AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene59378

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene59378.t1 MTR_5g020510 93.355 301 15 4 1 300 1 297 0.0 528
MS.gene59378.t1 MTR_4g134580 41.152 243 93 7 101 300 113 348 6.06e-52 175
MS.gene59378.t1 MTR_1g077020 41.000 200 98 2 101 300 9 188 3.25e-50 165
MS.gene59378.t1 MTR_5g032600 42.000 200 108 2 101 298 78 271 2.30e-47 160
MS.gene59378.t1 MTR_3g100650 41.284 218 104 4 91 298 70 273 4.57e-45 155
MS.gene59378.t1 MTR_7g010300 39.437 213 102 7 99 299 86 283 3.09e-44 154
MS.gene59378.t1 MTR_5g065440 39.623 212 112 5 101 298 58 267 1.10e-41 145
MS.gene59378.t1 MTR_2g076780 33.735 249 133 7 69 299 3 237 4.16e-40 140
MS.gene59378.t1 MTR_6g012280 38.208 212 107 5 101 302 91 288 5.66e-39 140
MS.gene59378.t1 MTR_8g069080 37.321 209 100 6 101 293 69 262 1.01e-38 138
MS.gene59378.t1 MTR_8g467340 61.404 57 22 0 236 292 271 327 5.33e-19 87.0
MS.gene59378.t1 MTR_8g467340 52.113 71 25 2 94 162 57 120 5.25e-18 84.3
MS.gene59378.t1 MTR_3g039810 53.846 65 30 0 90 154 9 73 1.21e-18 79.7
MS.gene59378.t1 MTR_6g073013 55.000 60 26 1 236 294 101 160 2.03e-18 81.6
MS.gene59378.t1 MTR_6g073013 61.538 52 15 2 101 149 19 68 4.51e-15 72.4
MS.gene59378.t1 MTR_8g442330 28.659 164 79 3 110 273 14 139 4.48e-18 79.7
MS.gene59378.t1 MTR_8g051480 48.387 62 31 1 237 298 68 128 2.18e-15 72.0
MS.gene59378.t1 MTR_8g069380 46.032 63 34 0 236 298 52 114 6.52e-15 70.5
MS.gene59378.t1 MTR_6g012220 57.143 49 17 1 101 149 21 65 1.13e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene59378.t1 AT2G18350 47.639 233 84 8 79 300 57 262 2.91e-58 188
MS.gene59378.t1 AT3G50890 36.981 265 121 7 45 297 12 242 9.45e-49 164
MS.gene59378.t1 AT2G02540 39.013 223 90 6 99 298 85 284 2.03e-48 164
MS.gene59378.t1 AT2G02540 39.013 223 90 6 99 298 85 284 2.03e-48 164
MS.gene59378.t1 AT4G24660 39.070 215 86 4 97 302 45 223 4.66e-48 161
MS.gene59378.t1 AT4G24660 39.810 211 82 4 97 298 45 219 7.65e-48 160
MS.gene59378.t1 AT1G14440 40.191 209 100 5 99 298 88 280 8.28e-45 155
MS.gene59378.t1 AT1G14440 40.191 209 100 5 99 298 88 280 8.28e-45 155
MS.gene59378.t1 AT1G69600 36.475 244 115 6 82 311 12 229 1.21e-43 150
MS.gene59378.t1 AT5G65410 38.389 211 103 4 91 297 65 252 1.56e-40 143
MS.gene59378.t1 AT3G28920 37.379 206 120 3 98 296 49 252 5.17e-40 142
MS.gene59378.t1 AT5G15210 34.137 249 124 6 69 292 2 235 4.91e-39 139
