.gene54939:CDS
GAACCATGTGAGATCTCATG+TGG 0.730676 4.3:-63386895 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GATCAAGAAACAAAAAATGA+GGG + chr4.3:63387252-63387271 MS.gene54939:CDS 25.0%
!!! ATTCTGTGTTTGTTGTATTT+CGG - chr4.3:63387026-63387045 None:intergenic 25.0%
AAAAATGTTCCGATCTTATC+AGG + chr4.3:63387354-63387373 MS.gene54939:CDS 30.0%
GGATCAAGAAACAAAAAATG+AGG + chr4.3:63387251-63387270 MS.gene54939:CDS 30.0%
TGAACACTTTGTTGCAATTT+GGG - chr4.3:63387453-63387472 None:intergenic 30.0%
TTACAAAGATGCGCAAAAAA+GGG + chr4.3:63387225-63387244 MS.gene54939:CDS 30.0%
TTGAACACTTTGTTGCAATT+TGG - chr4.3:63387454-63387473 None:intergenic 30.0%
TTTACAAAGATGCGCAAAAA+AGG + chr4.3:63387224-63387243 MS.gene54939:CDS 30.0%
! TGAGTATTAGTTTCAAGCTT+TGG - chr4.3:63386935-63386954 None:intergenic 30.0%
!! AAGCAAATTGATTTTGACGA+TGG - chr4.3:63386985-63387004 None:intergenic 30.0%
!! AGCAAATTGATTTTGACGAT+GGG - chr4.3:63386984-63387003 None:intergenic 30.0%
!! TTCTGTGTTTGTTGTATTTC+GGG - chr4.3:63387025-63387044 None:intergenic 30.0%
CAAAAAATGAGGGAAAACGA+TGG + chr4.3:63387262-63387281 MS.gene54939:CDS 35.0%
TACTCAAGCTGTAGACAATT+TGG + chr4.3:63386949-63386968 MS.gene54939:CDS 35.0%
TACTGCAAAAGAGACAATGA+TGG + chr4.3:63387397-63387416 MS.gene54939:CDS 35.0%
!! ACTTTGAAATTCCTTAGCAC+TGG - chr4.3:63387518-63387537 None:intergenic 35.0%
!!! ATCCAGGTGTTTTGATGTTA+TGG + chr4.3:63387197-63387216 MS.gene54939:CDS 35.0%
!!! ATTTTGACGATGGGTTGAAT+CGG - chr4.3:63386975-63386994 None:intergenic 35.0%
!!! CGAAGTTTTGTTTCATGGAT+AGG - chr4.3:63387051-63387070 None:intergenic 35.0%
!!! TCCAGGTGTTTTGATGTTAT+GGG + chr4.3:63387198-63387217 MS.gene54939:CDS 35.0%
AAAGATGCGCAAAAAAGGGA+AGG + chr4.3:63387229-63387248 MS.gene54939:CDS 40.0%
AAGATGCGCAAAAAAGGGAA+GGG + chr4.3:63387230-63387249 MS.gene54939:CDS 40.0%
GAAGATATGTCAAGAGATCC+AGG + chr4.3:63387181-63387200 MS.gene54939:CDS 40.0%
TTGCAATTTGGGCAGTGAAA+AGG - chr4.3:63387442-63387461 None:intergenic 40.0%
! TTCTCTGTTTGAGTTTGCAG+AGG - chr4.3:63387080-63387099 None:intergenic 40.0%
!! GTGTTTGTTGTATTTCGGGA+AGG - chr4.3:63387021-63387040 None:intergenic 40.0%
!! GTTTCAAGCTTTGGAGCAAT+CGG - chr4.3:63386926-63386945 None:intergenic 40.0%
!!! CCAGGTGTTTTGATGTTATG+GGG + chr4.3:63387199-63387218 MS.gene54939:CDS 40.0%
AATTGGATCTCTTGCGGGTT+GGG - chr4.3:63387129-63387148 None:intergenic 45.0%
