AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29298

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29298.t1 MTR_7g114060 100.000 139 0 0 1 139 1 139 3.00e-97 276
MS.gene29298.t1 MTR_7g114040 100.000 139 0 0 1 139 1 139 3.00e-97 276
MS.gene29298.t1 MTR_7g108320 95.775 142 3 1 1 139 1 142 4.40e-93 265
MS.gene29298.t1 MTR_7g093910 87.313 134 17 0 6 139 9 142 6.22e-82 237
MS.gene29298.t1 MTR_7g114050 87.023 131 6 2 9 139 11 130 3.86e-72 212
MS.gene29298.t1 MTR_2g082510 86.777 121 12 1 10 126 3 123 3.42e-69 204
MS.gene29298.t1 MTR_2g082220 84.921 126 11 2 10 129 3 126 4.30e-69 204
MS.gene29298.t1 MTR_2g096610 75.000 120 30 0 18 137 21 140 1.15e-59 181
MS.gene29298.t1 MTR_7g113160 76.068 117 28 0 9 125 16 132 3.78e-59 179
MS.gene29298.t1 MTR_4g063280 79.091 110 23 0 18 127 17 126 2.93e-58 177
MS.gene29298.t1 MTR_2g096570 81.132 106 20 0 19 124 23 128 5.36e-58 177
MS.gene29298.t1 MTR_4g063410 79.439 107 22 0 19 125 24 130 5.44e-58 177
MS.gene29298.t1 MTR_4g071150 80.374 107 21 0 19 125 24 130 6.46e-58 177
MS.gene29298.t1 MTR_4g064005 81.132 106 20 0 19 124 24 129 6.49e-58 177
MS.gene29298.t1 MTR_8g086640 81.132 106 20 0 19 124 24 129 7.30e-58 177
MS.gene29298.t1 MTR_4g064967 81.132 106 20 0 19 124 24 129 8.16e-58 176
MS.gene29298.t1 MTR_6g005150 61.345 119 37 2 19 136 26 136 5.87e-42 136
MS.gene29298.t1 MTR_1g011750 58.197 122 49 2 3 123 10 130 1.06e-39 130
MS.gene29298.t1 MTR_1g011850 58.197 122 49 2 3 123 10 130 1.06e-39 130
MS.gene29298.t1 MTR_1g114050 62.857 105 37 2 20 123 24 127 5.35e-38 125
MS.gene29298.t1 MTR_1g071040 63.462 104 36 2 21 123 28 130 1.15e-37 125
MS.gene29298.t1 MTR_4g063300 67.708 96 23 1 40 127 10 105 7.05e-36 120
MS.gene29298.t1 MTR_4g005910 88.889 45 5 0 82 126 4 48 6.44e-23 85.5
MS.gene29298.t1 MTR_7g010440 54.444 90 41 0 47 136 96 185 2.92e-22 89.7
MS.gene29298.t1 MTR_4g048490 44.860 107 30 2 19 125 26 103 2.83e-20 80.1
MS.gene29298.t1 MTR_1g069770 55.224 67 30 0 62 128 32 98 1.19e-18 75.9
MS.gene29298.t1 MTR_7g027610 41.818 110 32 3 18 123 13 94 8.02e-16 68.9
MS.gene29298.t1 MTR_0653s0030 52.830 53 25 0 50 102 43 95 4.63e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29298.t1 AT1G54690 92.958 142 7 1 1 139 1 142 2.22e-90 258
MS.gene29298.t1 AT1G08880 94.118 136 8 0 4 139 7 142 5.41e-90 258
MS.gene29298.t1 AT4G27230 86.290 124 13 1 10 129 3 126 4.66e-70 207
MS.gene29298.t1 AT4G27230 86.290 124 13 1 10 129 3 126 4.66e-70 207
MS.gene29298.t1 AT5G54640 82.946 129 19 1 1 129 1 126 1.59e-69 205
