AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene28398

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28398.t1 MTR_8g093500 92.562 242 15 2 1 240 21 261 1.13e-143 403
MS.gene28398.t1 MTR_3g101810 73.958 96 25 0 60 155 139 234 6.10e-47 157
MS.gene28398.t1 MTR_5g017210 68.627 102 32 0 60 161 105 206 2.32e-37 131
MS.gene28398.t1 MTR_8g015450 60.577 104 36 2 58 156 289 392 7.48e-29 113
MS.gene28398.t1 MTR_2g100490 62.105 95 35 1 63 156 260 354 1.08e-26 106
MS.gene28398.t1 MTR_7g069590 67.857 56 18 0 98 153 32 87 1.08e-20 85.5
MS.gene28398.t1 MTR_5g079500 41.085 129 64 3 58 174 182 310 1.11e-19 86.3
MS.gene28398.t1 MTR_1g018090 66.071 56 19 0 101 156 283 338 8.23e-19 84.7
MS.gene28398.t1 MTR_1g106460 41.176 102 59 1 56 156 201 302 8.54e-19 84.3
MS.gene28398.t1 MTR_5g005110 66.071 56 19 0 101 156 233 288 9.35e-19 84.0
MS.gene28398.t1 MTR_1g106470 66.071 56 19 0 101 156 205 260 3.17e-18 82.0
MS.gene28398.t1 MTR_3g103030 60.606 66 25 1 92 156 228 293 7.79e-18 81.3
MS.gene28398.t1 MTR_4g131160 50.667 75 37 0 80 154 187 261 2.11e-15 75.1
MS.gene28398.t1 MTR_4g131160 50.667 75 37 0 80 154 184 258 2.13e-15 75.1
MS.gene28398.t1 MTR_1g106480 54.237 59 27 0 96 154 73 131 9.81e-15 69.7
MS.gene28398.t1 MTR_1g080890 50.000 70 35 0 85 154 186 255 1.91e-13 69.3
MS.gene28398.t1 MTR_2g067000 58.491 53 22 0 103 155 168 220 2.57e-13 68.6
MS.gene28398.t1 MTR_2g089070 52.632 57 27 0 102 158 146 202 3.22e-13 68.2
MS.gene28398.t1 MTR_1g060700 59.259 54 22 0 102 155 357 410 3.26e-13 68.9
MS.gene28398.t1 MTR_4g033295 57.143 56 23 1 102 156 128 183 1.24e-11 62.0
MS.gene28398.t1 MTR_4g033295 50.000 70 30 2 102 170 128 193 2.45e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28398.t1 AT5G09750 83.178 107 11 1 65 164 92 198 2.11e-46 154
MS.gene28398.t1 AT4G00120 82.022 89 16 0 67 155 87 175 2.56e-46 153
MS.gene28398.t1 AT3G21330 52.985 134 55 1 56 189 233 358 3.17e-38 137
MS.gene28398.t1 AT5G67060 75.824 91 22 0 65 155 83 173 3.82e-36 128
MS.gene28398.t1 AT5G67060 75.824 91 22 0 65 155 95 185 5.54e-36 128
MS.gene28398.t1 AT3G50330 74.725 91 23 0 65 155 92 182 1.70e-35 126
MS.gene28398.t1 AT5G01305 64.179 67 24 0 90 156 35 101 3.34e-21 87.4
MS.gene28398.t1 AT5G43175 47.500 80 42 0 77 156 117 196 6.57e-19 82.8
MS.gene28398.t1 AT2G14760 67.857 56 18 0 101 156 246 301 6.63e-19 84.3
MS.gene28398.t1 AT4G33880 67.857 56 18 0 101 156 275 330 7.32e-19 84.7
