AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1092050


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1092050 MtrunA17_Chr1g0154241 90.541 222 13 1 4 217 36 257 4.45e-145 405
Msa1092050 MtrunA17_Chr1g0154101 58.801 267 55 6 4 216 197 462 4.82e-88 276
Msa1092050 MtrunA17_Chr1g0154101 70.161 124 29 1 4 119 40 163 4.30e-52 179
Msa1092050 MtrunA17_Chr1g0154211 61.607 224 69 4 4 216 37 254 4.16e-86 260
Msa1092050 MtrunA17_Chr1g0154251 57.269 227 75 6 4 209 41 266 5.54e-75 234
Msa1092050 MtrunA17_Chr1g0154111 59.009 222 54 5 4 216 41 234 1.64e-73 233
Msa1092050 MtrunA17_Chr1g0154111 58.636 220 70 7 4 217 368 572 1.18e-69 223
Msa1092050 MtrunA17_Chr1g0154191 57.333 225 45 6 4 216 37 222 5.44e-71 220
Msa1092050 MtrunA17_Chr1g0154151 52.423 227 53 6 1 216 16 198 2.42e-64 202
Msa1092050 MtrunA17_Chr1g0154171 54.464 224 53 6 4 216 37 222 1.73e-60 193
Msa1092050 MtrunA17_Chr1g0154131 51.961 204 38 5 4 198 197 349 1.63e-53 178
Msa1092050 MtrunA17_Chr1g0154131 66.400 125 34 1 4 120 40 164 5.43e-50 169
Msa1092050 MtrunA17_Chr1g0154161 73.333 105 19 2 4 100 45 148 9.28e-45 151
Msa1092050 MtrunA17_Chr1g0154071 65.289 121 34 2 4 116 170 290 3.95e-44 154
Msa1092050 MtrunA17_Chr1g0154071 69.307 101 23 2 4 96 42 142 2.12e-40 144
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1092050 AT4G33280.2 47.917 96 41 3 4 90 38 133 3.23e-21 89.4
Msa1092050 AT4G33280.1 47.917 96 41 3 4 90 38 133 6.77e-21 89.4
Msa1092050 AT4G33280.3 47.917 96 41 3 4 90 38 133 1.00e-20 89.7
Msa1092050 AT4G34400.2 37.681 69 43 0 4 72 30 98 9.45e-13 66.6
Msa1092050 AT4G34400.1 37.681 69 43 0 4 72 30 98 9.45e-13 66.6
Msa1092050 AT3G06220.1 28.829 111 61 2 5 106 25 126 1.01e-12 64.3
Msa1092050 AT3G06160.5 27.500 160 94 4 4 162 24 162 1.77e-11 62.8
Msa1092050 AT3G06160.4 27.500 160 94 4 4 162 24 162 1.77e-11 62.8
Msa1092050 AT3G06160.3 27.500 160 94 4 4 162 24 162 1.77e-11 62.8
Msa1092050 AT3G06160.1 27.500 160 94 4 4 162 39 177 2.06e-11 62.8
Msa1092050 AT3G06160.2 27.500 160 94 4 4 162 83 221 2.57e-11 62.4

Find 50 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACTCCACTAGGCCCTTTA+AGG 0.157742 7_3:+8100265 None:intergenic
CCTGAAAATGTGACCCTTAA+AGG 0.182662 7_3:-8100279 Msa1092050:CDS
GCTGGTCTTCCCCGCTTCTT+AGG 0.270434 7_3:+8099741 None:intergenic
AGTGGAGTTGTGTGGAATAT+AGG 0.300231 7_3:-8100252 Msa1092050:CDS
