AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1461660


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1461660 MtrunA17_Chr2g0331101 97.030 202 3 1 1 202 1 199 1.05e-146 405
Msa1461660 MtrunA17_Chr2g0331091 90.148 203 12 3 1 203 1 195 2.25e-131 367
Msa1461660 MtrunA17_Chr8g0340451 68.966 203 48 6 1 202 1 189 7.73e-97 279
Msa1461660 MtrunA17_Chr8g0340461 68.473 203 49 6 1 202 1 189 3.17e-96 278
Msa1461660 MtrunA17_Chr8g0340431 64.356 202 53 7 1 200 1 185 3.00e-84 247
Msa1461660 MtrunA17_Chr6g0486761 42.365 203 77 11 7 202 10 179 1.55e-38 131
Msa1461660 MtrunA17_Chr0c01g0489221 40.097 207 85 8 3 202 6 180 2.33e-38 131
Msa1461660 MtrunA17_Chr6g0486771 39.320 206 88 7 3 202 6 180 1.48e-37 129
Msa1461660 MtrunA17_Chr6g0486781 38.350 206 90 7 3 202 6 180 7.14e-36 124
Msa1461660 MtrunA17_Chr0c01g0489231 38.916 203 86 7 7 202 10 181 7.96e-36 124
Msa1461660 MtrunA17_Chr6g0486751 39.614 207 86 9 3 202 6 180 6.40e-35 122
Msa1461660 MtrunA17_Chr8g0390031 36.816 201 88 11 7 202 9 175 5.75e-29 106
Msa1461660 MtrunA17_Chr7g0252551 34.222 225 106 13 1 203 1 205 4.71e-21 86.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1461660 AT1G52140.1 47.196 214 88 8 1 202 1 201 1.68e-55 175
Msa1461660 AT3G16330.1 42.661 218 87 9 1 202 1 196 8.21e-44 145
Msa1461660 AT4G29110.1 39.706 204 87 7 1 202 14 183 2.29e-31 113

Find 55 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTCCCTTGATGCGGTAAAT+TGG 0.283815 tig0041641:+12424 Msa1461660:intergenic
TGCGGTGACGTTTCCCTATT+GGG 0.299531 tig0041641:+12364 Msa1461660:intergenic
TCTCCAGCACTGCCTGGATT+CGG 0.302018 tig0041641:-12207 Msa1461660:CDS
CTGCGGTGACGTTTCCCTAT+TGG 0.308179 tig0041641:+12363 Msa1461660:intergenic
CTCCAGCACTGCCTGGATTC+GGG 0.322990 tig0041641:-12206 Msa1461660:CDS
ATCAAGCTTGCTTCCTCAAT+TGG 0.341340 tig0041641:+12064 Msa1461660:intergenic
CCCTCAATTGCCTTACCATT+GGG 0.354815 tig0041641:+12178 Msa1461660:intergenic
TTCTCATCATCTTCTCTTAG+AGG 0.359691 tig0041641:+12138 Msa1461660:intergenic
CTGCTGAAGATTTCATAAAC+AGG 0.373468 tig0041641:-12095 Msa1461660:CDS
ATCAAAGAGAGTGTGGAGTA+TGG 0.418765 tig0041641:-12631 Msa1461660:CDS
GGCGTTTGAGCATCATGTTT+AGG 0.451131 tig0041641:+12550 Msa1461660:intergenic
CGTGGCTGTGGTGGCTGTGA+TGG 0.466817 tig0041641:+12484 Msa1461660:intergenic
