AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene86248

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86248.t1 MTR_5g032375 87.907 215 18 2 1 208 1 214 2.33e-135 378
MS.gene86248.t1 MTR_5g066080 40.994 161 74 2 45 184 37 197 6.50e-26 100
MS.gene86248.t1 MTR_1g093750 37.126 167 87 3 43 198 156 315 6.68e-25 99.8
MS.gene86248.t1 MTR_3g070970 35.673 171 86 4 45 198 73 236 2.17e-23 94.4
MS.gene86248.t1 MTR_2g015890 37.589 141 80 2 34 173 56 189 5.99e-21 87.8
MS.gene86248.t1 MTR_2g091190 39.583 144 72 3 40 177 54 188 3.16e-20 85.9
MS.gene86248.t1 MTR_4g079760 35.000 160 87 3 33 185 56 205 6.77e-18 79.7
MS.gene86248.t1 MTR_2g015890 40.000 120 64 2 34 152 56 168 1.71e-17 77.8
MS.gene86248.t1 MTR_4g087920 36.364 143 78 4 39 175 68 203 2.83e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86248.t1 AT4G38070 46.073 191 86 6 1 184 42 222 1.97e-45 151
MS.gene86248.t1 AT3G25710 43.478 138 68 3 43 177 130 260 9.39e-26 102
MS.gene86248.t1 AT1G68810 42.012 169 78 3 43 198 172 333 5.05e-25 100
MS.gene86248.t1 AT3G56770 33.333 174 93 6 40 200 39 202 1.92e-22 91.3
MS.gene86248.t1 AT2G40200 39.259 135 66 4 46 172 64 190 5.82e-20 85.1
MS.gene86248.t1 AT2G41130 35.838 173 93 5 39 200 60 225 1.39e-19 84.3

Find 48 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGGGCAGACAAATTGAATT+TGG 0.253589 5.1:+22935263 MS.gene86248:CDS
TGTCTGCCCCACCAGGAAAC+TGG 0.346018 5.1:-22935251 None:intergenic
TTGGACCCATAACACACTTC+TGG 0.378699 5.1:-22935430 None:intergenic
ACACTAACTTTGATCAAGTT+GGG 0.389149 5.1:-22934896 None:intergenic
AGGTGTTGAAAATGAAGGTT+TGG 0.393224 5.1:+22935452 MS.gene86248:CDS
AATGAAAGCCAAAGTTGTTA+AGG 0.399548 5.1:+22935380 MS.gene86248:CDS
GAAGAACCAGAAGTGTGTTA+TGG 0.408049 5.1:+22935424 MS.gene86248:CDS
CATCTCAACCTTAACAACTT+TGG 0.408942 5.1:-22935388 None:intergenic
AAGAACCAGAAGTGTGTTAT+GGG 0.427563 5.1:+22935425 MS.gene86248:CDS
TCAAAGGAGATCCAGTTTCC+TGG 0.436396 5.1:+22935240 MS.gene86248:CDS
CTATAACGCAGAAGCTCAAA+TGG 0.441129 5.1:+22934703 MS.gene86248:CDS
GACACTAACTTTGATCAAGT+TGG 0.443559 5.1:-22934897 None:intergenic
GATGAGGCGGTATACTCAAT+AGG 0.446628 5.1:+22935524 MS.gene86248:CDS
GGTGTTGAAAATGAAGGTTT+GGG 0.450241 5.1:+22935453 MS.gene86248:CDS
TTCAATTTGTCTGCCCCACC+AGG 0.456050 5.1:-22935258 None:intergenic
TACCGCCTCATCTTAAAGCT+TGG 0.493542 5.1:-22935513 None:intergenic
GATATAGATGACATCAATCC+TGG 0.505784 5.1:-22935342 None:intergenic
AGACGTAGAATGCGAATCAA+TGG 0.510341 5.1:+22934845 MS.gene86248:CDS
GTTTGCGAGATGAATGAACT+TGG 0.518532 5.1:-22934740 None:intergenic
AGGAAACTGGATCTCCTTTG+AGG 0.538324 5.1:-22935238 None:intergenic
CAAAGTTGTTAAGGTTGAGA+TGG 0.542500 5.1:+22935389 MS.gene86248:CDS
GTCCAAGGTGTTGAAAATGA+AGG 0.548376 5.1:+22935447 MS.gene86248:CDS
GGAAAAGTGTAATGATGAGG+AGG 0.576454 5.1:+22935284 MS.gene86248:CDS
TTGAGTTGTGAGGATAGACC+AGG 0.582755 5.1:+22935324 MS.gene86248:CDS
GGAGATCCAGTTTCCTGGTG+GGG 0.584829 5.1:+22935245 MS.gene86248:CDS
GGATCTCCTTTGAGGTAGCA+TGG 0.586127 5.1:-22935230 None:intergenic
AGAAGTGTGTTATGGGTCCA+AGG 0.587934 5.1:+22935432 MS.gene86248:CDS
CACTAACTTTGATCAAGTTG+GGG 0.594450 5.1:-22934895 None:intergenic
GGAGACTATCAAACAAGTGA+AGG 0.601788 5.1:+22935170 MS.gene86248:CDS
AGGAGATCCAGTTTCCTGGT+GGG 0.605957 5.1:+22935244 MS.gene86248:CDS
GTTGAGATGGTGACAGTGGG+TGG 0.609342 5.1:+22935402 MS.gene86248:CDS
GAAAAGTGTAATGATGAGGA+GGG 0.610839 5.1:+22935285 MS.gene86248:CDS
TAAGGTTGAGATGGTGACAG+TGG 0.619246 5.1:+22935398 MS.gene86248:CDS
TAACTTTGATCAAGTTGGGG+AGG 0.625634 5.1:-22934892 None:intergenic
TTTCTCGAAGCAAAGATCAA+AGG 0.627837 5.1:+22934775 MS.gene86248:CDS
GGACAAGGCATCAATACTAG+TGG 0.628919 5.1:+22935149 MS.gene86248:CDS
AGATAGCCATGCTACCTCAA+AGG 0.632769 5.1:+22935224 MS.gene86248:CDS
AAGGTTGAGATGGTGACAGT+GGG 0.645311 5.1:+22935399 MS.gene86248:CDS
CTCGAAGCAAAGATCAAAGG+CGG 0.646476 5.1:+22934778 MS.gene86248:CDS
AAGGAGATCCAGTTTCCTGG+TGG 0.648546 5.1:+22935243 MS.gene86248:CDS
AGCCAAGCTTTAAGATGAGG+CGG 0.655183 5.1:+22935511 MS.gene86248:CDS
AGTTGGGGAGGATACTGCGG+AGG 0.655539 5.1:-22934880 None:intergenic
ATAAGCCAAGCTTTAAGATG+AGG 0.659617 5.1:+22935508 MS.gene86248:CDS
TTTGGAAAAGTGTAATGATG+AGG 0.678742 5.1:+22935281 MS.gene86248:CDS
GAAAGCTACATTGAGTTGTG+AGG 0.689461 5.1:+22935314 MS.gene86248:CDS
TATTGATTAACAGAAGGACA+AGG 0.695632 5.1:+22935134 MS.gene86248:intron
TCAAGTTGGGGAGGATACTG+CGG 0.696028 5.1:-22934883 None:intergenic
GTTGGGGAGGATACTGCGGA+GGG 0.717546 5.1:-22934879 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAAATTTTGTTTTATAAAGT+TGG - chr5.1:22934940-22934959 None:intergenic 15.0%
!! TGTTTATTACCATTATTGTA+AGG + chr5.1:22934971-22934990 MS.gene86248:intron 20.0%
!!! ATATGTTATTGATTAACAGA+AGG + chr5.1:22935128-22935147 MS.gene86248:intron 20.0%
!!! GAAATCATGGTTTTTAATTT+TGG + chr5.1:22935045-22935064 MS.gene86248:intron 20.0%
!!! TAAATTTAGCAATCTTGTTT+AGG - chr5.1:22935106-22935125 None:intergenic 20.0%
AATGAAAGCCAAAGTTGTTA+AGG + chr5.1:22935380-22935399 MS.gene86248:CDS 30.0%
ACACTAACTTTGATCAAGTT+GGG - chr5.1:22934899-22934918 None:intergenic 30.0%
ACCATTATTGTAAGGAAGAA+CGG + chr5.1:22934979-22934998 MS.gene86248:intron 30.0%
! TATTGATTAACAGAAGGACA+AGG + chr5.1:22935134-22935153 MS.gene86248:intron 30.0%
! TTTGGAAAAGTGTAATGATG+AGG + chr5.1:22935281-22935300 MS.gene86248:CDS 30.0%
ACCGTTCTTCCTTACAATAA+TGG - chr5.1:22934983-22935002 None:intergenic 35.0%
CAAAGTTGTTAAGGTTGAGA+TGG + chr5.1:22935389-22935408 MS.gene86248:CDS 35.0%
CATCTCAACCTTAACAACTT+TGG - chr5.1:22935391-22935410 None:intergenic 35.0%
GACACTAACTTTGATCAAGT+TGG - chr5.1:22934900-22934919 None:intergenic 35.0%
GATATAGATGACATCAATCC+TGG - chr5.1:22935345-22935364 None:intergenic 35.0%
TTTCTCGAAGCAAAGATCAA+AGG + chr5.1:22934775-22934794 MS.gene86248:CDS 35.0%
! AACCTTCATTTTCAACACCT+TGG - chr5.1:22935452-22935471 None:intergenic 35.0%
! AAGAACCAGAAGTGTGTTAT+GGG + chr5.1:22935425-22935444 MS.gene86248:CDS 35.0%
! CACTAACTTTGATCAAGTTG+GGG - chr5.1:22934898-22934917 None:intergenic 35.0%
! GAAAAGTGTAATGATGAGGA+GGG + chr5.1:22935285-22935304 MS.gene86248:CDS 35.0%
! GGTGTTGAAAATGAAGGTTT+GGG + chr5.1:22935453-22935472 MS.gene86248:CDS 35.0%
!! AGGTGTTGAAAATGAAGGTT+TGG + chr5.1:22935452-22935471 MS.gene86248:CDS 35.0%
!! ATAAGCCAAGCTTTAAGATG+AGG + chr5.1:22935508-22935527 MS.gene86248:CDS 35.0%
AGACGTAGAATGCGAATCAA+TGG + chr5.1:22934845-22934864 MS.gene86248:CDS 40.0%
CTACATCGTGATTGCAATTG+CGG - chr5.1:22935023-22935042 None:intergenic 40.0%
CTATAACGCAGAAGCTCAAA+TGG + chr5.1:22934703-22934722 MS.gene86248:CDS 40.0%
GGAGACTATCAAACAAGTGA+AGG + chr5.1:22935170-22935189 MS.gene86248:CDS 40.0%
GTTTGCGAGATGAATGAACT+TGG - chr5.1:22934743-22934762 None:intergenic 40.0%
TCACGATGTAGTCGAAATCA+TGG + chr5.1:22935032-22935051 MS.gene86248:intron 40.0%
TGGGGCAGACAAATTGAATT+TGG + chr5.1:22935263-22935282 MS.gene86248:CDS 40.0%
! GAAAGCTACATTGAGTTGTG+AGG + chr5.1:22935314-22935333 MS.gene86248:CDS 40.0%
! GAAGAACCAGAAGTGTGTTA+TGG + chr5.1:22935424-22935443 MS.gene86248:CDS 40.0%
! GGAAAAGTGTAATGATGAGG+AGG + chr5.1:22935284-22935303 MS.gene86248:CDS 40.0%
!! GTCCAAGGTGTTGAAAATGA+AGG + chr5.1:22935447-22935466 MS.gene86248:CDS 40.0%
!! TAACTTTGATCAAGTTGGGG+AGG - chr5.1:22934895-22934914 None:intergenic 40.0%
AAGGTTGAGATGGTGACAGT+GGG + chr5.1:22935399-22935418 MS.gene86248:CDS 45.0%
AGATAGCCATGCTACCTCAA+AGG + chr5.1:22935224-22935243 MS.gene86248:CDS 45.0%
AGGAAACTGGATCTCCTTTG+AGG - chr5.1:22935241-22935260 None:intergenic 45.0%
CTCGAAGCAAAGATCAAAGG+CGG + chr5.1:22934778-22934797 MS.gene86248:CDS 45.0%
TAAGGTTGAGATGGTGACAG+TGG + chr5.1:22935398-22935417 MS.gene86248:CDS 45.0%
TACCGCCTCATCTTAAAGCT+TGG - chr5.1:22935516-22935535 None:intergenic 45.0%
TCAAAGGAGATCCAGTTTCC+TGG + chr5.1:22935240-22935259 MS.gene86248:CDS 45.0%
TTGGACCCATAACACACTTC+TGG - chr5.1:22935433-22935452 None:intergenic 45.0%
! AGAAGTGTGTTATGGGTCCA+AGG + chr5.1:22935432-22935451 MS.gene86248:CDS 45.0%
! GGACAAGGCATCAATACTAG+TGG + chr5.1:22935149-22935168 MS.gene86248:CDS 45.0%
! TTGAGTTGTGAGGATAGACC+AGG + chr5.1:22935324-22935343 MS.gene86248:CDS 45.0%
!! AGCCAAGCTTTAAGATGAGG+CGG + chr5.1:22935511-22935530 MS.gene86248:CDS 45.0%
AAGGAGATCCAGTTTCCTGG+TGG + chr5.1:22935243-22935262 MS.gene86248:CDS 50.0%
AGGAGATCCAGTTTCCTGGT+GGG + chr5.1:22935244-22935263 MS.gene86248:CDS 50.0%
TTCAATTTGTCTGCCCCACC+AGG - chr5.1:22935261-22935280 None:intergenic 50.0%
!! GGATCTCCTTTGAGGTAGCA+TGG - chr5.1:22935233-22935252 None:intergenic 50.0%
!! TCAAGTTGGGGAGGATACTG+CGG - chr5.1:22934886-22934905 None:intergenic 50.0%
GGAGATCCAGTTTCCTGGTG+GGG + chr5.1:22935245-22935264 MS.gene86248:CDS 55.0%
GTTGAGATGGTGACAGTGGG+TGG + chr5.1:22935402-22935421 MS.gene86248:CDS 55.0%
AGTTGGGGAGGATACTGCGG+AGG - chr5.1:22934883-22934902 None:intergenic 60.0%
GTTGGGGAGGATACTGCGGA+GGG - chr5.1:22934882-22934901 None:intergenic 60.0%
TGTCTGCCCCACCAGGAAAC+TGG - chr5.1:22935254-22935273 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 22934683 22935545 22934683 ID=MS.gene86248
chr5.1 mRNA 22934683 22935545 22934683 ID=MS.gene86248.t1;Parent=MS.gene86248
chr5.1 exon 22934683 22934910 22934683 ID=MS.gene86248.t1.exon1;Parent=MS.gene86248.t1
chr5.1 CDS 22934683 22934910 22934683 ID=cds.MS.gene86248.t1;Parent=MS.gene86248.t1
chr5.1 exon 22935147 22935545 22935147 ID=MS.gene86248.t1.exon2;Parent=MS.gene86248.t1
chr5.1 CDS 22935147 22935545 22935147 ID=cds.MS.gene86248.t1;Parent=MS.gene86248.t1
Gene Sequence

>MS.gene86248

ATGCAGCATGTTCGAAATTACTATAACGCAGAAGCTCAAATGGTAAGAAGCAACTTTCCAAGTTCATTCATCTCGCAAACATTCAAAAGCAGTTTCTCGAAGCAAAGATCAAAGGCGGAGAATAAATTACTAGCAGCTAAGAAACATAGTGAAGCAGAAAAGAGACGTAGAATGCGAATCAATGGTCAATATGACACCCTCCGCAGTATCCTCCCCAACTTGATCAAAGTTAGTGTCATTCATGAAAAATTAAACCAACTTTATAAAACAAAATTTCTTATATTTTTGTGTTTATTACCATTATTGTAAGGAAGAACGGTTAAATATGTTGACGTTGCCGCAATTGCAATCACGATGTAGTCGAAATCATGGTTTTTAATTTTGGCACTTGTGAAGTCAAGTTTTTAATGTTGTGATTTTCCTAAACAAGATTGCTAAATTTAGAATATGTTATTGATTAACAGAAGGACAAGGCATCAATACTAGTGGAGACTATCAAACAAGTGAAGGAGTTGAAGAAAAAAGCATCAAAACTAGAAGAAGATAGCCATGCTACCTCAAAGGAGATCCAGTTTCCTGGTGGGGCAGACAAATTGAATTTGGAAAAGTGTAATGATGAGGAGGGTCTAGTGAAAGCTACATTGAGTTGTGAGGATAGACCAGGATTGATGTCATCTATATCAAGAGCACTATTGTCAATGAAAGCCAAAGTTGTTAAGGTTGAGATGGTGACAGTGGGTGGAAGAACCAGAAGTGTGTTATGGGTCCAAGGTGTTGAAAATGAAGGTTTGGGAATGCTCAAGAGTACTTTGAAAGTTGTTATGCATAAGCCAAGCTTTAAGATGAGGCGGTATACTCAATAG
Protein sequence

>MS.gene86248.t1

MQHVRNYYNAEAQMVRSNFPSSFISQTFKSSFSKQRSKAENKLLAAKKHSEAEKRRRMRINGQYDTLRSILPNLIKKDKASILVETIKQVKELKKKASKLEEDSHATSKEIQFPGGADKLNLEKCNDEEGLVKATLSCEDRPGLMSSISRALLSMKAKVVKVEMVTVGGRTRSVLWVQGVENEGLGMLKSTLKVVMHKPSFKMRRYTQ