ATTTGTGGGAAGTGGTTCTC+CGG + chr4.3:63386854-63386873 MS.gene54939:CDS 45.0%
CACCAAGAGCCTGATAAGAT+CGG - chr4.3:63387366-63387385 None:intergenic 45.0%
CCCCATAACATCAAAACACC+TGG - chr4.3:63387202-63387221 None:intergenic 45.0%
GAACCATGTGAGATCTCATG+TGG - chr4.3:63386898-63386917 None:intergenic 45.0%
GATCTTATCAGGCTCTTGGT+GGG + chr4.3:63387365-63387384 MS.gene54939:CDS 45.0%
TTCCGATCTTATCAGGCTCT+TGG + chr4.3:63387361-63387380 MS.gene54939:CDS 45.0%
! CAAAGTGTTCAAGTCTGCTC+AGG + chr4.3:63387462-63387481 MS.gene54939:CDS 45.0%
! TCTGTTTGAGTTTGCAGAGG+AGG - chr4.3:63387077-63387096 None:intergenic 45.0%
!!! GGCAGCGAAGTTTTGTTTCA+TGG - chr4.3:63387056-63387075 None:intergenic 45.0%
AACGATGGCGAAAGCAGTAC+AGG + chr4.3:63387277-63387296 MS.gene54939:CDS 50.0%
AAGCCAGGTTCAACTGTGAG+AGG + chr4.3:63387326-63387345 MS.gene54939:CDS 50.0%
ACCCGCAAGAGATCCAATTG+CGG + chr4.3:63387130-63387149 MS.gene54939:CDS 50.0%
AGATCTCATGTGGCCTCCAA+GGG - chr4.3:63386888-63386907 None:intergenic 50.0%
AGGCCACATGAGATCTCACA+TGG + chr4.3:63386892-63386911 MS.gene54939:CDS 50.0%
AGGTTCAACTGTGAGAGGTG+CGG + chr4.3:63387331-63387350 MS.gene54939:CDS 50.0%
ATTAAGTTCGCGGCCGCAAT+TGG - chr4.3:63387146-63387165 None:intergenic 50.0%
CAATTGGATCTCTTGCGGGT+TGG - chr4.3:63387130-63387149 None:intergenic 50.0%
CGATCTTATCAGGCTCTTGG+TGG + chr4.3:63387364-63387383 MS.gene54939:CDS 50.0%
GGAAAGCCTGTGGGATTTGT+GGG + chr4.3:63386840-63386859 MS.gene54939:CDS 50.0%
GGTACACTCTTCCAGTGCTA+AGG + chr4.3:63387504-63387523 MS.gene54939:CDS 50.0%
TTCAAGTCTGCTCAGGCACT+CGG + chr4.3:63387469-63387488 MS.gene54939:CDS 50.0%
!!! TCTTGCGGGTTGGGTTTTTC+AGG - chr4.3:63387120-63387139 None:intergenic 50.0%
AAGAGCGATGGGAAAGCCTG+TGG + chr4.3:63386830-63386849 MS.gene54939:CDS 55.0%
AGAGCGATGGGAAAGCCTGT+GGG + chr4.3:63386831-63386850 MS.gene54939:CDS 55.0%
CAGCCGCAGCATTAAGTTCG+CGG - chr4.3:63387156-63387175 None:intergenic 55.0%
CCACTTCCCACAAATCCCAC+AGG - chr4.3:63386849-63386868 None:intergenic 55.0%
CCTGTGGGATTTGTGGGAAG+TGG + chr4.3:63386846-63386865 MS.gene54939:CDS 55.0%
GAGATCTCATGTGGCCTCCA+AGG - chr4.3:63386889-63386908 None:intergenic 55.0%
GCACCTCTCACAGTTGAACC+TGG - chr4.3:63387332-63387351 None:intergenic 55.0%
GCCGCAATTGGATCTCTTGC+GGG - chr4.3:63387134-63387153 None:intergenic 55.0%
GGCCGCAATTGGATCTCTTG+CGG - chr4.3:63387135-63387154 None:intergenic 55.0%