MS.gene29298.t1 AT1G51060 83.871 124 16 1 10 129 3 126 1.51e-68 203
MS.gene29298.t1 AT3G20670 84.677 124 15 1 10 129 3 126 4.76e-68 202
MS.gene29298.t1 AT5G59870 73.643 129 29 2 1 124 1 129 1.24e-60 184
MS.gene29298.t1 AT5G27670 73.438 128 29 1 2 124 3 130 4.78e-58 177
MS.gene29298.t1 AT5G02560 79.439 107 22 0 18 124 23 129 5.23e-57 174
MS.gene29298.t1 AT5G02560 64.885 131 22 1 18 124 23 153 1.37e-51 162
MS.gene29298.t1 AT2G38810 62.617 107 38 2 18 123 27 132 1.12e-38 127
MS.gene29298.t1 AT2G38810 62.617 107 38 2 18 123 27 132 1.12e-38 127
MS.gene29298.t1 AT2G38810 62.617 107 38 2 18 123 27 132 1.12e-38 127
MS.gene29298.t1 AT2G38810 62.617 107 38 2 18 123 27 132 1.12e-38 127
MS.gene29298.t1 AT1G52740 61.905 105 38 2 20 123 27 130 2.42e-38 127
MS.gene29298.t1 AT3G54560 60.952 105 39 2 20 123 29 132 4.94e-37 123
MS.gene29298.t1 AT3G54560 60.952 105 39 2 20 123 29 132 4.94e-37 123
MS.gene29298.t1 AT4G13570 43.220 118 65 2 1 117 2 118 3.98e-23 87.8
MS.gene29298.t1 AT4G13570 49.451 91 44 2 28 117 35 124 9.39e-22 84.3

Find 49 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCCCTTTCCAACCTTCTT+TGG 0.128920 7.2:+3344022 None:intergenic
TGCCCTTTCCAACCTTCTTT+GGG 0.261985 7.2:+3344023 None:intergenic
TGAAGAACTCAGCAAGCTTT+TGG 0.286717 7.2:-3344101 MS.gene29298:CDS
TGGTTTGCCTCTTCCACCTT+TGG 0.309774 7.2:+3344526 None:intergenic
AACACGTTCGGCGTATTTAC+CGG 0.321195 7.2:+3344424 None:intergenic
GGAAAGGGCAAAGGAGAAAT+TGG 0.326882 7.2:-3344010 MS.gene29298:CDS
TTTACCGGCCTTGAGGAATC+TGG 0.369624 7.2:+3344439 None:intergenic
AAGACCTGCCTTTGAAGATC+TGG 0.371894 7.2:+3344484 None:intergenic
AGCAAAGTCTGATGAATATT+AGG 0.375759 7.2:+3344046 None:intergenic
TGAAGATCTGGAAACCGATT+TGG 0.392248 7.2:+3344496 None:intergenic
GAAACCGATTTGGCAGCCTT+TGG 0.410658 7.2:+3344506 None:intergenic
TCCACCTTTGGTTGTTCCAG+TGG 0.430840 7.2:+3344538 None:intergenic
CAAACCAAAGGCTGCCAAAT+CGG 0.434148 7.2:-3344510 MS.gene29298:CDS
GGCACATTCAGCTTGCTGTT+AGG 0.440630 7.2:-3344129 MS.gene29298:CDS
TCAGACTTTGCTCCCAAAGA+AGG 0.448013 7.2:-3344035 MS.gene29298:CDS
AGCTCCGGCACCAACACGTT+CGG 0.461862 7.2:+3344412 None:intergenic
AGGACGGCGGAGAGGTAGAC+AGG 0.463287 7.2:+3344389 None:intergenic
CAGCAAGCTGAATGTGCCTT+GGG 0.478109 7.2:+3344134 None:intergenic
GGAACTGTGACCATTGCTAA+TGG 0.483635 7.2:-3344079 MS.gene29298:CDS
CTCCCAAAGAAGGTTGGAAA+GGG 0.488096 7.2:-3344025 MS.gene29298:CDS
ACAGCAAGCTGAATGTGCCT+TGG 0.510267 7.2:+3344133 None:intergenic
