AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060879


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060879.t1 MTR_2g103380 99.153 118 1 0 1 118 1 118 3.74e-84 241
MS.gene060879.t1 MTR_4g011060 60.684 117 34 2 1 117 1 105 6.50e-41 132
MS.gene060879.t1 MTR_4g114050 43.548 124 41 5 1 118 1 101 3.25e-23 86.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060879.t1 AT1G80180 48.551 138 51 6 1 118 1 138 1.34e-30 106
MS.gene060879.t1 AT1G15400 49.180 122 44 5 1 105 1 121 9.27e-29 102
MS.gene060879.t1 AT1G15400 49.180 122 44 5 1 105 1 121 1.10e-28 101
MS.gene060879.t1 AT1G15400 49.180 122 44 5 1 105 1 121 1.54e-28 101
MS.gene060879.t1 AT5G20100 47.273 110 42 5 3 108 2 99 1.27e-18 75.5

Find 29 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGGTTCATCAGGGTTTGTT+TGG 0.296640 2.1:-2433381 MS.gene060879:CDS
TTCAGAAGACAAGGTTCATC+AGG 0.369694 2.1:-2433391 MS.gene060879:CDS
GTTCTTGTTGATTCTGACTC+TGG 0.396706 2.1:+2433320 None:intergenic
AGGTTCATCAGGGTTTGTTT+GGG 0.404671 2.1:-2433380 MS.gene060879:CDS
CTCCTAGGATTTCTGCCTGT+GGG 0.417892 2.1:-2433150 MS.gene060879:CDS
CTTCTCTGAACAGTATTGAT+TGG 0.435131 2.1:+2433238 None:intergenic
CGTTCTAACGGTGGAGGACG+TGG 0.452280 2.1:-2433214 MS.gene060879:CDS
AACTACCTTGATCGATGCTT+AGG 0.486228 2.1:+2433085 None:intergenic
TTGGGAAAGTAGGGGAGAAG+AGG 0.507939 2.1:-2433114 MS.gene060879:CDS
CGATTGAGCCACCGTCTCCT+AGG 0.529012 2.1:-2433165 MS.gene060879:CDS
AACCCACAGGCAGAAATCCT+AGG 0.546823 2.1:+2433148 None:intergenic
GGAGACGGTGGCTCAATCGC+CGG 0.558530 2.1:+2433169 None:intergenic
CCGTACCGGAAAAGTTTCTC+CGG 0.558933 2.1:-2433188 MS.gene060879:CDS
AAAAGCACCACAAAACCCAC+AGG 0.561933 2.1:+2433135 None:intergenic
GATGCAACATCACCACAGCT+TGG 0.569916 2.1:-2433262 MS.gene060879:CDS
GGAGGACGTGGTTACCGTAC+CGG 0.573123 2.1:-2433202 MS.gene060879:CDS
TCTCCTAGGATTTCTGCCTG+TGG 0.574828 2.1:-2433151 MS.gene060879:CDS
AACCACCTAAGCATCGATCA+AGG 0.579242 2.1:-2433090 MS.gene060879:CDS
TCAGAAGACAAGGTTCATCA+GGG 0.600967 2.1:-2433390 MS.gene060879:CDS
TACCTTGATCGATGCTTAGG+TGG 0.600976 2.1:+2433088 None:intergenic
AGAAGTCGTTCTAACGGTGG+AGG 0.607642 2.1:-2433220 MS.gene060879:CDS
ACAGAGAAACCAGACATGGA+AGG 0.634834 2.1:-2433436 None:intergenic
GTTCAGAGAAGTCGTTCTAA+CGG 0.637358 2.1:-2433226 MS.gene060879:CDS
CAGGCAGAAATCCTAGGAGA+CGG 0.637647 2.1:+2433154 None:intergenic
GCAGTATCATTCAGAAGACA+AGG 0.648817 2.1:-2433400 MS.gene060879:CDS
CAGAGAAGTCGTTCTAACGG+TGG 0.679356 2.1:-2433223 MS.gene060879:CDS
GCAGAAATCCTAGGAGACGG+TGG 0.696269 2.1:+2433157 None:intergenic
GCTGTGGTGATGTTGCATCA+CGG 0.699454 2.1:+2433266 None:intergenic
GTATTGATTGGTCCAAGCTG+TGG 0.700900 2.1:+2433250 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTTCTCTGAACAGTATTGAT+TGG + chr2.1:2433273-2433292 None:intergenic 35.0%
GCAGTATCATTCAGAAGACA+AGG - chr2.1:2433108-2433127 MS.gene060879:CDS 40.0%
GTTCAGAGAAGTCGTTCTAA+CGG - chr2.1:2433282-2433301 MS.gene060879:CDS 40.0%
TCAGAAGACAAGGTTCATCA+GGG - chr2.1:2433118-2433137 MS.gene060879:CDS 40.0%
TTCAGAAGACAAGGTTCATC+AGG - chr2.1:2433117-2433136 MS.gene060879:CDS 40.0%