MS.gene59378.t1 AT5G60480 35.814 215 95 6 87 292 23 203 5.71e-36 129
MS.gene59378.t1 AT5G42780 30.457 197 113 5 101 295 64 238 1.25e-26 105
MS.gene59378.t1 AT1G75240 76.471 51 12 0 101 151 76 126 6.54e-23 97.1
MS.gene59378.t1 AT5G39760 55.385 65 29 0 236 300 200 264 3.73e-20 89.7
MS.gene59378.t1 AT1G74660 53.448 58 27 0 97 154 35 92 1.26e-18 80.1
MS.gene59378.t1 AT1G14687 27.551 196 102 6 101 293 7 165 1.48e-18 82.0
MS.gene59378.t1 AT1G74660 53.448 58 27 0 97 154 35 92 1.61e-17 77.0
MS.gene59378.t1 AT3G28917 54.098 61 27 1 95 154 27 87 1.32e-16 74.7
MS.gene59378.t1 AT1G18835 51.852 54 23 1 101 154 26 76 1.94e-13 65.5

Find 57 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATGTCACAGACAACTTT+AGG 0.301821 5.4:+12454808 MS.gene59378:CDS
CCGTCCATGATGATGACTTT+TGG 0.355768 5.4:+12455396 MS.gene59378:CDS
AGAGTTTCACAACCTAGTTC+TGG 0.368324 5.4:+12455363 MS.gene59378:CDS
AAGATGGTGTTGGAAGATTA+AGG 0.378783 5.4:-12455329 None:intergenic
GTTGTTGCAGCCGTTAGATC+TGG 0.406325 5.4:-12455000 None:intergenic
CTTACCCTCTTCTTCAAAAC+CGG 0.408989 5.4:-12455495 None:intergenic
GCTTAAAAGTGGATAATTGC+AGG 0.412519 5.4:+12455777 MS.gene59378:CDS
TAGTAGTAGTAGTATGGTTA+GGG 0.429477 5.4:-12454921 None:intergenic
CGGTTGCTGCGGCGTCTGTA+TGG 0.433418 5.4:-12455475 None:intergenic
ATGGAGTTTGCTGAAAAGAT+TGG 0.437625 5.4:+12455552 MS.gene59378:CDS
CATACAGACGCCGCAGCAAC+CGG 0.441402 5.4:+12455476 MS.gene59378:CDS
GAGGAATACTATGTTGTTGT+TGG 0.445811 5.4:-12455251 None:intergenic
AGTGAAGATCTCAACATGTT+TGG 0.446843 5.4:+12455441 MS.gene59378:CDS
ATGGGAAGCCACGTGGTAGA+TGG 0.447420 5.4:+12455132 MS.gene59378:CDS
GTTGATGATGTTATTTGTTG+TGG 0.461191 5.4:-12455060 None:intergenic
GATGTTATTTGTTGTGGCTG+AGG 0.462310 5.4:-12455054 None:intergenic
CGTGGTTTCTCAGACATTCT+CGG 0.464493 5.4:-12455101 None:intergenic
TCAAGTTGGTATCAAGAGAC+AGG 0.468371 5.4:+12455623 MS.gene59378:CDS
GGGGTACCTTCTTCACCGCT+TGG 0.472411 5.4:-12455171 None:intergenic
ACTTGAGGTGGTGGTGGAGT+TGG 0.474110 5.4:-12454859 None:intergenic
GAGAAACCACGCGGCAAGCA+TGG 0.475746 5.4:+12455113 MS.gene59378:CDS
CAGCACATTTGAAATATTGT+GGG 0.475954 5.4:-12455191 None:intergenic
GCAGCACATTTGAAATATTG+TGG 0.476946 5.4:-12455192 None:intergenic
TCTTCACTTGATGATTCAGC+TGG 0.479858 5.4:-12455426 None:intergenic
GTGTGAACTTGAGGTGGTGG+TGG 0.490980 5.4:-12454865 None:intergenic
TTCACAACCTAGTTCTGGAC+AGG 0.499932 5.4:+12455368 MS.gene59378:CDS