ACCCTCAATTGCCTTACCAT+TGG 0.467623 tig0041641:+12177 Msa1461660:intergenic
GTCAAAGGGCAAACTAATGA+TGG 0.467955 tig0041641:-12574 Msa1461660:CDS
GCCTTCTTCATGTTGAGAAA+AGG 0.468789 tig0041641:-12600 Msa1461660:CDS
TGAAGAAATTGTTGTGATTG+TGG 0.472141 tig0041641:+12334 Msa1461660:intergenic
AGGTGGAGCCGCCGTGGCTG+TGG 0.473691 tig0041641:+12472 Msa1461660:intergenic
CCCTTGATGCGGTAAATTGG+TGG 0.485419 tig0041641:+12427 Msa1461660:intergenic
GCCCAATGGTAAGGCAATTG+AGG 0.485585 tig0041641:-12179 Msa1461660:CDS
GAAGCATCTCCAGCACTGCC+TGG 0.487263 tig0041641:-12213 Msa1461660:CDS
GAGTGCAATGAAGGCCGTGC+TGG 0.499574 tig0041641:-12265 Msa1461660:CDS
CATCACAGCCACCACAGCCA+CGG 0.499967 tig0041641:-12483 Msa1461660:CDS
TCATCTTCTCTTAGAGGGAA+TGG 0.502641 tig0041641:+12144 Msa1461660:intergenic
CCCAATGGTAAGGCAATTGA+GGG 0.507064 tig0041641:-12178 Msa1461660:CDS
GTCGTGAGAGCGGCTTGAGG+TGG 0.508313 tig0041641:+12455 Msa1461660:intergenic
ATTGGGCTACGCCCGAATCC+AGG 0.513644 tig0041641:+12195 Msa1461660:intergenic
GAAGGACGATCAAGTTGATA+AGG 0.519057 tig0041641:-12118 Msa1461660:CDS
GGCTGTGGTGGCTGTGATGG+TGG 0.525762 tig0041641:+12487 Msa1461660:intergenic
TCTCATCATCTTCTCTTAGA+GGG 0.530370 tig0041641:+12139 Msa1461660:intergenic
CACACTCTCTTTGATATCAC+TGG 0.533500 tig0041641:+12639 Msa1461660:intergenic
TTGAGAAAAGGCATGTCAAA+GGG 0.534014 tig0041641:-12588 Msa1461660:CDS
GCCACCAATTTACCGCATCA+AGG 0.534674 tig0041641:-12428 Msa1461660:CDS
TGGAGCCGCCGTGGCTGTGG+TGG 0.543982 tig0041641:+12475 Msa1461660:intergenic
CGCTCATACGCCACCTACAC+AGG 0.551605 tig0041641:-12307 Msa1461660:CDS
GTTGAGAAAAGGCATGTCAA+AGG 0.559027 tig0041641:-12589 Msa1461660:CDS
GTGGAACATTAGATTGGCAA+TGG 0.565737 tig0041641:+12506 Msa1461660:intergenic
AAACGCCGAAGCAAGCTCGC+CGG 0.566114 tig0041641:-12534 Msa1461660:CDS
GTGATGGTGGAACATTAGAT+TGG 0.566670 tig0041641:+12500 Msa1461660:intergenic
TCGGGCGTAGCCCAATGGTA+AGG 0.575007 tig0041641:-12188 Msa1461660:CDS
GGCGACAATGAGTGCAATGA+AGG 0.584967 tig0041641:-12274 Msa1461660:CDS
TGGATTCGGGCGTAGCCCAA+TGG 0.585672 tig0041641:-12193 Msa1461660:CDS
ACATCATCGTCCTGTGTAGG+TGG 0.587034 tig0041641:+12297 Msa1461660:intergenic
TCAAAGGGCAAACTAATGAT+GGG 0.588410 tig0041641:-12573 Msa1461660:CDS
CCACCAATTTACCGCATCAA+GGG 0.590913 tig0041641:-12427 Msa1461660:CDS
CAGTGATATCAAAGAGAGTG+TGG 0.593721 tig0041641:-12638 Msa1461660:CDS
TCTAAGAGAAGATGATGAGA+AGG 0.594411 tig0041641:-12136 Msa1461660:CDS
GGCTTGAGGTGGAGCCGCCG+TGG 0.620681 tig0041641:+12466 Msa1461660:intergenic
GGTGGCGTGAGTCGTGAGAG+CGG 0.626926 tig0041641:+12445 Msa1461660:intergenic
TGTGATTGTGGTTGTTGCTG+CGG 0.635520 tig0041641:+12346 Msa1461660:intergenic
GCCACATCATCGTCCTGTGT+AGG 0.639849 tig0041641:+12294 Msa1461660:intergenic
ATTGTTAAGCATCTCCAGCA+CGG 0.641871 tig0041641:+12251 Msa1461660:intergenic
CACAGCCACCACAGCCACGG+CGG 0.652559 tig0041641:-12480 Msa1461660:CDS
ACCTACACAGGACGATGATG+TGG 0.656484 tig0041641:-12295 Msa1461660:CDS
TGAGTCGTGAGAGCGGCTTG+AGG 0.683296 tig0041641:+12452 Msa1461650:intergenic
GAATTCATACTCCCTTGATG+CGG 0.696823 tig0041641:+12416 Msa1461650:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGAAGAAATTGTTGTGATTG+TGG + tig0041641:12388-12407 Msa1461660:intergenic 30.0%
! TTGAGAAAAGGCATGTCAAA+GGG - tig0041641:12131-12150 Msa1461660:CDS 35.0%
TCAAAGGGCAAACTAATGAT+GGG - tig0041641:12146-12165 Msa1461660:CDS 35.0%
TCTCATCATCTTCTCTTAGA+GGG + tig0041641:12583-12602 Msa1461660:intergenic 35.0%
TTCTCATCATCTTCTCTTAG+AGG + tig0041641:12584-12603 Msa1461660:intergenic 35.0%
TCTAAGAGAAGATGATGAGA+AGG - tig0041641:12583-12602 Msa1461660:CDS 35.0%
CTGCTGAAGATTTCATAAAC+AGG - tig0041641:12624-12643 Msa1461660:CDS 35.0%
CACACTCTCTTTGATATCAC+TGG + tig0041641:12083-12102 Msa1456740:intergenic 40.0%
CAGTGATATCAAAGAGAGTG+TGG - tig0041641:12081-12100 Msa1461660:CDS 40.0%
! ATCAAAGAGAGTGTGGAGTA+TGG - tig0041641:12088-12107 Msa1461660:CDS 40.0%
GCCTTCTTCATGTTGAGAAA+AGG - tig0041641:12119-12138 Msa1461660:CDS 40.0%
! GCCTTTTCTCAACATGAAGA+AGG + tig0041641:12123-12142 Msa1461660:intergenic 40.0%
! GTTGAGAAAAGGCATGTCAA+AGG - tig0041641:12130-12149 Msa1461660:CDS 40.0%
GTCAAAGGGCAAACTAATGA+TGG - tig0041641:12145-12164 Msa1461660:CDS 40.0%
! TAGATTGGCAATGGCTTTTC+CGG + tig0041641:12207-12226 Msa1461660:intergenic 40.0%
GTGGAACATTAGATTGGCAA+TGG + tig0041641:12216-12235 Msa1461660:intergenic 40.0%
!! GTGATGGTGGAACATTAGAT+TGG + tig0041641:12222-12241 Msa1461660:intergenic 40.0%
GAATTCATACTCCCTTGATG+CGG + tig0041641:12306-12325 Msa1461660:intergenic 40.0%
CCTATTGGGAAAAAGTGATG+GGG + tig0041641:12344-12363 Msa1461660:intergenic 40.0%
CCCTATTGGGAAAAAGTGAT+GGG + tig0041641:12345-12364 Msa1461660:intergenic 40.0%
!!! CCCATCACTTTTTCCCAATA+GGG - tig0041641:12342-12361 Msa1461660:CDS 40.0%
TCCCTATTGGGAAAAAGTGA+TGG + tig0041641:12346-12365 Msa1461660:intergenic 40.0%
ATTGTTAAGCATCTCCAGCA+CGG + tig0041641:12471-12490 Msa1461660:intergenic 40.0%
TCATCTTCTCTTAGAGGGAA+TGG + tig0041641:12578-12597 Msa1461660:intergenic 40.0%
!! GAAGGACGATCAAGTTGATA+AGG - tig0041641:12601-12620 Msa1461660:CDS 40.0%
! ACAGGTTTTACAGCCAATTG+AGG - tig0041641:12642-12661 Msa1461660:CDS 40.0%
GGCGTTTGAGCATCATGTTT+AGG + tig0041641:12172-12191 Msa1461660:intergenic 45.0%
CCACCAATTTACCGCATCAA+GGG - tig0041641:12292-12311 Msa1461660:CDS 45.0%
ACTCCCTTGATGCGGTAAAT+TGG + tig0041641:12298-12317 Msa1461660:intergenic 45.0%
!!! CCCCATCACTTTTTCCCAAT+AGG - tig0041641:12341-12360 Msa1461660:CDS 45.0%
TGTGATTGTGGTTGTTGCTG+CGG + tig0041641:12376-12395 Msa1461660:intergenic 45.0%
CCCTCAATTGCCTTACCATT+GGG + tig0041641:12544-12563 Msa1461660:intergenic 45.0%
CCCAATGGTAAGGCAATTGA+GGG - tig0041641:12541-12560 Msa1461660:CDS 45.0%
ACCCTCAATTGCCTTACCAT+TGG + tig0041641:12545-12564 Msa1461660:intergenic 45.0%
GCCACCAATTTACCGCATCA+AGG - tig0041641:12291-12310 Msa1461660:CDS 50.0%
CCCTTGATGCGGTAAATTGG+TGG + tig0041641:12295-12314 Msa1461660:intergenic 50.0%
TGCGGTGACGTTTCCCTATT+GGG + tig0041641:12358-12377 Msa1461660:intergenic 50.0%
ACATCATCGTCCTGTGTAGG+TGG + tig0041641:12425-12444 Msa1461660:intergenic 50.0%
ACCTACACAGGACGATGATG+TGG - tig0041641:12424-12443 Msa1461660:CDS 50.0%
GGCGACAATGAGTGCAATGA+AGG - tig0041641:12445-12464 Msa1461660:CDS 50.0%
GCCCAATGGTAAGGCAATTG+AGG - tig0041641:12540-12559 Msa1461660:CDS 50.0%
!! CTTTTCCGGCGAGCTTGCTT+CGG + tig0041641:12193-12212 Msa1461660:intergenic 55.0%
CTGCGGTGACGTTTCCCTAT+TGG + tig0041641:12359-12378 Msa1461660:intergenic 55.0%
GCCACATCATCGTCCTGTGT+AGG + tig0041641:12428-12447 Msa1461660:intergenic 55.0%
TCTCCAGCACTGCCTGGATT+CGG - tig0041641:12512-12531 Msa1461660:CDS 55.0%
AAACGCCGAAGCAAGCTCGC+CGG - tig0041641:12185-12204 Msa1461660:CDS 60.0%
CATCACAGCCACCACAGCCA+CGG - tig0041641:12236-12255 Msa1461660:CDS 60.0%
TGAGTCGTGAGAGCGGCTTG+AGG + tig0041641:12270-12289 Msa1461660:intergenic 60.0%
CGCTCATACGCCACCTACAC+AGG - tig0041641:12412-12431 Msa1461660:CDS 60.0%
GAGTGCAATGAAGGCCGTGC+TGG - tig0041641:12454-12473 Msa1461660:CDS 60.0%
! GAAGCATCTCCAGCACTGCC+TGG - tig0041641:12506-12525 Msa1461660:CDS 60.0%
CTCCAGCACTGCCTGGATTC+GGG - tig0041641:12513-12532 Msa1461660:CDS 60.0%
ATTGGGCTACGCCCGAATCC+AGG + tig0041641:12527-12546 Msa1461660:intergenic 60.0%
TGGATTCGGGCGTAGCCCAA+TGG - tig0041641:12526-12545 Msa1461660:CDS 60.0%
TCGGGCGTAGCCCAATGGTA+AGG - tig0041641:12531-12550 Msa1461660:CDS 60.0%
GGCTGTGGTGGCTGTGATGG+TGG + tig0041641:12235-12254 Msa1461660:intergenic 65.0%
CGTGGCTGTGGTGGCTGTGA+TGG + tig0041641:12238-12257 Msa1461660:intergenic 65.0%
GTCGTGAGAGCGGCTTGAGG+TGG + tig0041641:12267-12286 Msa1461660:intergenic 65.0%
GGTGGCGTGAGTCGTGAGAG+CGG + tig0041641:12277-12296 Msa1461660:intergenic 65.0%
CACAGCCACCACAGCCACGG+CGG - tig0041641:12239-12258 Msa1461660:CDS 70.0%
CGCCCGAATCCAGGCAGTGC+TGG + tig0041641:12518-12537 Msa1461660:intergenic 70.0%
TGGAGCCGCCGTGGCTGTGG+TGG + tig0041641:12247-12266 Msa1461660:intergenic 75.0%
AGGTGGAGCCGCCGTGGCTG+TGG + tig0041641:12250-12269 Msa1461660:intergenic 75.0%
GGCTTGAGGTGGAGCCGCCG+TGG + tig0041641:12256-12275 Msa1461660:intergenic 75.0%
Chromosome Type Strat End Strand Name
tig0041641 gene 12065 12676 12065 ID=Msa1461660;Name=Msa1461660
tig0041641 mRNA 12065 12676 12065 ID=Msa1461660-mRNA-1;Parent=Msa1461660;Name=Msa1461660-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|203
tig0041641 exon 12065 12676 12065 ID=Msa1461660-mRNA-1:exon:23269;Parent=Msa1461660-mRNA-1
tig0041641 CDS 12065 12676 12065 ID=Msa1461660-mRNA-1:cds;Parent=Msa1461660-mRNA-1
Gene Sequence

>Msa1461660

ATGGAAAACAATCTACCAGTGATATCAAAGAGAGTGTGGAGTATGGTACGTGTAGCCTTCTTCATGTTGAGAAAAGGCATGTCAAAGGGCAAACTAATGATGGGCCTAAACATGATGCTCAAACGCCGAAGCAAGCTCGCCGGAAAAGCCATTGCCAATCTAATGTTCCACCATCACAGCCACCACAGCCACGGCGGCTCCACCTCAAGCCGCTCTCACGACTCACGCCACCAATTTACCGCATCAAGGGAGTATGAATTCAGCTGCAGCAACACTCCCCATCACTTTTTCCCAATAGGGAAACGTCACCGCAGCAACAACCACAATCACAACAATTTCTTCACTTGCGCTCATACGCCACCTACACAGGACGATGATGTGGCGACAATGAGTGCAATGAAGGCCGTGCTGGAGATGCTTAACAATGATCAAGCAATCGTAGAAGCATCTCCAGCACTGCCTGGATTCGGGCGTAGCCCAATGGTAAGGCAATTGAGGGTGACTGACTCACCATTCCCTCTAAGAGAAGATGATGAGAAGGACGATCAAGTTGATAAGGCTGCTGAAGATTTCATAAACAGGTTTTACAGCCAATTGAGGAAGCAAGCTTGA

Protein sequence

>Msa1461660

MENNLPVISKRVWSMVRVAFFMLRKGMSKGKLMMGLNMMLKRRSKLAGKAIANLMFHHHSHHSHGGSTSSRSHDSRHQFTASREYEFSCSNTPHHFFPIGKRHRSNNHNHNNFFTCAHTPPTQDDDVATMSAMKAVLEMLNNDQAIVEASPALPGFGRSPMVRQLRVTDSPFPLREDDEKDDQVDKAAEDFINRFYSQLRKQA*