CCCGCTTTCTCGCATATATA+AGG 0.321213 7_3:+8100086 None:intergenic
AACTTCGTTAACAGGCTTCT+TGG 0.341598 7_3:+8099776 None:intergenic
CCAGGCGTAACTTCGTTAAC+AGG 0.352395 7_3:+8099768 None:intergenic
GTCTTCCCCGCTTCTTAGGC+TGG 0.353235 7_3:+8099745 None:intergenic
AATGCGGTTCTGAGAAATTT+CGG 0.363117 7_3:-8099950 Msa1092050:CDS
CCCCGCTTCTTAGGCTGGCC+AGG 0.381562 7_3:+8099750 None:intergenic
CCAGCAAAATCAGCTACTTC+TGG 0.385623 7_3:-8099723 Msa1092050:CDS
CTGAAAATGTGACCCTTAAA+GGG 0.403312 7_3:-8100278 Msa1092050:CDS
GTGGAGTTGTGTGGAATATA+GGG 0.421556 7_3:-8100251 Msa1092050:CDS
TTTGTTAGAAAATGTGGAAA+AGG 0.421612 7_3:-8100056 Msa1092050:CDS
GCATCAGCCATGACCTGCTC+AGG 0.424246 7_3:+8099840 None:intergenic
TGAGTCTGCTTCCCCTGAGC+AGG 0.449413 7_3:-8099853 Msa1092050:CDS
GCGAGAAAGCAATTGTTGAT+TGG 0.450466 7_3:-8099701 Msa1092050:CDS
GACATTGTTTACTTCACAAA+CGG 0.457173 7_3:-8100213 Msa1092050:CDS
TGCTTCCCCTGAGCAGGTCA+TGG 0.458901 7_3:-8099847 Msa1092050:CDS
GAAGTCAACACTGCTTCTAA+TGG 0.464985 7_3:-8099981 Msa1092050:CDS
GCCTGGCCAGCCTAAGAAGC+GGG 0.466869 7_3:-8099751 Msa1092050:CDS
TCTTACTTTGTTAGAAAATG+TGG 0.473474 7_3:-8100062 Msa1092050:CDS
CGAGAAAGCAATTGTTGATT+GGG 0.485091 7_3:-8099700 Msa1092050:CDS
GCGGTTCCCTCCCAAACAAC+CGG 0.485847 7_3:-8099807 Msa1092050:CDS
AACTCCACTAGGCCCTTTAA+GGG 0.492023 7_3:+8100266 None:intergenic
TACTTCACAAACGGTTGGCA+AGG 0.517034 7_3:-8100204 Msa1092050:CDS
CCTGTTAACGAAGTTACGCC+TGG 0.535294 7_3:-8099768 Msa1092050:CDS
AATGAAAAGACTTATAATGC+TGG 0.548214 7_3:-8099879 Msa1092050:CDS
ATATTCCACACAACTCCACT+AGG 0.554654 7_3:+8100255 None:intergenic
ACCTTATATATGCGAGAAAG+CGG 0.555289 7_3:-8100087 Msa1092050:CDS
TTGTTTACTTCACAAACGGT+TGG 0.559837 7_3:-8100209 Msa1092050:CDS
CATCAGCCATGACCTGCTCA+GGG 0.563227 7_3:+8099841 None:intergenic
CGCCTGGCCAGCCTAAGAAG+CGG 0.563693 7_3:-8099752 Msa1092050:CDS
GAAAGCAATTGTTGATTGGG+TGG 0.568458 7_3:-8099697 Msa1092050:CDS
AATCACTCTCTTTCAAAGAG+TGG 0.568664 7_3:+8100169 None:intergenic
CCTTATATATGCGAGAAAGC+GGG 0.572083 7_3:-8100086 Msa1092050:CDS
TATAGGGCTGACAACTAAAG+AGG 0.573508 7_3:-8100235 Msa1092050:CDS
GGCTGATGCAGTCACTATTG+CGG 0.596142 7_3:-8099826 Msa1092050:CDS
TACTGAGCAAGAGGGAGACA+AGG 0.597506 7_3:-8100030 Msa1092050:CDS
AAAAGGTCATACTGAGCAAG+AGG 0.610370 7_3:-8100039 Msa1092050:CDS
AAGGGCCTAGTGGAGTTGTG+TGG 0.623981 7_3:-8100260 Msa1092050:CDS
GTGACCCTTAAAGGGCCTAG+TGG 0.625534 7_3:-8100270 Msa1092050:CDS
GCTTGTAGCAAGGAAAACTC+AGG 0.631925 7_3:-8099675 Msa1092050:CDS
CCTGGCCAGCCTAAGAAGCG+GGG 0.640983 7_3:-8099750 Msa1092050:CDS
GCAAGAGGGAGACAAGGCAA+AGG 0.642426 7_3:-8100024 Msa1092050:CDS
GTCAACACTGCTTCTAATGG+CGG 0.645750 7_3:-8099978 Msa1092050:CDS
TGATTGGGTGGCTTGTAGCA+AGG 0.654638 7_3:-8099685 Msa1092050:CDS
TCTAATGGCGGTGTTGAATG+CGG 0.661026 7_3:-8099966 Msa1092050:CDS
AAAGGTCATACTGAGCAAGA+GGG 0.680883 7_3:-8100038 Msa1092050:CDS
ATCAGCCATGACCTGCTCAG+GGG 0.726483 7_3:+8099842 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTGAAGATTTAATATTTCA+TGG - chr7_3:8099941-8099960 Msa1092050:CDS 15.0%
!! ATGTTTATACATTTATTTGC+AGG - chr7_3:8099712-8099731 Msa1092050:CDS 20.0%
!!! AAATTGTCTGAAAATGTTTT+AGG + chr7_3:8099743-8099762 None:intergenic 20.0%
!!! TTTTCATTGGTATTTTCAAA+AGG + chr7_3:8100164-8100183 None:intergenic 20.0%
!!! TTCCTTTTTTTCAAGTACAA+TGG - chr7_3:8099908-8099927 Msa1092050:CDS 25.0%
! TCTTACTTTGTTAGAAAATG+TGG - chr7_3:8099993-8100012 Msa1092050:CDS 25.0%
! TTTGTTAGAAAATGTGGAAA+AGG - chr7_3:8099999-8100018 Msa1092050:CDS 25.0%
!! AGCATTATAAGTCTTTTCAT+TGG + chr7_3:8100177-8100196 None:intergenic 25.0%
! AATGAAAAGACTTATAATGC+TGG - chr7_3:8100176-8100195 Msa1092050:CDS 25.0%
GACATTGTTTACTTCACAAA+CGG - chr7_3:8099842-8099861 Msa1092050:CDS 30.0%
!! TTTTCAAAAGGTACAGCTAA+TGG + chr7_3:8100152-8100171 None:intergenic 30.0%
CTGAAAATGTGACCCTTAAA+GGG - chr7_3:8099777-8099796 Msa1092050:CDS 35.0%
TTGTTTACTTCACAAACGGT+TGG - chr7_3:8099846-8099865 Msa1092050:CDS 35.0%
AATCACTCTCTTTCAAAGAG+TGG + chr7_3:8099889-8099908 None:intergenic 35.0%
CGCCATTGTACTTGAAAAAA+AGG + chr7_3:8099913-8099932 None:intergenic 35.0%
ACCTTATATATGCGAGAAAG+CGG - chr7_3:8099968-8099987 Msa1092050:CDS 35.0%
!! AATGCGGTTCTGAGAAATTT+CGG - chr7_3:8100105-8100124 Msa1092050:intron 35.0%
! CGAGAAAGCAATTGTTGATT+GGG - chr7_3:8100355-8100374 Msa1092050:intron 35.0%
!! CCTTTAAGGGTCACATTTTC+AGG + chr7_3:8099779-8099798 None:intergenic 40.0%
CCTGAAAATGTGACCCTTAA+AGG - chr7_3:8099776-8099795 Msa1092050:CDS 40.0%
ATATTCCACACAACTCCACT+AGG + chr7_3:8099803-8099822 None:intergenic 40.0%
AGTGGAGTTGTGTGGAATAT+AGG - chr7_3:8099803-8099822 Msa1092050:CDS 40.0%
GTGGAGTTGTGTGGAATATA+GGG - chr7_3:8099804-8099823 Msa1092050:CDS 40.0%
TATAGGGCTGACAACTAAAG+AGG - chr7_3:8099820-8099839 Msa1092050:CDS 40.0%
CCTTATATATGCGAGAAAGC+GGG - chr7_3:8099969-8099988 Msa1092050:CDS 40.0%
AAAAGGTCATACTGAGCAAG+AGG - chr7_3:8100016-8100035 Msa1092050:CDS 40.0%
AAAGGTCATACTGAGCAAGA+GGG - chr7_3:8100017-8100036 Msa1092050:CDS 40.0%
GAAGTCAACACTGCTTCTAA+TGG - chr7_3:8100074-8100093 Msa1092050:CDS 40.0%
AACTTCGTTAACAGGCTTCT+TGG + chr7_3:8100282-8100301 None:intergenic 40.0%
GCGAGAAAGCAATTGTTGAT+TGG - chr7_3:8100354-8100373 Msa1092050:intron 40.0%
! GAAAGCAATTGTTGATTGGG+TGG - chr7_3:8100358-8100377 Msa1092050:intron 40.0%
AACTCCACTAGGCCCTTTAA+GGG + chr7_3:8099792-8099811 None:intergenic 45.0%
TACTTCACAAACGGTTGGCA+AGG - chr7_3:8099851-8099870 Msa1092050:CDS 45.0%
CCCGCTTTCTCGCATATATA+AGG + chr7_3:8099972-8099991 None:intergenic 45.0%
GTCAACACTGCTTCTAATGG+CGG - chr7_3:8100077-8100096 Msa1092050:CDS 45.0%
! TCTAATGGCGGTGTTGAATG+CGG - chr7_3:8100089-8100108 Msa1092050:CDS 45.0%
!! TTTTTGCCGGTTGTTTGGGA+GGG + chr7_3:8100257-8100276 None:intergenic 45.0%
!! GGTCTTTTTGCCGGTTGTTT+GGG + chr7_3:8100261-8100280 None:intergenic 45.0%
!! TGGTCTTTTTGCCGGTTGTT+TGG + chr7_3:8100262-8100281 None:intergenic 45.0%
!! AGGCTTCTTGGTCTTTTTGC+CGG + chr7_3:8100270-8100289 None:intergenic 45.0%
!! CCAGAAGTAGCTGATTTTGC+TGG + chr7_3:8100335-8100354 None:intergenic 45.0%
CCAGCAAAATCAGCTACTTC+TGG - chr7_3:8100332-8100351 Msa1092050:intron 45.0%
GCTTGTAGCAAGGAAAACTC+AGG - chr7_3:8100380-8100399 Msa1092050:intron 45.0%
CAACTCCACTAGGCCCTTTA+AGG + chr7_3:8099793-8099812 None:intergenic 50.0%
TACTGAGCAAGAGGGAGACA+AGG - chr7_3:8100025-8100044 Msa1092050:CDS 50.0%
GGCTGATGCAGTCACTATTG+CGG - chr7_3:8100229-8100248 Msa1092050:CDS 50.0%
!! CTTTTTGCCGGTTGTTTGGG+AGG + chr7_3:8100258-8100277 None:intergenic 50.0%
CCAGGCGTAACTTCGTTAAC+AGG + chr7_3:8100290-8100309 None:intergenic 50.0%
CCTGTTAACGAAGTTACGCC+TGG - chr7_3:8100287-8100306 Msa1092050:CDS 50.0%
! TGATTGGGTGGCTTGTAGCA+AGG - chr7_3:8100370-8100389 Msa1092050:intron 50.0%
GTGACCCTTAAAGGGCCTAG+TGG - chr7_3:8099785-8099804 Msa1092050:CDS 55.0%
AAGGGCCTAGTGGAGTTGTG+TGG - chr7_3:8099795-8099814 Msa1092050:CDS 55.0%
GCAAGAGGGAGACAAGGCAA+AGG - chr7_3:8100031-8100050 Msa1092050:CDS 55.0%
ATCAGCCATGACCTGCTCAG+GGG + chr7_3:8100216-8100235 None:intergenic 55.0%
CATCAGCCATGACCTGCTCA+GGG + chr7_3:8100217-8100236 None:intergenic 55.0%
TGAGTCTGCTTCCCCTGAGC+AGG - chr7_3:8100202-8100221 Msa1092050:CDS 60.0%
TGCTTCCCCTGAGCAGGTCA+TGG - chr7_3:8100208-8100227 Msa1092050:CDS 60.0%