ATGACAGGTCTTTGAGAAGA+AGG 0.512659 5.4:-12454973 None:intergenic
TTCATGCCAAGCGGTGAAGA+AGG 0.514566 5.4:+12455165 MS.gene59378:CDS
TGGAGTTTGCTGAAAAGATT+GGG 0.549528 5.4:+12455553 MS.gene59378:CDS
AGAAACCACGCGGCAAGCAT+GGG 0.549901 5.4:+12455114 MS.gene59378:CDS
GGTGGAACCTGTCCAGAACT+AGG 0.552234 5.4:-12455375 None:intergenic
ATACACTTGGTGCTTAAAAG+TGG 0.558616 5.4:+12455766 MS.gene59378:CDS
GTTAGATCTGGATCTATGAC+AGG 0.562020 5.4:-12454988 None:intergenic
AGGCGAAACTCGCATACACT+TGG 0.566495 5.4:+12455753 MS.gene59378:CDS
GAAGGTGCAAGATGTGGTGG+TGG 0.572439 5.4:-12454955 None:intergenic
TGAGATGAAGAAGATGGTGT+TGG 0.575563 5.4:-12455339 None:intergenic
TGATCCAAAAGTCATCATCA+TGG 0.575663 5.4:-12455400 None:intergenic
TTCTTCAAAACCGGTTGCTG+CGG 0.576173 5.4:-12455486 None:intergenic
AATGTGTGAACTTGAGGTGG+TGG 0.602598 5.4:-12454868 None:intergenic
TGTCATAGATCCAGATCTAA+CGG 0.606727 5.4:+12454990 MS.gene59378:CDS
AAGACTAATGTGTGAACTTG+AGG 0.616691 5.4:-12454874 None:intergenic
CCAAAAGTCATCATCATGGA+CGG 0.622115 5.4:-12455396 None:intergenic
AGCCACGTGGTAGATGGATG+TGG 0.625991 5.4:+12455138 MS.gene59378:CDS
ACTCTTTGAGATGAAGAAGA+TGG 0.637378 5.4:-12455345 None:intergenic
GGCTTCCCATGCTTGCCGCG+TGG 0.643184 5.4:-12455119 None:intergenic
GAAGAAGGTGCAAGATGTGG+TGG 0.651537 5.4:-12454958 None:intergenic
AGCACATTTGAAATATTGTG+GGG 0.654466 5.4:-12455190 None:intergenic
ACATGCTGAACATGTTGTTG+AGG 0.672696 5.4:-12455270 None:intergenic
AGTTTGCTGAAAAGATTGGG+TGG 0.678186 5.4:+12455556 MS.gene59378:CDS
CATCATCAAAACAACAACAA+CGG 0.680341 5.4:+12455303 MS.gene59378:CDS
AAAGTCATCATCATGGACGG+TGG 0.680716 5.4:-12455393 None:intergenic
TGAGAAGAAGGTGCAAGATG+TGG 0.685772 5.4:-12454961 None:intergenic
GGCAAGCATGGGAAGCCACG+TGG 0.697743 5.4:+12455125 MS.gene59378:CDS
ACTAATGTGTGAACTTGAGG+TGG 0.703165 5.4:-12454871 None:intergenic
CACCACATCCATCTACCACG+TGG 0.722647 5.4:-12455140 None:intergenic
TGTGGTGAATTCATGCCAAG+CGG 0.769326 5.4:+12455156 MS.gene59378:CDS
AGAATGTCTGAGAAACCACG+CGG 0.882510 5.4:+12455104 MS.gene59378:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGTTTTGATGATGATAATT+AGG - chr5.4:12455297-12455316 None:intergenic 20.0%
!!! TTTTTTTCAAAAAAGCTTAG+AGG + chr5.4:12455733-12455752 MS.gene59378:intron 20.0%
!! TATGTTTTCGATGGAAATTA+CGG - chr5.4:12455230-12455249 None:intergenic 25.0%
CATCATCAAAACAACAACAA+CGG + chr5.4:12455303-12455322 MS.gene59378:CDS 30.0%