! AAGGTTCATCAGGGTTTGTT+TGG - chr2.1:2433127-2433146 MS.gene060879:CDS 40.0%
! AGGTTCATCAGGGTTTGTTT+GGG - chr2.1:2433128-2433147 MS.gene060879:CDS 40.0%
!! GTTCTTGTTGATTCTGACTC+TGG + chr2.1:2433191-2433210 None:intergenic 40.0%
TACCTTGATCGATGCTTAGG+TGG + chr2.1:2433423-2433442 None:intergenic 45.0%
! AATCGCCGGAGAAACTTTTC+CGG + chr2.1:2433328-2433347 None:intergenic 45.0%
! ATTTCTGCCTGTGGGTTTTG+TGG - chr2.1:2433366-2433385 MS.gene060879:CDS 45.0%
!! AAAAGCACCACAAAACCCAC+AGG + chr2.1:2433376-2433395 None:intergenic 45.0%
!! AACCACCTAAGCATCGATCA+AGG - chr2.1:2433418-2433437 MS.gene060879:CDS 45.0%
!! GTATTGATTGGTCCAAGCTG+TGG + chr2.1:2433261-2433280 None:intergenic 45.0%
!! GTGGGTTTTGTGGTGCTTTT+GGG - chr2.1:2433376-2433395 MS.gene060879:CDS 45.0%
!! GTGGTGCTTTTGGGAAAGTA+GGG - chr2.1:2433385-2433404 MS.gene060879:CDS 45.0%
!! TGGTGCTTTTGGGAAAGTAG+GGG - chr2.1:2433386-2433405 MS.gene060879:CDS 45.0%
!! TGTGGGTTTTGTGGTGCTTT+TGG - chr2.1:2433375-2433394 MS.gene060879:CDS 45.0%
!! TGTGGTGCTTTTGGGAAAGT+AGG - chr2.1:2433384-2433403 MS.gene060879:CDS 45.0%
AACCCACAGGCAGAAATCCT+AGG + chr2.1:2433363-2433382 None:intergenic 50.0%
AGAAGTCGTTCTAACGGTGG+AGG - chr2.1:2433288-2433307 MS.gene060879:CDS 50.0%
CAGAGAAGTCGTTCTAACGG+TGG - chr2.1:2433285-2433304 MS.gene060879:CDS 50.0%
CAGGCAGAAATCCTAGGAGA+CGG + chr2.1:2433357-2433376 None:intergenic 50.0%
CCGTACCGGAAAAGTTTCTC+CGG - chr2.1:2433320-2433339 MS.gene060879:CDS 50.0%
CTCCTAGGATTTCTGCCTGT+GGG - chr2.1:2433358-2433377 MS.gene060879:CDS 50.0%
GATGCAACATCACCACAGCT+TGG - chr2.1:2433246-2433265 MS.gene060879:CDS 50.0%
TCTCCTAGGATTTCTGCCTG+TGG - chr2.1:2433357-2433376 MS.gene060879:CDS 50.0%
TTGGGAAAGTAGGGGAGAAG+AGG - chr2.1:2433394-2433413 MS.gene060879:CDS 50.0%
! CCGGAGAAACTTTTCCGGTA+CGG + chr2.1:2433323-2433342 None:intergenic 50.0%
! GCTGTGGTGATGTTGCATCA+CGG + chr2.1:2433245-2433264 None:intergenic 50.0%
GCAGAAATCCTAGGAGACGG+TGG + chr2.1:2433354-2433373 None:intergenic 55.0%
CGATTGAGCCACCGTCTCCT+AGG - chr2.1:2433343-2433362 MS.gene060879:CDS 60.0%
CGTTCTAACGGTGGAGGACG+TGG - chr2.1:2433294-2433313 MS.gene060879:CDS 60.0%
GGAGGACGTGGTTACCGTAC+CGG - chr2.1:2433306-2433325 MS.gene060879:CDS 60.0%
GGAGACGGTGGCTCAATCGC+CGG + chr2.1:2433342-2433361 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 2433087 2433443 2433087 ID=MS.gene060879
chr2.1 mRNA 2433087 2433443 2433087 ID=MS.gene060879.t1;Parent=MS.gene060879
chr2.1 exon 2433087 2433443 2433087 ID=MS.gene060879.t1.exon1;Parent=MS.gene060879.t1
chr2.1 CDS 2433087 2433443 2433087 ID=cds.MS.gene060879.t1;Parent=MS.gene060879.t1
Gene Sequence

>MS.gene060879

ATGGAAGGTTTACAAAGATCTGCAGTATCATTCAGAAGACAAGGTTCATCAGGGTTTGTTTGGGATGATAGATTTCTACAAGAAGAAATAAACAAGATGAACCAGAGTCAGAATCAACAAGAACAAGAAGACAAAGATGAAATCAAAGAGATGAACCGTGATGCAACATCACCACAGCTTGGACCAATCAATACTGTTCAGAGAAGTCGTTCTAACGGTGGAGGACGTGGTTACCGTACCGGAAAAGTTTCTCCGGCGATTGAGCCACCGTCTCCTAGGATTTCTGCCTGTGGGTTTTGTGGTGCTTTTGGGAAAGTAGGGGAGAAGAGGAAACCACCTAAGCATCGATCAAGGTAG

Protein sequence

>MS.gene060879.t1

MEGLQRSAVSFRRQGSSGFVWDDRFLQEEINKMNQSQNQQEQEDKDEIKEMNRDATSPQLGPINTVQRSRSNGGGRGYRTGKVSPAIEPPSPRISACGFCGAFGKVGEKRKPPKHRSR