GGGAAAGCCTGTGGGATTTG+TGG + chr4.3:63386839-63386858 MS.gene54939:CDS 55.0%
TTCGGGAAGGCAAGTCTGTG+AGG - chr4.3:63387008-63387027 None:intergenic 55.0%
!! CACAAGCAGACTCTGAAGCC+AGG + chr4.3:63387311-63387330 MS.gene54939:CDS 55.0%
!!! GCGGGTTGGGTTTTTCAGGT+TGG - chr4.3:63387116-63387135 None:intergenic 55.0%
AAGTCTGCTCAGGCACTCGG+TGG + chr4.3:63387472-63387491 MS.gene54939:CDS 60.0%
CGGCCGCGAACTTAATGCTG+CGG + chr4.3:63387150-63387169 MS.gene54939:CDS 60.0%
GTGGGAAGTGGTTCTCCGGT+GGG + chr4.3:63386858-63386877 MS.gene54939:CDS 60.0%
TGTGGGAAGTGGTTCTCCGG+TGG + chr4.3:63386857-63386876 MS.gene54939:CDS 60.0%
TTCTCCGGTGGGAAAGCCCT+TGG + chr4.3:63386869-63386888 MS.gene54939:CDS 60.0%
! AGGCACTCGGTGGACACAAG+AGG + chr4.3:63387482-63387501 MS.gene54939:CDS 60.0%
! GGCACTCGGTGGACACAAGA+GGG + chr4.3:63387483-63387502 MS.gene54939:CDS 60.0%
GCCTCCAAGGGCTTTCCCAC+CGG - chr4.3:63386876-63386895 None:intergenic 65.0%
TCCGGTGGGAAAGCCCTTGG+AGG + chr4.3:63386872-63386891 MS.gene54939:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 63386824 63387555 63386824 ID=MS.gene54939
chr4.3 mRNA 63386824 63387555 63386824 ID=MS.gene54939.t1;Parent=MS.gene54939
chr4.3 exon 63386824 63387555 63386824 ID=MS.gene54939.t1.exon1;Parent=MS.gene54939.t1
chr4.3 CDS 63386824 63387555 63386824 ID=cds.MS.gene54939.t1;Parent=MS.gene54939.t1
Gene Sequence

>MS.gene54939

ATGGAGAAGAGCGATGGGAAAGCCTGTGGGATTTGTGGGAAGTGGTTCTCCGGTGGGAAAGCCCTTGGAGGCCACATGAGATCTCACATGGTTCATTTGCCGATTGCTCCAAAGCTTGAAACTAATACTCAAGCTGTAGACAATTTGGCCGATTCAACCCATCGTCAAAATCAATTTGCTTCCTCACAGACTTGCCTTCCCGAAATACAACAAACACAGAATTTCCTATCCATGAAACAAAACTTCGCTGCCTCCTCTGCAAACTCAAACAGAGAAAATGAATCTGTGTCCAACCTGAAAAACCCAACCCGCAAGAGATCCAATTGCGGCCGCGAACTTAATGCTGCGGCTGATACAGAAGATATGTCAAGAGATCCAGGTGTTTTGATGTTATGGGGATTTTACAAAGATGCGCAAAAAAGGGAAGGGATCAAGAAACAAAAAATGAGGGAAAACGATGGCGAAAGCAGTACAGGTGACTCGCTTGCACAAGCAGACTCTGAAGCCAGGTTCAACTGTGAGAGGTGCGGAAAAATGTTCCGATCTTATCAGGCTCTTGGTGGGCACAGAGTATACTGCAAAAGAGACAATGATGGTGATTTAATAGATCAGAAACCTTTTCACTGCCCAAATTGCAACAAAGTGTTCAAGTCTGCTCAGGCACTCGGTGGACACAAGAGGGTACACTCTTCCAGTGCTAAGGAATTTCAAAGTGTGCCACACCCGTATTGA
Protein sequence

>MS.gene54939.t1

MEKSDGKACGICGKWFSGGKALGGHMRSHMVHLPIAPKLETNTQAVDNLADSTHRQNQFASSQTCLPEIQQTQNFLSMKQNFAASSANSNRENESVSNLKNPTRKRSNCGRELNAAADTEDMSRDPGVLMLWGFYKDAQKREGIKKQKMRENDGESSTGDSLAQADSEARFNCERCGKMFRSYQALGGHRVYCKRDNDGDLIDQKPFHCPNCNKVFKSAQALGGHKRVHSSSAKEFQSVPHPY