GTTTCCAGATCTTCAAAGGC+AGG 0.515636 7.2:-3344488 MS.gene29298:CDS
GATCAGAAAATGAGCTCCAC+TGG 0.517370 7.2:-3344554 None:intergenic
ACTTTGCTCCCAAAGAAGGT+TGG 0.520151 7.2:-3344031 MS.gene29298:CDS
GGAACAACCAAAGGTGGAAG+AGG 0.533476 7.2:-3344533 MS.gene29298:CDS
TACGCCGAACGTGTTGGTGC+CGG 0.543181 7.2:-3344416 MS.gene29298:CDS
ATCGGTTTCCAGATCTTCAA+AGG 0.543380 7.2:-3344492 MS.gene29298:CDS
ATCGCCAGATTCCTCAAGGC+CGG 0.565542 7.2:-3344443 MS.gene29298:CDS
GCTCCCAAAGAAGGTTGGAA+AGG 0.567735 7.2:-3344026 MS.gene29298:CDS
CGGCGTATTTACCGGCCTTG+AGG 0.577173 7.2:+3344432 None:intergenic
GAATCTGGCGATTCTTCCGA+CGG 0.592664 7.2:+3344454 None:intergenic
GGTAAATACGCCGAACGTGT+TGG 0.593895 7.2:-3344422 MS.gene29298:CDS
GGAGAGGTAGACAGGAGCTC+CGG 0.601992 7.2:+3344397 None:intergenic
AGCTCCACTGGAACAACCAA+AGG 0.603686 7.2:-3344542 MS.gene29298:CDS
CCTTGAGTATCTCGCTGCTG+AGG 0.612329 7.2:-3344369 MS.gene29298:intron
AAGAAGGTTGGAAAGGGCAA+AGG 0.616375 7.2:-3344019 MS.gene29298:CDS
AAGAATCGCCAGATTCCTCA+AGG 0.631643 7.2:-3344447 MS.gene29298:CDS
TCCACTGGAACAACCAAAGG+TGG 0.637545 7.2:-3344539 MS.gene29298:CDS
CCTCAGCAGCGAGATACTCA+AGG 0.638807 7.2:+3344369 None:intergenic
GAAACCCTAAAATTCTTGAG+AGG 0.640292 7.2:+3343982 None:intergenic
CAGAACACCACCATTAGCAA+TGG 0.646082 7.2:+3344069 None:intergenic
AGGTGGAAGAGGCAAACCAA+AGG 0.648004 7.2:-3344522 MS.gene29298:CDS
AGAAGAATCGTATTGTCCCA+AGG 0.648823 7.2:-3344150 MS.gene29298:CDS
AATCTGGCGATTCTTCCGAC+GGG 0.649569 7.2:+3344455 None:intergenic
GCAGGTCTTCAATTTCCCGT+CGG 0.653866 7.2:-3344470 MS.gene29298:CDS
GATACTCAAGGACGGCGGAG+AGG 0.669935 7.2:+3344381 None:intergenic
AGCAGCGAGATACTCAAGGA+CGG 0.684917 7.2:+3344373 None:intergenic
ACTGTGACCATTGCTAATGG+TGG 0.694716 7.2:-3344076 MS.gene29298:CDS
AGCGAGATACTCAAGGACGG+CGG 0.736224 7.2:+3344376 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATCTTTTTTGTTTAATTTA+GGG - chr7.2:3344217-3344236 MS.gene29298:intron 10.0%
!!! CTATCTTTTTTGTTTAATTT+AGG - chr7.2:3344216-3344235 MS.gene29298:intron 15.0%
!! AAAGATAGTGAAAGAAAAAT+TGG + chr7.2:3344204-3344223 None:intergenic 20.0%
!! ATATGAATCTGATAATTGAA+AGG - chr7.2:3344286-3344305 MS.gene29298:intron 20.0%
!!! ATTTTTTGTTGATTAGGTTT+TGG - chr7.2:3344330-3344349 MS.gene29298:intron 20.0%
!!! CTGTTAATTTTTTGTTGATT+AGG - chr7.2:3344324-3344343 MS.gene29298:intron 20.0%
!!! GAATTGTCTTTGTTTTATTA+GGG - chr7.2:3344259-3344278 MS.gene29298:intron 20.0%
!!! CGAATTGTCTTTGTTTTATT+AGG - chr7.2:3344258-3344277 MS.gene29298:intron 25.0%