GCATCAGCCATGACCTGCTC+AGG + chr7_3:8100218-8100237 None:intergenic 60.0%
GCGGTTCCCTCCCAAACAAC+CGG - chr7_3:8100248-8100267 Msa1092050:CDS 60.0%
GTCTTCCCCGCTTCTTAGGC+TGG + chr7_3:8100313-8100332 None:intergenic 60.0%
!! GCTGGTCTTCCCCGCTTCTT+AGG + chr7_3:8100317-8100336 None:intergenic 60.0%
CGCCTGGCCAGCCTAAGAAG+CGG - chr7_3:8100303-8100322 Msa1092050:CDS 65.0%
GCCTGGCCAGCCTAAGAAGC+GGG - chr7_3:8100304-8100323 Msa1092050:CDS 65.0%
CCTGGCCAGCCTAAGAAGCG+GGG - chr7_3:8100305-8100324 Msa1092050:CDS 65.0%
! CCCCGCTTCTTAGGCTGGCC+AGG + chr7_3:8100308-8100327 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 8099671 8100406 8099671 ID=Msa1092050;Name=Msa1092050
chr7_3 mRNA 8099671 8100406 8099671 ID=Msa1092050-mRNA-1;Parent=Msa1092050;Name=Msa1092050-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|0|0|0.66|0.5|0.33|3|0|217
chr7_3 exon 8100398 8100406 8100398 ID=Msa1092050-mRNA-1:exon:2423;Parent=Msa1092050-mRNA-1
chr7_3 exon 8100138 8100343 8100138 ID=Msa1092050-mRNA-1:exon:2422;Parent=Msa1092050-mRNA-1
chr7_3 exon 8099671 8100109 8099671 ID=Msa1092050-mRNA-1:exon:2421;Parent=Msa1092050-mRNA-1
chr7_3 CDS 8100398 8100406 8100398 ID=Msa1092050-mRNA-1:cds;Parent=Msa1092050-mRNA-1
chr7_3 CDS 8100138 8100343 8100138 ID=Msa1092050-mRNA-1:cds;Parent=Msa1092050-mRNA-1
chr7_3 CDS 8099671 8100109 8099671 ID=Msa1092050-mRNA-1:cds;Parent=Msa1092050-mRNA-1
Gene Sequence

>Msa1092050

ATGACTAGTGCACTTCCTAAAACATTTTCAGACAATTTAAAGAAAAAGTTGCCTGAAAATGTGACCCTTAAAGGGCCTAGTGGAGTTGTGTGGAATATAGGGCTGACAACTAAAGAGGACATTGTTTACTTCACAAACGGTTGGCAAGGATTTGTGAATGACCACTCTTTGAAAGAGAGTGATTTCCTTTTTTTCAAGTACAATGGCGAATCATTACCTTATATATGCGAGAAAGCGGGCTCTTACTTTGTTAGAAAATGTGGAAAAGGTCATACTGAGCAAGAGGGAGACAAGGCAAAGGTTGCAAAGAATTCTATTGAAGAAGTCAACACTGCTTCTAATGGCGGTGTTGAATGCGGTTCTGAGAAATTTCGGAAGCTTGACACAATAAGAACACCATTAGCTGTACCTTTTGAAAATACCAATGAAAAGACTTATAATGCTGGTGTTGAGTCTGCTTCCCCTGAGCAGGTCATGGCTGATGCAGTCACTATTGCGGTTCCCTCCCAAACAACCGGCAAAAAGACCAAGAAGCCTGTTAACGAAGTTACGCCTGGCCAGCCTAAGAAGCGGGGAAGACCAGCAAAATCAGCTACTTCTGGCGAGAAAGCAATTGTTGATTGGGTGGCTTGTAGCAAGGAAAACTCAGGTTAA

Protein sequence

>Msa1092050

MTSALPKTFSDNLKKKLPENVTLKGPSGVVWNIGLTTKEDIVYFTNGWQGFVNDHSLKESDFLFFKYNGESLPYICEKAGSYFVRKCGKGHTEQEGDKAKVAKNSIEEVNTASNGGVECGSEKFRKLDTIRTPLAVPFENTNEKTYNAGVESASPEQVMADAVTIAVPSQTTGKKTKKPVNEVTPGQPKKRGRPAKSATSGEKAIVDWVACSKENSG*