AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0270350

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0270350 MtrunA17_Chr4g0046521 47.917 192 86 4 32 222 26 204 2.03e-60 189
Msa0270350 MtrunA17_Chr2g0282811 48.187 193 85 3 33 222 28 208 3.96e-60 188
Msa0270350 MtrunA17_Chr2g0282791 47.120 191 89 2 32 222 27 205 9.74e-59 184
Msa0270350 MtrunA17_Chr4g0040531 43.784 185 89 4 40 222 32 203 1.22e-48 159
Msa0270350 MtrunA17_Chr2g0286871 40.000 190 99 3 33 222 13 187 2.39e-43 145
Msa0270350 MtrunA17_Chr5g0419161 39.683 189 99 4 33 218 38 214 1.35e-41 141
Msa0270350 MtrunA17_Chr7g0217511 39.153 189 100 4 33 218 38 214 1.65e-39 135
Msa0270350 MtrunA17_Chr4g0066491 37.186 199 111 4 24 222 15 199 4.75e-38 132
Msa0270350 MtrunA17_Chr4g0066481 39.344 183 97 4 40 222 29 197 7.87e-38 131
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0270350 AT3G02430.1 52.535 217 93 3 6 222 7 213 2.35e-71 217
Msa0270350 AT4G24310.1 53.394 221 84 4 2 222 6 207 3.52e-70 214
Msa0270350 AT4G18425.1 49.153 177 76 4 47 222 48 211 1.43e-53 172
Msa0270350 AT5G46090.1 45.078 193 92 4 31 222 33 212 2.85e-52 169
Msa0270350 AT4G28485.2 44.670 197 94 5 29 222 14 198 7.16e-45 149
Msa0270350 AT3G21550.1 42.614 176 84 3 45 220 14 172 4.63e-39 134
Msa0270350 AT1G09157.1 38.889 180 108 2 40 218 61 239 5.06e-37 130
Msa0270350 AT3G21520.1 38.418 177 94 3 43 219 26 187 4.13e-36 127
Msa0270350 AT5G39650.1 38.889 180 108 2 40 218 62 240 5.17e-36 128
Msa0270350 AT5G27370.1 37.705 183 103 5 43 218 8 186 1.95e-29 109
Msa0270350 AT4G28485.1 44.545 110 50 2 113 222 65 163 5.86e-20 84.0

Find 60 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTTCAGATTGCTTATTAT+TGG 0.102422 2_3:+1602698 None:intergenic
GTACTCCTAGTAATTATATT+TGG 0.194804 2_3:+1602023 None:intergenic
CTAGTAATTATATTTGGAAT+TGG 0.267098 2_3:+1602029 None:intergenic
TGTTCTTTGCTGTTGCATTA+AGG 0.305960 2_3:-1602227 Msa0270350:CDS
GATATTGTGCCCCTCGGAAT+TGG 0.326356 2_3:-1602144 Msa0270350:CDS
GGTGCAGGTGTAGGTGTAAC+AGG 0.338425 2_3:+1602063 None:intergenic
TGAAGACTGGCGTGAGAATC+TGG 0.355118 2_3:+1602535 None:intergenic
TAGTCACACGGCGTGGTTGC+GGG 0.359159 2_3:+1602178 None:intergenic
GTTCTTTGCTGTTGCATTAA+GGG 0.365115 2_3:-1602226 Msa0270350:CDS
ATGCTTCCTTGCTTGTTTCA+CGG 0.371761 2_3:-1602442 Msa0270350:CDS