AGCAAAGTCTGATGAATATT+AGG + chr7.2:3344490-3344509 None:intergenic 30.0%
CAAAGACAATTCGATTGAAT+TGG + chr7.2:3344251-3344270 None:intergenic 30.0%
!!! TGTTGATTAGGTTTTGGAAT+TGG - chr7.2:3344336-3344355 MS.gene29298:intron 30.0%
AGAAGAATCGTATTGTCCCA+AGG - chr7.2:3344383-3344402 MS.gene29298:CDS 40.0%
TGAAGATCTGGAAACCGATT+TGG + chr7.2:3344040-3344059 None:intergenic 40.0%
! ATCGGTTTCCAGATCTTCAA+AGG - chr7.2:3344041-3344060 MS.gene29298:CDS 40.0%
! GAAGAACTCAGCAAGCTTTT+GGG - chr7.2:3344433-3344452 MS.gene29298:CDS 40.0%
! TGAAGAACTCAGCAAGCTTT+TGG - chr7.2:3344432-3344451 MS.gene29298:CDS 40.0%
!!! GATTAGGTTTTGGAATTGGC+TGG - chr7.2:3344340-3344359 MS.gene29298:intron 40.0%
AACACGTTCGGCGTATTTAC+CGG + chr7.2:3344112-3344131 None:intergenic 45.0%
AAGAAGGTTGGAAAGGGCAA+AGG - chr7.2:3344514-3344533 MS.gene29298:CDS 45.0%
AAGAATCGCCAGATTCCTCA+AGG - chr7.2:3344086-3344105 MS.gene29298:CDS 45.0%
ACTGTGACCATTGCTAATGG+TGG - chr7.2:3344457-3344476 MS.gene29298:CDS 45.0%
ACTTTGCTCCCAAAGAAGGT+TGG - chr7.2:3344502-3344521 MS.gene29298:CDS 45.0%
CAAACCAAAGGCTGCCAAAT+CGG - chr7.2:3344023-3344042 MS.gene29298:CDS 45.0%
CAGAACACCACCATTAGCAA+TGG + chr7.2:3344467-3344486 None:intergenic 45.0%
CTCCCAAAGAAGGTTGGAAA+GGG - chr7.2:3344508-3344527 MS.gene29298:CDS 45.0%
GGAAAGGGCAAAGGAGAAAT+TGG - chr7.2:3344523-3344542 MS.gene29298:CDS 45.0%
GGAACTGTGACCATTGCTAA+TGG - chr7.2:3344454-3344473 MS.gene29298:CDS 45.0%
GTTTCCAGATCTTCAAAGGC+AGG - chr7.2:3344045-3344064 MS.gene29298:CDS 45.0%
TCAGACTTTGCTCCCAAAGA+AGG - chr7.2:3344498-3344517 MS.gene29298:CDS 45.0%
TGCCCTTTCCAACCTTCTTT+GGG + chr7.2:3344513-3344532 None:intergenic 45.0%
TTGCCCTTTCCAACCTTCTT+TGG + chr7.2:3344514-3344533 None:intergenic 45.0%
! AAGACCTGCCTTTGAAGATC+TGG + chr7.2:3344052-3344071 None:intergenic 45.0%
AATCTGGCGATTCTTCCGAC+GGG + chr7.2:3344081-3344100 None:intergenic 50.0%
ACAGCAAGCTGAATGTGCCT+TGG + chr7.2:3344403-3344422 None:intergenic 50.0%
AGCAGCGAGATACTCAAGGA+CGG + chr7.2:3344163-3344182 None:intergenic 50.0%
AGCTCCACTGGAACAACCAA+AGG - chr7.2:3343991-3344010 MS.gene29298:CDS 50.0%
AGGTGGAAGAGGCAAACCAA+AGG - chr7.2:3344011-3344030 MS.gene29298:CDS 50.0%
CAGCAAGCTGAATGTGCCTT+GGG + chr7.2:3344402-3344421 None:intergenic 50.0%
GAATCTGGCGATTCTTCCGA+CGG + chr7.2:3344082-3344101 None:intergenic 50.0%
GCAGGTCTTCAATTTCCCGT+CGG - chr7.2:3344063-3344082 MS.gene29298:CDS 50.0%
GCTCCCAAAGAAGGTTGGAA+AGG - chr7.2:3344507-3344526 MS.gene29298:CDS 50.0%
GGAACAACCAAAGGTGGAAG+AGG - chr7.2:3344000-3344019 MS.gene29298:CDS 50.0%