MS.gene28398.t1 AT1G27740 50.704 71 35 0 86 156 161 231 1.04e-17 80.1
MS.gene28398.t1 AT1G66470 64.815 54 19 0 101 154 204 257 1.56e-17 80.5
MS.gene28398.t1 AT5G37800 52.778 72 26 1 83 154 200 263 1.75e-17 80.1
MS.gene28398.t1 AT4G30980 59.091 66 26 1 90 154 127 192 2.25e-16 77.4
MS.gene28398.t1 AT4G30980 59.091 66 26 1 90 154 175 240 4.17e-16 77.0
MS.gene28398.t1 AT2G24260 62.963 54 20 0 101 154 44 97 4.74e-16 75.5
MS.gene28398.t1 AT2G24260 49.333 75 32 1 86 154 126 200 9.91e-16 75.9
MS.gene28398.t1 AT2G14760 55.072 69 18 1 101 156 246 314 1.38e-15 75.5
MS.gene28398.t1 AT5G58010 52.113 71 33 1 85 154 91 161 5.93e-15 73.2

Find 51 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTATGAATTCTTCTGGAATT+TGG 0.166878 4.4:+9110819 MS.gene28398:CDS
GGTTCACTCAGTGACATATT+AGG 0.250977 4.4:+9110893 MS.gene28398:CDS
TTGTTATTGTCTCCTTCTTC+TGG 0.266342 4.4:+9111313 MS.gene28398:CDS
TGTTCCTGGTGGAACTAAAA+TGG 0.289003 4.4:+9111135 MS.gene28398:CDS
CAAGTTCCTATGAATTCTTC+TGG 0.298023 4.4:+9110812 MS.gene28398:CDS
ATCATGCTGTTGTAGCTATT+TGG 0.316175 4.4:-9110845 None:intergenic
CTTCTTCTGGTTGTGACGTC+TGG 0.336110 4.4:+9111326 MS.gene28398:CDS
GTGGAAGTGAGTAGTAAATT+TGG 0.351622 4.4:-9111358 None:intergenic
ATTCGAACGTTTCTTCGCTT+TGG 0.353088 4.4:-9111034 None:intergenic
TGTCTAGCTGCAACACTTTG+TGG 0.381712 4.4:-9111067 None:intergenic
ATCCTTCAAAGACTTGTTCC+TGG 0.399593 4.4:+9111121 MS.gene28398:CDS
GAAGAACAAGAAGAAGAGTT+AGG 0.401481 4.4:+9110938 MS.gene28398:CDS
AGAAGAGTTAGGAGCTATGA+AGG 0.405429 4.4:+9110949 MS.gene28398:CDS
GTTCACTCAGTGACATATTA+GGG 0.414540 4.4:+9110894 MS.gene28398:CDS
GATCTTGTTGGAGAATAATA+CGG 0.432514 4.4:-9110784 None:intergenic
GTTCTTCTACATCTTCGATT+CGG 0.433352 4.4:-9110922 None:intergenic
TCCGGCGTCAAATTGAATTC+CGG 0.435839 4.4:-9111407 None:intergenic
AGTAGTAAATTTGGTGCAAA+AGG 0.442540 4.4:-9111349 None:intergenic
CAAATTCCAGAAGAATTCAT+AGG 0.451806 4.4:-9110818 None:intergenic
CAGAAGAATTCATAGGAACT+TGG 0.471897 4.4:-9110811 None:intergenic
CACCAGGAACAAGTCTTTGA+AGG 0.481487 4.4:-9111123 None:intergenic
GAACTTGGTGGTGATCTTGT+TGG 0.483925 4.4:-9110796 None:intergenic
CAAGATTGCAGCTATGCAAC+CGG 0.495861 4.4:+9110982 MS.gene28398:CDS
GCACCACCACCACCTTCATC+AGG 0.499844 4.4:+9110872 MS.gene28398:CDS
GTCCACTGTGGCAGCTGTTG+TGG 0.509617 4.4:-9111377 None:intergenic
CAGACGTCACAACCAGAAGA+AGG 0.532660 4.4:-9111325 None:intergenic
TAGCTACAACAGCATGATCA+TGG 0.539866 4.4:+9110850 MS.gene28398:CDS
ATGCTGTTGTAGCTATTTGG+TGG 0.542016 4.4:-9110842 None:intergenic
GAACCTGATGAAGGTGGTGG+TGG 0.552409 4.4:-9110875 None:intergenic
ATGAACATGTGAATGTCCTC+CGG 0.556908 4.4:-9111425 None:intergenic
CAAGAACTTAACATAACGAA+TGG 0.583966 4.4:-9111182 None:intergenic
GCCACAGTGGACTTACCCGC+CGG 0.587259 4.4:+9111388 MS.gene28398:CDS
TCACATGTTCATGCTTGTGA+AGG 0.591006 4.4:+9111436 MS.gene28398:CDS
AAGAATTCATAGGAACTTGG+TGG 0.592411 4.4:-9110808 None:intergenic
ACTCACTAATTACCTCATGA+TGG 0.592814 4.4:-9111474 None:intergenic
GGAATTCAATTTGACGCCGG+AGG 0.597336 4.4:+9111409 MS.gene28398:CDS
GACAATAACAAAGCACTAGG+AGG 0.606861 4.4:-9111301 None:intergenic
GGAGACAATAACAAAGCACT+AGG 0.609214 4.4:-9111304 None:intergenic
GCCGGAATTCAATTTGACGC+CGG 0.611764 4.4:+9111406 MS.gene28398:CDS
GGCGTCAAATTGAATTCCGG+CGG 0.614451 4.4:-9111404 None:intergenic
CTTCAAAGACTTGTTCCTGG+TGG 0.627271 4.4:+9111124 MS.gene28398:CDS
GCGTCAAATTGAATTCCGGC+GGG 0.629380 4.4:-9111403 None:intergenic
GTTGCTGGGTCGATATCCAC+CGG 0.629556 4.4:-9111001 None:intergenic
ATCAAGCTTTAACCATCATG+AGG 0.658321 4.4:+9111462 MS.gene28398:CDS
TTAATGCATTGTGATGAAAG+TGG 0.662271 4.4:-9111271 None:intergenic
TCACTGAGTGAACCTGATGA+AGG 0.669394 4.4:-9110884 None:intergenic
GATTGCAGCTATGCAACCGG+TGG 0.671341 4.4:+9110985 MS.gene28398:CDS
TTCCACAACAGCTGCCACAG+TGG 0.676021 4.4:+9111375 MS.gene28398:CDS
AGTGAACCTGATGAAGGTGG+TGG 0.679836 4.4:-9110878 None:intergenic
CTGAGTGAACCTGATGAAGG+TGG 0.711599 4.4:-9110881 None:intergenic
TCCGGCGGGTAAGTCCACTG+TGG 0.807057 4.4:-9111389 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAAATTCCAGAAGAATTCAT+AGG - chr4.4:9110821-9110840 None:intergenic 30.0%
CAAGAACTTAACATAACGAA+TGG - chr4.4:9111185-9111204 None:intergenic 30.0%
GATCTTGTTGGAGAATAATA+CGG - chr4.4:9110787-9110806 None:intergenic 30.0%
TTAATGCATTGTGATGAAAG+TGG - chr4.4:9111274-9111293 None:intergenic 30.0%
!! AGTAGTAAATTTGGTGCAAA+AGG - chr4.4:9111352-9111371 None:intergenic 30.0%
!! CTATGAATTCTTCTGGAATT+TGG + chr4.4:9110819-9110838 MS.gene28398:CDS 30.0%
!!! TGTTGTTGTTGTTGATTTTG+AGG - chr4.4:9111238-9111257 None:intergenic 30.0%
AAGAATTCATAGGAACTTGG+TGG - chr4.4:9110811-9110830 None:intergenic 35.0%
ACTCACTAATTACCTCATGA+TGG - chr4.4:9111477-9111496 None:intergenic 35.0%
ATCATGCTGTTGTAGCTATT+TGG - chr4.4:9110848-9110867 None:intergenic 35.0%