TAGTAATTATATTTGGAATT+GGG 0.375012 2_3:+1602030 None:intergenic
CCATGGCATCGCAACCTTCA+AGG 0.392282 2_3:-1602385 Msa0270350:CDS
GTAGTATCTGGAGCATTAAC+GGG 0.406461 2_3:-1602606 Msa0270350:CDS
AAATGCATGTACAAAGTCAA+TGG 0.433016 2_3:+1602263 None:intergenic
AGTAGTATCTGGAGCATTAA+CGG 0.435471 2_3:-1602607 Msa0270350:CDS
CGACGGTCAGTAGTAGTATC+TGG 0.437746 2_3:-1602618 Msa0270350:CDS
TTAGTCACACGGCGTGGTTG+CGG 0.444013 2_3:+1602177 None:intergenic
TTGGAATTGGGTGCAGCAGC+AGG 0.459846 2_3:+1602042 None:intergenic
TTGGGTGCAGCAGCAGGTGC+AGG 0.468002 2_3:+1602048 None:intergenic
TCGCAACCTTCAAGGGTCTC+TGG 0.469635 2_3:-1602377 Msa0270350:CDS
GCAGCAGCACATGGAATTAG+TGG 0.477735 2_3:-1602654 Msa0270350:CDS
CAATTCCAAATATAATTACT+AGG 0.486361 2_3:-1602028 None:intergenic
GCAGCAGCAGGTGCAGGTGT+AGG 0.488422 2_3:+1602054 None:intergenic
GCAACCACGCCGTGTGACTA+AGG 0.489093 2_3:-1602175 Msa0270350:CDS
CATGGCATCGCAACCTTCAA+GGG 0.499059 2_3:-1602384 Msa0270350:CDS
GCTCCGTTGTTTGTGAAGAC+TGG 0.503057 2_3:+1602522 None:intergenic
AAATAGCCAGAGACCCTTGA+AGG 0.509853 2_3:+1602371 None:intergenic
CCAACCACTAGACATGGGAT+TGG 0.514072 2_3:-1602090 Msa0270350:CDS
TTATACTTGCTCAACTCAGC+TGG 0.520275 2_3:+1602294 None:intergenic
GGGAAGTAAGTTTGCCAAGT+TGG 0.532415 2_3:+1602578 None:intergenic
AATGCATGTACAAAGTCAAT+GGG 0.533496 2_3:+1602264 None:intergenic
GCGTGAGAATCTGGAATGCT+AGG 0.537937 2_3:+1602544 None:intergenic
ATTAACGGGGACAGCCAACT+TGG 0.539398 2_3:-1602592 Msa0270350:CDS
AATAAGCAATCTGAAGCAGA+TGG 0.548858 2_3:-1602693 Msa0270350:CDS
TCCATGACATTGACATTGAC+GGG 0.550083 2_3:+1602339 None:intergenic
AGTTGAGCAAGTATAAGATC+AGG 0.557038 2_3:-1602287 Msa0270350:CDS
CCAATCCCATGTCTAGTGGT+TGG 0.561333 2_3:+1602090 None:intergenic
GTCCATGACATTGACATTGA+CGG 0.563837 2_3:+1602338 None:intergenic
GTTCTTGATATTGTGCCCCT+CGG 0.569071 2_3:-1602150 Msa0270350:CDS
CCTTGAAGGTTGCGATGCCA+TGG 0.569779 2_3:+1602385 None:intergenic
ACCCGTCAATGTCAATGTCA+TGG 0.570259 2_3:-1602340 Msa0270350:CDS
ACAGTGAATAATGCATCAGA+TGG 0.586121 2_3:-1602417 Msa0270350:CDS
TTGGCAAACTTACTTCCCAC+AGG 0.590824 2_3:-1602573 Msa0270350:CDS
GAATGCTAGGAGTGTTCCTG+TGG 0.592747 2_3:+1602557 None:intergenic
ATGAGATTGCAAGCAAGATG+AGG 0.612498 2_3:+1602463 None:intergenic
GTAGCCAATCCCATGTCTAG+TGG 0.615835 2_3:+1602086 None:intergenic
AAGTGTGAGAATGCGAGTAA+CGG 0.616907 2_3:+1602491 None:intergenic
GCATAGGAATCCAATTCCGA+GGG 0.617670 2_3:+1602134 None:intergenic
TGCATAGGAATCCAATTCCG+AGG 0.619320 2_3:+1602133 None:intergenic
CAAGAACCTCCTTAGTCACA+CGG 0.627426 2_3:+1602166 None:intergenic
CTGTGTCCGTGAAACAAGCA+AGG 0.639798 2_3:+1602436 None:intergenic
ACCTCCTTAGTCACACGGCG+TGG 0.648095 2_3:+1602171 None:intergenic
ACGCCAGTCTTCACAAACAA+CGG 0.649231 2_3:-1602525 Msa0270350:CDS
GTGGTAGACGACGACGACGA+CGG 0.670485 2_3:-1602635 Msa0270350:CDS
TAGTATCTGGAGCATTAACG+GGG 0.687598 2_3:-1602605 Msa0270350:CDS
TCAGATGGAAGAATCTACCA+TGG 0.695565 2_3:-1602402 Msa0270350:CDS
ACCACGCCGTGTGACTAAGG+AGG 0.698128 2_3:-1602172 Msa0270350:CDS
GTGCAGGTGTAGGTGTAACA+GGG 0.699596 2_3:+1602064 None:intergenic
AATGCTAGGAGTGTTCCTGT+GGG 0.719785 2_3:+1602558 None:intergenic
CATAGGAATCCAATTCCGAG+GGG 0.764587 2_3:+1602135 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAGTAATTATATTTGGAATT+GGG + chr2_3:1602722-1602741 None:intergenic 15.0%
!!! CTAGTAATTATATTTGGAAT+TGG + chr2_3:1602723-1602742 None:intergenic 20.0%
TGCTTCAGATTGCTTATTAT+TGG + chr2_3:1602054-1602073 None:intergenic 30.0%
AATGCATGTACAAAGTCAAT+GGG + chr2_3:1602488-1602507 None:intergenic 30.0%
AAATGCATGTACAAAGTCAA+TGG + chr2_3:1602489-1602508 None:intergenic 30.0%
! AATAAGCAATCTGAAGCAGA+TGG - chr2_3:1602056-1602075 Msa0270350:CDS 35.0%
! AGTAGTATCTGGAGCATTAA+CGG - chr2_3:1602142-1602161 Msa0270350:CDS 35.0%
ACAGTGAATAATGCATCAGA+TGG - chr2_3:1602332-1602351 Msa0270350:CDS 35.0%
AGTTGAGCAAGTATAAGATC+AGG - chr2_3:1602462-1602481 Msa0270350:CDS 35.0%
!! TGTTCTTTGCTGTTGCATTA+AGG - chr2_3:1602522-1602541 Msa0270350:CDS 35.0%
!! GTTCTTTGCTGTTGCATTAA+GGG - chr2_3:1602523-1602542 Msa0270350:CDS 35.0%
! TTTTTCCAACCACTAGACAT+GGG - chr2_3:1602654-1602673 Msa0270350:CDS 35.0%
! GTAGTATCTGGAGCATTAAC+GGG - chr2_3:1602143-1602162 Msa0270350:CDS 40.0%
! TAGTATCTGGAGCATTAACG+GGG - chr2_3:1602144-1602163 Msa0270350:CDS 40.0%
AAGTGTGAGAATGCGAGTAA+CGG + chr2_3:1602261-1602280 None:intergenic 40.0%
ATGAGATTGCAAGCAAGATG+AGG + chr2_3:1602289-1602308 None:intergenic 40.0%
ATGCTTCCTTGCTTGTTTCA+CGG - chr2_3:1602307-1602326 Msa0270350:CDS 40.0%
TCAGATGGAAGAATCTACCA+TGG - chr2_3:1602347-1602366 Msa0270350:CDS 40.0%
TCCATGACATTGACATTGAC+GGG + chr2_3:1602413-1602432 None:intergenic 40.0%
GTCCATGACATTGACATTGA+CGG + chr2_3:1602414-1602433 None:intergenic 40.0%
TTATACTTGCTCAACTCAGC+TGG + chr2_3:1602458-1602477 None:intergenic 40.0%
CGACAAAAAGCAAAGTGCAT+AGG + chr2_3:1602634-1602653 None:intergenic 40.0%
! GTTTTTCCAACCACTAGACA+TGG - chr2_3:1602653-1602672 Msa0270350:CDS 40.0%
GGGAAGTAAGTTTGCCAAGT+TGG + chr2_3:1602174-1602193 None:intergenic 45.0%
TTGGCAAACTTACTTCCCAC+AGG - chr2_3:1602176-1602195 Msa0270350:CDS 45.0%
!! AATGCTAGGAGTGTTCCTGT+GGG + chr2_3:1602194-1602213 None:intergenic 45.0%
ACGCCAGTCTTCACAAACAA+CGG - chr2_3:1602224-1602243 Msa0270350:CDS 45.0%
AAATAGCCAGAGACCCTTGA+AGG + chr2_3:1602381-1602400 None:intergenic 45.0%
ACCCGTCAATGTCAATGTCA+TGG - chr2_3:1602409-1602428 Msa0270350:CDS 45.0%
CAAGAACCTCCTTAGTCACA+CGG + chr2_3:1602586-1602605 None:intergenic 45.0%
GTTCTTGATATTGTGCCCCT+CGG - chr2_3:1602599-1602618 Msa0270350:CDS 45.0%
CATAGGAATCCAATTCCGAG+GGG + chr2_3:1602617-1602636 None:intergenic 45.0%
GCATAGGAATCCAATTCCGA+GGG + chr2_3:1602618-1602637 None:intergenic 45.0%
TGCATAGGAATCCAATTCCG+AGG + chr2_3:1602619-1602638 None:intergenic 45.0%
GCAGCAGCACATGGAATTAG+TGG - chr2_3:1602095-1602114 Msa0270350:CDS 50.0%
CGACGGTCAGTAGTAGTATC+TGG - chr2_3:1602131-1602150 Msa0270350:CDS 50.0%
ATTAACGGGGACAGCCAACT+TGG - chr2_3:1602157-1602176 Msa0270350:CDS 50.0%
!! GAATGCTAGGAGTGTTCCTG+TGG + chr2_3:1602195-1602214 None:intergenic 50.0%
! GCGTGAGAATCTGGAATGCT+AGG + chr2_3:1602208-1602227 None:intergenic 50.0%
TGAAGACTGGCGTGAGAATC+TGG + chr2_3:1602217-1602236 None:intergenic 50.0%
GCTCCGTTGTTTGTGAAGAC+TGG + chr2_3:1602230-1602249 None:intergenic 50.0%
CTGTGTCCGTGAAACAAGCA+AGG + chr2_3:1602316-1602335 None:intergenic 50.0%
CATGGCATCGCAACCTTCAA+GGG - chr2_3:1602365-1602384 Msa0270350:CDS 50.0%
GATATTGTGCCCCTCGGAAT+TGG - chr2_3:1602605-1602624 Msa0270350:CDS 50.0%
CCAATCCCATGTCTAGTGGT+TGG + chr2_3:1602662-1602681 None:intergenic 50.0%
CCAACCACTAGACATGGGAT+TGG - chr2_3:1602659-1602678 Msa0270350:CDS 50.0%
GTAGCCAATCCCATGTCTAG+TGG + chr2_3:1602666-1602685 None:intergenic 50.0%
GTGCAGGTGTAGGTGTAACA+GGG + chr2_3:1602688-1602707 None:intergenic 50.0%
CCTTGAAGGTTGCGATGCCA+TGG + chr2_3:1602367-1602386 None:intergenic 55.0%
CCATGGCATCGCAACCTTCA+AGG - chr2_3:1602364-1602383 Msa0270350:CDS 55.0%
TCGCAACCTTCAAGGGTCTC+TGG - chr2_3:1602372-1602391 Msa0270350:CDS 55.0%
TTAGTCACACGGCGTGGTTG+CGG + chr2_3:1602575-1602594 None:intergenic 55.0%
GGTGCAGGTGTAGGTGTAAC+AGG + chr2_3:1602689-1602708 None:intergenic 55.0%
TTGGAATTGGGTGCAGCAGC+AGG + chr2_3:1602710-1602729 None:intergenic 55.0%
TCAGCAGCAGCAGCAGCACA+TGG - chr2_3:1602086-1602105 Msa0270350:CDS 60.0%
GTGGTAGACGACGACGACGA+CGG - chr2_3:1602114-1602133 Msa0270350:CDS 60.0%
TAGTCACACGGCGTGGTTGC+GGG + chr2_3:1602574-1602593 None:intergenic 60.0%
GCAACCACGCCGTGTGACTA+AGG - chr2_3:1602574-1602593 Msa0270350:CDS 60.0%
ACCACGCCGTGTGACTAAGG+AGG - chr2_3:1602577-1602596 Msa0270350:CDS 60.0%
ACCTCCTTAGTCACACGGCG+TGG + chr2_3:1602581-1602600 None:intergenic 60.0%
GCAGCAGCAGGTGCAGGTGT+AGG + chr2_3:1602698-1602717 None:intergenic 65.0%
TTGGGTGCAGCAGCAGGTGC+AGG + chr2_3:1602704-1602723 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 1602029 1602742 1602029 ID=Msa0270350;Name=Msa0270350
chr2_3 mRNA 1602029 1602742 1602029 ID=Msa0270350-mRNA-1;Parent=Msa0270350;Name=Msa0270350-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|-1|0|1|-1|1|1|0|237
chr2_3 exon 1602029 1602742 1602029 ID=Msa0270350-mRNA-1:exon:769;Parent=Msa0270350-mRNA-1
chr2_3 CDS 1602029 1602742 1602029 ID=Msa0270350-mRNA-1:cds;Parent=Msa0270350-mRNA-1
Gene Sequence

>Msa0270350

ATGTCGGTTACACAACGTCGATCCAATAATAAGCAATCTGAAGCAGATGGATCATCATCAGCAGCAGCAGCAGCACATGGAATTAGTGGTAGACGACGACGACGACGGTCAGTAGTAGTATCTGGAGCATTAACGGGGACAGCCAACTTGGCAAACTTACTTCCCACAGGAACACTCCTAGCATTCCAGATTCTCACGCCAGTCTTCACAAACAACGGAGCTTGTGACTCCGTTACTCGCATTCTCACACTTGTACTCCTCATCTTGCTTGCAATCTCATGCTTCCTTGCTTGTTTCACGGACACAGTGAATAATGCATCAGATGGAAGAATCTACCATGGCATCGCAACCTTCAAGGGTCTCTGGCTATTTGATTACTCACCCGTCAATGTCAATGTCATGGACAGTAGTAGTACAATAATATTACCAGCTGAGTTGAGCAAGTATAAGATCAGGCCCATTGACTTTGTACATGCATTTTTGTCTGTCTTTGTGTTCTTTGCTGTTGCATTAAGGGATAACAATGTGTTGACATGTTATTACCCGCAACCACGCCGTGTGACTAAGGAGGTTCTTGATATTGTGCCCCTCGGAATTGGATTCCTATGCACTTTGCTTTTTGTCGTTTTTCCAACCACTAGACATGGGATTGGCTACCCTGTTACACCTACACCTGCACCTGCTGCTGCACCCAATTCCAAATATAATTACTAG
Protein sequence

>Msa0270350

MSVTQRRSNNKQSEADGSSSAAAAAHGISGRRRRRRSVVVSGALTGTANLANLLPTGTLLAFQILTPVFTNNGACDSVTRILTLVLLILLAISCFLACFTDTVNNASDGRIYHGIATFKGLWLFDYSPVNVNVMDSSSTIILPAELSKYKIRPIDFVHAFLSVFVFFAVALRDNNVLTCYYPQPRRVTKEVLDIVPLGIGFLCTLLFVVFPTTRHGIGYPVTPTPAPAAAPNSKYNY*