GATTAGTAGTAGTAGTAGTA+TGG - chr5.4:12454930-12454949 None:intergenic 30.0%
TAGTAGTAGTAGTATGGTTA+GGG - chr5.4:12454924-12454943 None:intergenic 30.0%
! AGCACATTTGAAATATTGTG+GGG - chr5.4:12455193-12455212 None:intergenic 30.0%
! CAGCACATTTGAAATATTGT+GGG - chr5.4:12455194-12455213 None:intergenic 30.0%
!! GTTGATGATGTTATTTGTTG+TGG - chr5.4:12455063-12455082 None:intergenic 30.0%
AAGACTAATGTGTGAACTTG+AGG - chr5.4:12454877-12454896 None:intergenic 35.0%
AAGATGTCACAGACAACTTT+AGG + chr5.4:12454808-12454827 MS.gene59378:CDS 35.0%
AGTGAAGATCTCAACATGTT+TGG + chr5.4:12455441-12455460 MS.gene59378:CDS 35.0%
GAGGAATACTATGTTGTTGT+TGG - chr5.4:12455254-12455273 None:intergenic 35.0%
GCAACAAAAAGATAGGATGA+TGG + chr5.4:12455533-12455552 MS.gene59378:CDS 35.0%
GCTTAAAAGTGGATAATTGC+AGG + chr5.4:12455777-12455796 MS.gene59378:CDS 35.0%
GTAGTAGTAGTAGTATGGTT+AGG - chr5.4:12454925-12454944 None:intergenic 35.0%
TCTCACAGCAACAAAAAGAT+AGG + chr5.4:12455526-12455545 MS.gene59378:CDS 35.0%
TGATCCAAAAGTCATCATCA+TGG - chr5.4:12455403-12455422 None:intergenic 35.0%
TGTCATAGATCCAGATCTAA+CGG + chr5.4:12454990-12455009 MS.gene59378:CDS 35.0%
! AAGATGGTGTTGGAAGATTA+AGG - chr5.4:12455332-12455351 None:intergenic 35.0%
! GCAGCACATTTGAAATATTG+TGG - chr5.4:12455195-12455214 None:intergenic 35.0%
! GTTGTTGGATATGTTTTCGA+TGG - chr5.4:12455239-12455258 None:intergenic 35.0%
!! ACTCTTTGAGATGAAGAAGA+TGG - chr5.4:12455348-12455367 None:intergenic 35.0%
!! ATACACTTGGTGCTTAAAAG+TGG + chr5.4:12455766-12455785 MS.gene59378:CDS 35.0%
!! ATGGAGTTTGCTGAAAAGAT+TGG + chr5.4:12455552-12455571 MS.gene59378:CDS 35.0%
!! TGGAGTTTGCTGAAAAGATT+GGG + chr5.4:12455553-12455572 MS.gene59378:CDS 35.0%
!!! CAACAGTTTTGTTCTCAAGT+TGG + chr5.4:12455609-12455628 MS.gene59378:CDS 35.0%
ACATGCTGAACATGTTGTTG+AGG - chr5.4:12455273-12455292 None:intergenic 40.0%
ACTAATGTGTGAACTTGAGG+TGG - chr5.4:12454874-12454893 None:intergenic 40.0%
AGAGTTTCACAACCTAGTTC+TGG + chr5.4:12455363-12455382 MS.gene59378:CDS 40.0%
CCAAAAGTCATCATCATGGA+CGG - chr5.4:12455399-12455418 None:intergenic 40.0%
CTTACCCTCTTCTTCAAAAC+CGG - chr5.4:12455498-12455517 None:intergenic 40.0%
GTTAGATCTGGATCTATGAC+AGG - chr5.4:12454991-12455010 None:intergenic 40.0%
TGAGATGAAGAAGATGGTGT+TGG - chr5.4:12455342-12455361 None:intergenic 40.0%
! ATGACAGGTCTTTGAGAAGA+AGG - chr5.4:12454976-12454995 None:intergenic 40.0%
! TCTTCACTTGATGATTCAGC+TGG - chr5.4:12455429-12455448 None:intergenic 40.0%
! TGGTTAGGGTGTGAATTTTG+AGG - chr5.4:12454910-12454929 None:intergenic 40.0%
!! AGTTTGCTGAAAAGATTGGG+TGG + chr5.4:12455556-12455575 MS.gene59378:CDS 40.0%
!! GATGTTATTTGTTGTGGCTG+AGG - chr5.4:12455057-12455076 None:intergenic 40.0%
!! TCAAGTTGGTATCAAGAGAC+AGG + chr5.4:12455623-12455642 MS.gene59378:CDS 40.0%
!! TTAGGGTGTGAATTTTGAGG+TGG - chr5.4:12454907-12454926 None:intergenic 40.0%
!!! TAGGGTGTGAATTTTGAGGT+GGG - chr5.4:12454906-12454925 None:intergenic 40.0%
AAAGTCATCATCATGGACGG+TGG - chr5.4:12455396-12455415 None:intergenic 45.0%
AATGTGTGAACTTGAGGTGG+TGG - chr5.4:12454871-12454890 None:intergenic 45.0%
AGAATGTCTGAGAAACCACG+CGG + chr5.4:12455104-12455123 MS.gene59378:CDS 45.0%
CGTGGTTTCTCAGACATTCT+CGG - chr5.4:12455104-12455123 None:intergenic 45.0%
TGTGGTGAATTCATGCCAAG+CGG + chr5.4:12455156-12455175 MS.gene59378:CDS 45.0%
TTCTTCAAAACCGGTTGCTG+CGG - chr5.4:12455489-12455508 None:intergenic 45.0%
! TGAGAAGAAGGTGCAAGATG+TGG - chr5.4:12454964-12454983 None:intergenic 45.0%
!! CCGTCCATGATGATGACTTT+TGG + chr5.4:12455396-12455415 MS.gene59378:CDS 45.0%
!! TTCACAACCTAGTTCTGGAC+AGG + chr5.4:12455368-12455387 MS.gene59378:CDS 45.0%
!!! AGCAACCGGTTTTGAAGAAG+AGG + chr5.4:12455490-12455509 MS.gene59378:CDS 45.0%
!!! CGGTTTTGAAGAAGAGGGTA+AGG + chr5.4:12455496-12455515 MS.gene59378:CDS 45.0%
!!! GCAACCGGTTTTGAAGAAGA+GGG + chr5.4:12455491-12455510 MS.gene59378:CDS 45.0%
AGGCGAAACTCGCATACACT+TGG + chr5.4:12455753-12455772 MS.gene59378:CDS 50.0%
GTTGTTGCAGCCGTTAGATC+TGG - chr5.4:12455003-12455022 None:intergenic 50.0%
TTCATGCCAAGCGGTGAAGA+AGG + chr5.4:12455165-12455184 MS.gene59378:CDS 50.0%
! GAAGAAGGTGCAAGATGTGG+TGG - chr5.4:12454961-12454980 None:intergenic 50.0%
AGAAACCACGCGGCAAGCAT+GGG + chr5.4:12455114-12455133 MS.gene59378:CDS 55.0%
AGCCACGTGGTAGATGGATG+TGG + chr5.4:12455138-12455157 MS.gene59378:CDS 55.0%
ATGGGAAGCCACGTGGTAGA+TGG + chr5.4:12455132-12455151 MS.gene59378:CDS 55.0%
CACCACATCCATCTACCACG+TGG - chr5.4:12455143-12455162 None:intergenic 55.0%
GGTGGAACCTGTCCAGAACT+AGG - chr5.4:12455378-12455397 None:intergenic 55.0%
! GAAGGTGCAAGATGTGGTGG+TGG - chr5.4:12454958-12454977 None:intergenic 55.0%
! GTGTGAACTTGAGGTGGTGG+TGG - chr5.4:12454868-12454887 None:intergenic 55.0%
!! ACTTGAGGTGGTGGTGGAGT+TGG - chr5.4:12454862-12454881 None:intergenic 55.0%
CATACAGACGCCGCAGCAAC+CGG + chr5.4:12455476-12455495 MS.gene59378:CDS 60.0%
GAGAAACCACGCGGCAAGCA+TGG + chr5.4:12455113-12455132 MS.gene59378:CDS 60.0%
! GGGGTACCTTCTTCACCGCT+TGG - chr5.4:12455174-12455193 None:intergenic 60.0%
CGGTTGCTGCGGCGTCTGTA+TGG - chr5.4:12455478-12455497 None:intergenic 65.0%
GGCAAGCATGGGAAGCCACG+TGG + chr5.4:12455125-12455144 MS.gene59378:CDS 65.0%
GGCTTCCCATGCTTGCCGCG+TGG - chr5.4:12455122-12455141 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 12454799 12455817 12454799 ID=MS.gene59378
chr5.4 mRNA 12454799 12455817 12454799 ID=MS.gene59378.t1;Parent=MS.gene59378
chr5.4 exon 12454799 12455697 12454799 ID=MS.gene59378.t1.exon1;Parent=MS.gene59378.t1
chr5.4 CDS 12454799 12455697 12454799 ID=cds.MS.gene59378.t1;Parent=MS.gene59378.t1
chr5.4 exon 12455748 12455817 12455748 ID=MS.gene59378.t1.exon2;Parent=MS.gene59378.t1
chr5.4 CDS 12455748 12455817 12455748 ID=cds.MS.gene59378.t1;Parent=MS.gene59378.t1
Gene Sequence

>MS.gene59378

ATGGAAACAAAGATGTCACAGACAACTTTAGGTTACAATAGAGATTCTTCTTCTTCTTCACCAACTCCACCACCACCTCAAGTTCACACATTAGTCTTCAATAACCCACCTCAAAATTCACACCCTAACCATACTACTACTACTACTAATCTTTATCCACCACCACATCTTGCACCTTCTTCTCAAAGACCTGTCATAGATCCAGATCTAACGGCTGCAACAACAACAGCAAACACTTCTACAATAACAACACAACCTCAGCCACAACAAATAACATCATCAACAACAACAAAAATATGTTACCGAGAATGTCTGAGAAACCACGCGGCAAGCATGGGAAGCCACGTGGTAGATGGATGTGGTGAATTCATGCCAAGCGGTGAAGAAGGTACCCCACAATATTTCAAATGTGCTGCTTGTGATTGTCACCGTAATTTCCATCGAAAACATATCCAACAACAACATAGTATTCCTCAACAACATGTTCAGCATGTTCCTAATTATCATCATCAAAACAACAACAACGGTCACCTTAATCTTCCAACACCATCTTCTTCATCTCAAAGAGTTTCACAACCTAGTTCTGGACAGGTTCCACCGTCCATGATGATGACTTTTGGATCAGTTCCAGCTGAATCATCAAGTGAAGATCTCAACATGTTTGGTGCACAATTTTCCATACAGACGCCGCAGCAACCGGTTTTGAAGAAGAGGGTAAGGACGAAATTCTCACAGCAACAAAAAGATAGGATGATGGAGTTTGCTGAAAAGATTGGGTGGAAGATTCAGAAACATGATGAACAAGAAGTGCAACAGTTTTGTTCTCAAGTTGGTATCAAGAGACAGGTTTTTAAAGTTTTTATGCATAATAACAAACAAGCTATGAAGAAACAGCAAATGTAAGCTTAGTTATAATAAACTAATTTCATTATTATTTTTTTCAAAAAAGCTTAGAGGCGAAACTCGCATACACTTGGTGCTTAAAAGTGGATAATTGCAGGTTCAAACTCGCACTCTAG
Protein sequence

>MS.gene59378.t1

METKMSQTTLGYNRDSSSSSPTPPPPQVHTLVFNNPPQNSHPNHTTTTTNLYPPPHLAPSSQRPVIDPDLTAATTTANTSTITTQPQPQQITSSTTTKICYRECLRNHAASMGSHVVDGCGEFMPSGEEGTPQYFKCAACDCHRNFHRKHIQQQHSIPQQHVQHVPNYHHQNNNNGHLNLPTPSSSSQRVSQPSSGQVPPSMMMTFGSVPAESSSEDLNMFGAQFSIQTPQQPVLKKRVRTKFSQQQKDRMMEFAEKIGWKIQKHDEQEVQQFCSQVGIKRQVFKVFMHNNKQAMKKQQILEAKLAYTWCLKVDNCRFKLAL