CAAGTTCCTATGAATTCTTC+TGG + chr4.4:9110812-9110831 MS.gene28398:CDS 35.0%
CAGAAGAATTCATAGGAACT+TGG - chr4.4:9110814-9110833 None:intergenic 35.0%
GAAGAACAAGAAGAAGAGTT+AGG + chr4.4:9110938-9110957 MS.gene28398:CDS 35.0%
GTGGAAGTGAGTAGTAAATT+TGG - chr4.4:9111361-9111380 None:intergenic 35.0%
GTTCACTCAGTGACATATTA+GGG + chr4.4:9110894-9110913 MS.gene28398:CDS 35.0%
GTTCTTCTACATCTTCGATT+CGG - chr4.4:9110925-9110944 None:intergenic 35.0%
! ATCAAGCTTTAACCATCATG+AGG + chr4.4:9111462-9111481 MS.gene28398:CDS 35.0%
! TTGTTATTGTCTCCTTCTTC+TGG + chr4.4:9111313-9111332 MS.gene28398:CDS 35.0%
!!! TTGTTGTTGATTTTGAGGAG+TGG - chr4.4:9111233-9111252 None:intergenic 35.0%
AGAAGAGTTAGGAGCTATGA+AGG + chr4.4:9110949-9110968 MS.gene28398:CDS 40.0%
ATGAACATGTGAATGTCCTC+CGG - chr4.4:9111428-9111447 None:intergenic 40.0%
ATGCTGTTGTAGCTATTTGG+TGG - chr4.4:9110845-9110864 None:intergenic 40.0%
ATTCGAACGTTTCTTCGCTT+TGG - chr4.4:9111037-9111056 None:intergenic 40.0%
GGTTCACTCAGTGACATATT+AGG + chr4.4:9110893-9110912 MS.gene28398:CDS 40.0%
TAGCTACAACAGCATGATCA+TGG + chr4.4:9110850-9110869 MS.gene28398:CDS 40.0%
TCACATGTTCATGCTTGTGA+AGG + chr4.4:9111436-9111455 MS.gene28398:CDS 40.0%
TGTTCCTGGTGGAACTAAAA+TGG + chr4.4:9111135-9111154 MS.gene28398:CDS 40.0%
! ATCCTTCAAAGACTTGTTCC+TGG + chr4.4:9111121-9111140 MS.gene28398:CDS 40.0%
! GACAATAACAAAGCACTAGG+AGG - chr4.4:9111304-9111323 None:intergenic 40.0%
! GGAGACAATAACAAAGCACT+AGG - chr4.4:9111307-9111326 None:intergenic 40.0%
!! TTGGTTTTCGAATCGTTGCT+GGG - chr4.4:9111018-9111037 None:intergenic 40.0%
!!! GTATCCATTTTAGTTCCACC+AGG - chr4.4:9111142-9111161 None:intergenic 40.0%
!!! TTTGGTTTTCGAATCGTTGC+TGG - chr4.4:9111019-9111038 None:intergenic 40.0%
CAAGATTGCAGCTATGCAAC+CGG + chr4.4:9110982-9111001 MS.gene28398:CDS 45.0%
CACCAGGAACAAGTCTTTGA+AGG - chr4.4:9111126-9111145 None:intergenic 45.0%
TCACTGAGTGAACCTGATGA+AGG - chr4.4:9110887-9110906 None:intergenic 45.0%
TCCGGCGTCAAATTGAATTC+CGG - chr4.4:9111410-9111429 None:intergenic 45.0%
TGTCTAGCTGCAACACTTTG+TGG - chr4.4:9111070-9111089 None:intergenic 45.0%
! CTTCAAAGACTTGTTCCTGG+TGG + chr4.4:9111124-9111143 MS.gene28398:CDS 45.0%
!! GAACTTGGTGGTGATCTTGT+TGG - chr4.4:9110799-9110818 None:intergenic 45.0%
AGTGAACCTGATGAAGGTGG+TGG - chr4.4:9110881-9110900 None:intergenic 50.0%
CAGACGTCACAACCAGAAGA+AGG - chr4.4:9111328-9111347 None:intergenic 50.0%
CTGAGTGAACCTGATGAAGG+TGG - chr4.4:9110884-9110903 None:intergenic 50.0%
GCCGGAATTCAATTTGACGC+CGG + chr4.4:9111406-9111425 MS.gene28398:CDS 50.0%
GCGTCAAATTGAATTCCGGC+GGG - chr4.4:9111406-9111425 None:intergenic 50.0%
GGAATTCAATTTGACGCCGG+AGG + chr4.4:9111409-9111428 MS.gene28398:CDS 50.0%
GGCGTCAAATTGAATTCCGG+CGG - chr4.4:9111407-9111426 None:intergenic 50.0%
! CTTCTTCTGGTTGTGACGTC+TGG + chr4.4:9111326-9111345 MS.gene28398:CDS 50.0%
GATTGCAGCTATGCAACCGG+TGG + chr4.4:9110985-9111004 MS.gene28398:CDS 55.0%
GTTGCTGGGTCGATATCCAC+CGG - chr4.4:9111004-9111023 None:intergenic 55.0%
TTCCACAACAGCTGCCACAG+TGG + chr4.4:9111375-9111394 MS.gene28398:CDS 55.0%
! GAACCTGATGAAGGTGGTGG+TGG - chr4.4:9110878-9110897 None:intergenic 55.0%
GCACCACCACCACCTTCATC+AGG + chr4.4:9110872-9110891 MS.gene28398:CDS 60.0%
GTCCACTGTGGCAGCTGTTG+TGG - chr4.4:9111380-9111399 None:intergenic 60.0%
TCCGGCGGGTAAGTCCACTG+TGG - chr4.4:9111392-9111411 None:intergenic 65.0%
! GCCACAGTGGACTTACCCGC+CGG + chr4.4:9111388-9111407 MS.gene28398:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 9110764 9111498 9110764 ID=MS.gene28398
chr4.4 mRNA 9110764 9111498 9110764 ID=MS.gene28398.t1;Parent=MS.gene28398
chr4.4 exon 9110764 9111498 9110764 ID=MS.gene28398.t1.exon1;Parent=MS.gene28398.t1
chr4.4 CDS 9110764 9111498 9110764 ID=cds.MS.gene28398.t1;Parent=MS.gene28398.t1
Gene Sequence

>MS.gene28398

ATGGAAACAAATGAACAAAACCGTATTATTCTCCAACAAGATCACCACCAAGTTCCTATGAATTCTTCTGGAATTTGGCCACCAAATAGCTACAACAGCATGATCATGGCACCACCACCACCTTCATCAGGTTCACTCAGTGACATATTAGGGATCAACCGAATCGAAGATGTAGAAGAACAAGAAGAAGAGTTAGGAGCTATGAAGGAAATGATGTACAAGATTGCAGCTATGCAACCGGTGGATATCGACCCAGCAACGATTCGAAAACCAAAGCGAAGAAACGTTCGAATCAGCGATGATCCACAAAGTGTTGCAGCTAGACATAGAAGAGAAAGAATCAGTGAGAAGATTCGTATCCTTCAAAGACTTGTTCCTGGTGGAACTAAAATGGATACAGCTTCTATGCTTGATGAAGCCATTCGTTATGTTAAGTTCTTGAAGAGACAAATCAAGTTGCTTCAATCCACTCCTCAAAATCAACAACAACAACAACGCATTCAATTGCCACTTTCATCACAATGCATTAATTCTACTCCTCCTAGTGCTTTGTTATTGTCTCCTTCTTCTGGTTGTGACGTCTGGCCTTTTGCACCAAATTTACTACTCACTTCCACAACAGCTGCCACAGTGGACTTACCCGCCGGAATTCAATTTGACGCCGGAGGACATTCACATGTTCATGCTTGTGAAGGCTCATCAAGCTTTAACCATCATGAGGTAATTAGTGAGTGA
Protein sequence

>MS.gene28398.t1

METNEQNRIILQQDHHQVPMNSSGIWPPNSYNSMIMAPPPPSSGSLSDILGINRIEDVEEQEEELGAMKEMMYKIAAMQPVDIDPATIRKPKRRNVRISDDPQSVAARHRRERISEKIRILQRLVPGGTKMDTASMLDEAIRYVKFLKRQIKLLQSTPQNQQQQQRIQLPLSSQCINSTPPSALLLSPSSGCDVWPFAPNLLLTSTTAATVDLPAGIQFDAGGHSHVHACEGSSSFNHHEVISE