GGTAAATACGCCGAACGTGT+TGG - chr7.2:3344111-3344130 MS.gene29298:CDS 50.0%
TCCACCTTTGGTTGTTCCAG+TGG + chr7.2:3343998-3344017 None:intergenic 50.0%
TCCACTGGAACAACCAAAGG+TGG - chr7.2:3343994-3344013 MS.gene29298:CDS 50.0%
TTTACCGGCCTTGAGGAATC+TGG + chr7.2:3344097-3344116 None:intergenic 50.0%
! TGGTTTGCCTCTTCCACCTT+TGG + chr7.2:3344010-3344029 None:intergenic 50.0%
!! GAAACCGATTTGGCAGCCTT+TGG + chr7.2:3344030-3344049 None:intergenic 50.0%
!! GGCACATTCAGCTTGCTGTT+AGG - chr7.2:3344404-3344423 MS.gene29298:CDS 50.0%
AGCGAGATACTCAAGGACGG+CGG + chr7.2:3344160-3344179 None:intergenic 55.0%
ATCGCCAGATTCCTCAAGGC+CGG - chr7.2:3344090-3344109 MS.gene29298:CDS 55.0%
CCTCAGCAGCGAGATACTCA+AGG + chr7.2:3344167-3344186 None:intergenic 55.0%
CCTTGAGTATCTCGCTGCTG+AGG - chr7.2:3344164-3344183 MS.gene29298:CDS 55.0%
AGCTCCGGCACCAACACGTT+CGG + chr7.2:3344124-3344143 None:intergenic 60.0%
CGGCGTATTTACCGGCCTTG+AGG + chr7.2:3344104-3344123 None:intergenic 60.0%
GATACTCAAGGACGGCGGAG+AGG + chr7.2:3344155-3344174 None:intergenic 60.0%
GGAGAGGTAGACAGGAGCTC+CGG + chr7.2:3344139-3344158 None:intergenic 60.0%
! TACGCCGAACGTGTTGGTGC+CGG - chr7.2:3344117-3344136 MS.gene29298:CDS 60.0%
AGGACGGCGGAGAGGTAGAC+AGG + chr7.2:3344147-3344166 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 3343988 3344567 3343988 ID=MS.gene29298
chr7.2 mRNA 3343988 3344567 3343988 ID=MS.gene29298.t1;Parent=MS.gene29298
chr7.2 exon 3344370 3344567 3344370 ID=MS.gene29298.t1.exon1;Parent=MS.gene29298.t1
chr7.2 CDS 3344370 3344567 3344370 ID=cds.MS.gene29298.t1;Parent=MS.gene29298.t1
chr7.2 exon 3343988 3344209 3343988 ID=MS.gene29298.t1.exon2;Parent=MS.gene29298.t1
chr7.2 CDS 3343988 3344209 3343988 ID=cds.MS.gene29298.t1;Parent=MS.gene29298.t1
Gene Sequence

>MS.gene29298

ATGAGCTCCACTGGAACAACCAAAGGTGGAAGAGGCAAACCAAAGGCTGCCAAATCGGTTTCCAGATCTTCAAAGGCAGGTCTTCAATTTCCCGTCGGAAGAATCGCCAGATTCCTCAAGGCCGGTAAATACGCCGAACGTGTTGGTGCCGGAGCTCCTGTCTACCTCTCCGCCGTCCTTGAGTATCTCGCTGCTGAGGTTTGTTTCTTTTCTCCAATTTTTCTTTCACTATCTTTTTTGTTTAATTTAGGGTTCTAGATCCAATTCAATCGAATTGTCTTTGTTTTATTAGGGTTTTATATGAATCTGATAATTGAAAGGTAGAAACTCAATTTTCTGTTAATTTTTTGTTGATTAGGTTTTGGAATTGGCTGGAAACGCTGCTAGAGACAACAAGAAGAATCGTATTGTCCCAAGGCACATTCAGCTTGCTGTTAGGAACGATGAAGAACTCAGCAAGCTTTTGGGAACTGTGACCATTGCTAATGGTGGTGTTCTGCCTAATATTCATCAGACTTTGCTCCCAAAGAAGGTTGGAAAGGGCAAAGGAGAAATTGGATCTGCCTCTCAAGAATTTTAG
Protein sequence

>MS.gene29298.t1

MSSTGTTKGGRGKPKAAKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQTLLPKKVGKGKGEIGSASQEF