AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0158450


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0158450 MtrunA17_Chr1g0170581 88.664 247 28 0 1 247 1 247 2.62e-161 446
Msa0158450 MtrunA17_Chr1g0170591 86.066 244 26 1 1 244 1 236 9.39e-153 424
Msa0158450 MtrunA17_Chr1g0170571 86.066 244 26 1 1 244 1 236 7.60e-145 404
Msa0158450 MtrunA17_Chr7g0256671 57.371 251 88 6 1 241 1 242 9.27e-65 202
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0158450 AT3G56970.1 41.036 251 133 6 1 240 1 247 2.71e-54 175
Msa0158450 AT3G56980.1 40.076 262 129 6 1 242 1 254 2.15e-44 150
Msa0158450 AT2G41240.1 37.603 242 147 2 1 242 1 238 3.56e-44 149
Msa0158450 AT2G41240.2 37.190 242 147 3 1 242 1 237 1.08e-41 142
Msa0158450 AT5G04150.2 44.654 159 86 1 61 219 82 238 2.48e-35 126
Msa0158450 AT5G04150.1 42.541 181 99 3 61 239 82 259 4.06e-35 126

Find 38 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCACATGTTTCTGTATTTC+TGG 0.048296 1_4:+27732778 None:intergenic
TGATGATGGTTATGGCTTAT+TGG 0.233335 1_4:+27733199 None:intergenic
CGAGAAGTTGTTATCAATAA+TGG 0.272808 1_4:-27732333 Msa0158450:CDS
GTTTCTTCATCTCAAACCTT+TGG 0.309294 1_4:-27732517 Msa0158450:CDS
AGTACTCTTGAAATTGTTGC+TGG 0.363324 1_4:+27732811 None:intergenic
TCAATAGTGTCTTTGTAGAA+TGG 0.399191 1_4:+27733172 None:intergenic
ATGGCTTATTGGCTCTTCAA+AGG 0.435523 1_4:+27733210 None:intergenic
TCTTCCTGTTTCAGATCAAA+TGG 0.439923 1_4:-27732984 Msa0158450:intron
ATGGATTCTGATGATGGTTA+TGG 0.442376 1_4:+27733191 None:intergenic
TTGTTATGTTTCGAAAATGA+TGG 0.448403 1_4:-27732556 Msa0158450:CDS
AGTACCATTTGATCTGAAAC+AGG 0.450182 1_4:+27732980 None:intergenic
TCTTCATCTCAAACCTTTGG+AGG 0.450222 1_4:-27732514 Msa0158450:CDS
TCGAAACATAACAAAATCTC+AGG 0.458685 1_4:+27732565 None:intergenic
GTTGTTATCAATAATGGAAA+AGG 0.460271 1_4:-27732327 Msa0158450:CDS
ATCTCAAACCTTTGGAGGGA+GGG 0.471487 1_4:-27732509 Msa0158450:CDS
AAGAAACATTTAGCAACAAA+AGG 0.474589 1_4:+27732533 None:intergenic
TGGCTTATTGGCTCTTCAAA+GGG 0.488560 1_4:+27733211 None:intergenic
TGTAGAATGGATTCTGATGA+TGG 0.499558 1_4:+27733185 None:intergenic
ATAATAACTTCATTTACTTG+TGG 0.512712 1_4:+27732712 None:intergenic
CATAACAAAATCTCAGGTAG+TGG 0.513867 1_4:+27732571 None:intergenic
ACAAATTATTCATCTTCTTG+CGG 0.523820 1_4:+27733026 None:intergenic
CTTCATCTCAAACCTTTGGA+GGG 0.524238 1_4:-27732513 Msa0158450:CDS
CATGCAAAGGTCACTGCTTG+TGG 0.541878 1_4:+27733087 None:intergenic
AAGAAACATAGTTACAACTC+TGG 0.547575 1_4:-27732670 Msa0158450:CDS
CATCTCAAACCTTTGGAGGG+AGG 0.551061 1_4:-27732510 Msa0158450:CDS
AGTGTAACATGAAATCTGAA+TGG 0.555088 1_4:+27732606 None:intergenic
CATCCAATTGTTGAAAACAT+AGG 0.558093 1_4:+27733235 None:intergenic
AGGAAGAAGTGAACGAAGAG+AGG 0.567551 1_4:+27733000 None:intergenic
GTAGAAGACCCTCCCTCCAA+AGG 0.574235 1_4:+27732501 None:intergenic
CCAATTGTTGAAAACATAGG+AGG 0.582074 1_4:+27733238 None:intergenic
TCTCAGGTAGTGGAATCTTG+TGG 0.593592 1_4:+27732581 None:intergenic
CACAAGCAGTGACCTTTGCA+TGG 0.598738 1_4:-27733086 Msa0158450:CDS
TTATCAATAATGGAAAAGGA+AGG 0.604075 1_4:-27732323 Msa0158450:CDS
GTCACTGCTTGTGGATTGTG+AGG 0.612584 1_4:+27733096 None:intergenic
GAAATACAGAAACATGTGGA+AGG 0.627895 1_4:-27732775 Msa0158450:CDS
ACCAGAAATACAGAAACATG+TGG 0.649518 1_4:-27732779 Msa0158450:CDS
CAAGCTTCTTGACCATGCAA+AGG 0.654337 1_4:+27733074 None:intergenic
TCACTGCTTGTGGATTGTGA+GGG 0.698792 1_4:+27733097 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTAATTTTCTTAGAACTA+TGG - chr1_4:27732672-27732691 Msa0158450:CDS 15.0%
!!! TTTTAATTTTCTTAGAACTA+TGG - chr1_4:27732672-27732691 Msa0158450:CDS 15.0%
!! ATAATAACTTCATTTACTTG+TGG + chr1_4:27732848-27732867 None:intergenic 20.0%
!! AATGTGTAAATAGTAAATTC+AGG - chr1_4:27733125-27733144 Msa0158450:CDS 20.0%
!! ATAATAACTTCATTTACTTG+TGG + chr1_4:27732848-27732867 None:intergenic 20.0%
!! AATGTGTAAATAGTAAATTC+AGG - chr1_4:27733125-27733144 Msa0158450:CDS 20.0%
! ACAAATTATTCATCTTCTTG+CGG + chr1_4:27732534-27732553 None:intergenic 25.0%
! TTGTTATGTTTCGAAAATGA+TGG - chr1_4:27733001-27733020 Msa0158450:CDS 25.0%
! AAGAAACATTTAGCAACAAA+AGG + chr1_4:27733027-27733046 None:intergenic 25.0%
!! ATTTAACTAAAAGCTCCTTT+TGG - chr1_4:27733152-27733171 Msa0158450:CDS 25.0%
!! TTTAACTAAAAGCTCCTTTT+GGG - chr1_4:27733153-27733172 Msa0158450:CDS 25.0%
! CAACTTCTCGTTTAAAAAAT+CGG + chr1_4:27733214-27733233 None:intergenic 25.0%
!! GTTGTTATCAATAATGGAAA+AGG - chr1_4:27733230-27733249 Msa0158450:CDS 25.0%
!! TTATCAATAATGGAAAAGGA+AGG - chr1_4:27733234-27733253 Msa0158450:CDS 25.0%
! ACAAATTATTCATCTTCTTG+CGG + chr1_4:27732534-27732553 None:intergenic 25.0%
! TTGTTATGTTTCGAAAATGA+TGG - chr1_4:27733001-27733020 Msa0158450:CDS 25.0%
! AAGAAACATTTAGCAACAAA+AGG + chr1_4:27733027-27733046 None:intergenic 25.0%
!! ATTTAACTAAAAGCTCCTTT+TGG - chr1_4:27733152-27733171 Msa0158450:CDS 25.0%
!! TTTAACTAAAAGCTCCTTTT+GGG - chr1_4:27733153-27733172 Msa0158450:CDS 25.0%
! CAACTTCTCGTTTAAAAAAT+CGG + chr1_4:27733214-27733233 None:intergenic 25.0%
!! GTTGTTATCAATAATGGAAA+AGG - chr1_4:27733230-27733249 Msa0158450:CDS 25.0%
!! TTATCAATAATGGAAAAGGA+AGG - chr1_4:27733234-27733253 Msa0158450:CDS 25.0%
CATCCAATTGTTGAAAACAT+AGG + chr1_4:27732325-27732344 None:intergenic 30.0%
! CTATGTTTTCAACAATTGGA+TGG - chr1_4:27732323-27732342 Msa0158450:CDS 30.0%
TCAATAGTGTCTTTGTAGAA+TGG + chr1_4:27732388-27732407 None:intergenic 30.0%
!! TCATTTTGATGATCAAGTAG+AGG - chr1_4:27732417-27732436 Msa0158450:intron 30.0%
AAGAAACATAGTTACAACTC+TGG - chr1_4:27732887-27732906 Msa0158450:intron 30.0%
! GTTTTGTAGTTTCAACAAGT+AGG - chr1_4:27732909-27732928 Msa0158450:intron 30.0%
AGTGTAACATGAAATCTGAA+TGG + chr1_4:27732954-27732973 None:intergenic 30.0%
TCGAAACATAACAAAATCTC+AGG + chr1_4:27732995-27733014 None:intergenic 30.0%
! CTTCTACAATTTGCATTTTC+AGG - chr1_4:27733072-27733091 Msa0158450:CDS 30.0%
CGAGAAGTTGTTATCAATAA+TGG - chr1_4:27733224-27733243 Msa0158450:CDS 30.0%
CATCCAATTGTTGAAAACAT+AGG + chr1_4:27732325-27732344 None:intergenic 30.0%
! CTATGTTTTCAACAATTGGA+TGG - chr1_4:27732323-27732342 Msa0158450:CDS 30.0%
TCAATAGTGTCTTTGTAGAA+TGG + chr1_4:27732388-27732407 None:intergenic 30.0%
!! TCATTTTGATGATCAAGTAG+AGG - chr1_4:27732417-27732436 Msa0158450:intron 30.0%
AAGAAACATAGTTACAACTC+TGG - chr1_4:27732887-27732906 Msa0158450:intron 30.0%
! GTTTTGTAGTTTCAACAAGT+AGG - chr1_4:27732909-27732928 Msa0158450:intron 30.0%
AGTGTAACATGAAATCTGAA+TGG + chr1_4:27732954-27732973 None:intergenic 30.0%
TCGAAACATAACAAAATCTC+AGG + chr1_4:27732995-27733014 None:intergenic 30.0%
! CTTCTACAATTTGCATTTTC+AGG - chr1_4:27733072-27733091 Msa0158450:CDS 30.0%
CGAGAAGTTGTTATCAATAA+TGG - chr1_4:27733224-27733243 Msa0158450:CDS 30.0%
CCAATTGTTGAAAACATAGG+AGG + chr1_4:27732322-27732341 None:intergenic 35.0%
! CCTCCTATGTTTTCAACAAT+TGG - chr1_4:27732319-27732338 Msa0158450:CDS 35.0%
!! TGATGATGGTTATGGCTTAT+TGG + chr1_4:27732361-27732380 None:intergenic 35.0%
!! ATGGATTCTGATGATGGTTA+TGG + chr1_4:27732369-27732388 None:intergenic 35.0%
! TGTAGAATGGATTCTGATGA+TGG + chr1_4:27732375-27732394 None:intergenic 35.0%
TCTTCCTGTTTCAGATCAAA+TGG - chr1_4:27732573-27732592 Msa0158450:CDS 35.0%
! AGTACCATTTGATCTGAAAC+AGG + chr1_4:27732580-27732599 None:intergenic 35.0%
AGTACTCTTGAAATTGTTGC+TGG + chr1_4:27732749-27732768 None:intergenic 35.0%
ACCAGAAATACAGAAACATG+TGG - chr1_4:27732778-27732797 Msa0158450:CDS 35.0%
! TCCACATGTTTCTGTATTTC+TGG + chr1_4:27732782-27732801 None:intergenic 35.0%
GAAATACAGAAACATGTGGA+AGG - chr1_4:27732782-27732801 Msa0158450:CDS 35.0%
CATAACAAAATCTCAGGTAG+TGG + chr1_4:27732989-27733008 None:intergenic 35.0%
GTTTCTTCATCTCAAACCTT+TGG - chr1_4:27733040-27733059 Msa0158450:CDS 35.0%
CCAATTGTTGAAAACATAGG+AGG + chr1_4:27732322-27732341 None:intergenic 35.0%
! CCTCCTATGTTTTCAACAAT+TGG - chr1_4:27732319-27732338 Msa0158450:CDS 35.0%
!! TGATGATGGTTATGGCTTAT+TGG + chr1_4:27732361-27732380 None:intergenic 35.0%
!! ATGGATTCTGATGATGGTTA+TGG + chr1_4:27732369-27732388 None:intergenic 35.0%
! TGTAGAATGGATTCTGATGA+TGG + chr1_4:27732375-27732394 None:intergenic 35.0%
TCTTCCTGTTTCAGATCAAA+TGG - chr1_4:27732573-27732592 Msa0158450:CDS 35.0%
! AGTACCATTTGATCTGAAAC+AGG + chr1_4:27732580-27732599 None:intergenic 35.0%
AGTACTCTTGAAATTGTTGC+TGG + chr1_4:27732749-27732768 None:intergenic 35.0%
ACCAGAAATACAGAAACATG+TGG - chr1_4:27732778-27732797 Msa0158450:CDS 35.0%
! TCCACATGTTTCTGTATTTC+TGG + chr1_4:27732782-27732801 None:intergenic 35.0%
GAAATACAGAAACATGTGGA+AGG - chr1_4:27732782-27732801 Msa0158450:CDS 35.0%
CATAACAAAATCTCAGGTAG+TGG + chr1_4:27732989-27733008 None:intergenic 35.0%
GTTTCTTCATCTCAAACCTT+TGG - chr1_4:27733040-27733059 Msa0158450:CDS 35.0%
!! TGGCTTATTGGCTCTTCAAA+GGG + chr1_4:27732349-27732368 None:intergenic 40.0%
!! ATGGCTTATTGGCTCTTCAA+AGG + chr1_4:27732350-27732369 None:intergenic 40.0%
TCTTCATCTCAAACCTTTGG+AGG - chr1_4:27733043-27733062 Msa0158450:CDS 40.0%
CTTCATCTCAAACCTTTGGA+GGG - chr1_4:27733044-27733063 Msa0158450:CDS 40.0%
!! TGGCTTATTGGCTCTTCAAA+GGG + chr1_4:27732349-27732368 None:intergenic 40.0%
!! ATGGCTTATTGGCTCTTCAA+AGG + chr1_4:27732350-27732369 None:intergenic 40.0%
TCTTCATCTCAAACCTTTGG+AGG - chr1_4:27733043-27733062 Msa0158450:CDS 40.0%
CTTCATCTCAAACCTTTGGA+GGG - chr1_4:27733044-27733063 Msa0158450:CDS 40.0%
! TCACTGCTTGTGGATTGTGA+GGG + chr1_4:27732463-27732482 None:intergenic 45.0%
CAAGCTTCTTGACCATGCAA+AGG + chr1_4:27732486-27732505 None:intergenic 45.0%
AGGAAGAAGTGAACGAAGAG+AGG + chr1_4:27732560-27732579 None:intergenic 45.0%
!! TCTCAGGTAGTGGAATCTTG+TGG + chr1_4:27732979-27732998 None:intergenic 45.0%
! ATCTCAAACCTTTGGAGGGA+GGG - chr1_4:27733048-27733067 Msa0158450:CDS 45.0%
! TCACTGCTTGTGGATTGTGA+GGG + chr1_4:27732463-27732482 None:intergenic 45.0%
CAAGCTTCTTGACCATGCAA+AGG + chr1_4:27732486-27732505 None:intergenic 45.0%
AGGAAGAAGTGAACGAAGAG+AGG + chr1_4:27732560-27732579 None:intergenic 45.0%
!! TCTCAGGTAGTGGAATCTTG+TGG + chr1_4:27732979-27732998 None:intergenic 45.0%
! ATCTCAAACCTTTGGAGGGA+GGG - chr1_4:27733048-27733067 Msa0158450:CDS 45.0%
! GTCACTGCTTGTGGATTGTG+AGG + chr1_4:27732464-27732483 None:intergenic 50.0%
CATGCAAAGGTCACTGCTTG+TGG + chr1_4:27732473-27732492 None:intergenic 50.0%
CACAAGCAGTGACCTTTGCA+TGG - chr1_4:27732471-27732490 Msa0158450:intron 50.0%
! CATCTCAAACCTTTGGAGGG+AGG - chr1_4:27733047-27733066 Msa0158450:CDS 50.0%
!!! GCTCCTTTTGGGTTTTCTGC+AGG - chr1_4:27733164-27733183 Msa0158450:CDS 50.0%
CCACCTGCAGAAAACCCAAA+AGG + chr1_4:27733170-27733189 None:intergenic 50.0%
!!! CCTTTTGGGTTTTCTGCAGG+TGG - chr1_4:27733167-27733186 Msa0158450:CDS 50.0%
! GTCACTGCTTGTGGATTGTG+AGG + chr1_4:27732464-27732483 None:intergenic 50.0%
CATGCAAAGGTCACTGCTTG+TGG + chr1_4:27732473-27732492 None:intergenic 50.0%
CACAAGCAGTGACCTTTGCA+TGG - chr1_4:27732471-27732490 Msa0158450:intron 50.0%
! CATCTCAAACCTTTGGAGGG+AGG - chr1_4:27733047-27733066 Msa0158450:CDS 50.0%
!!! GCTCCTTTTGGGTTTTCTGC+AGG - chr1_4:27733164-27733183 Msa0158450:CDS 50.0%
CCACCTGCAGAAAACCCAAA+AGG + chr1_4:27733170-27733189 None:intergenic 50.0%
!!! CCTTTTGGGTTTTCTGCAGG+TGG - chr1_4:27733167-27733186 Msa0158450:CDS 50.0%
GTAGAAGACCCTCCCTCCAA+AGG + chr1_4:27733059-27733078 None:intergenic 55.0%
GTAGAAGACCCTCCCTCCAA+AGG + chr1_4:27733059-27733078 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 27732304 27733275 27732304 ID=Msa0158450;Name=Msa0158450
chr1_4 mRNA 27732304 27733275 27732304 ID=Msa0158450-mRNA-1;Parent=Msa0158450;Name=Msa0158450-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0|0|1|1|1|3|0|247
chr1_4 exon 27732985 27733275 27732985 ID=Msa0158450-mRNA-1:exon:9028;Parent=Msa0158450-mRNA-1
chr1_4 exon 27732486 27732848 27732486 ID=Msa0158450-mRNA-1:exon:9027;Parent=Msa0158450-mRNA-1
chr1_4 exon 27732304 27732393 27732304 ID=Msa0158450-mRNA-1:exon:9026;Parent=Msa0158450-mRNA-1
chr1_4 CDS 27732985 27733275 27732985 ID=Msa0158450-mRNA-1:cds;Parent=Msa0158450-mRNA-1
chr1_4 CDS 27732486 27732848 27732486 ID=Msa0158450-mRNA-1:cds;Parent=Msa0158450-mRNA-1
chr1_4 CDS 27732304 27732393 27732304 ID=Msa0158450-mRNA-1:cds;Parent=Msa0158450-mRNA-1
Gene Sequence

>Msa0158450

ATGTTAGCGATATCTCCTCCTATGTTTTCAACAATTGGATGGCCCTTTGAAGAGCCAATAAGCCATAACCATCATCAGAATCCATTCTACAAAGACACTATTGATCAATTATTTCATTTTGATGATCAAGTAGAGGCAGAAATTAATTCAACAGATCCCTCACAATCCACAAGCAGTGACCTTTGCATGGTCAAGAAGCTTGTTCATAATGCTAGTGAACGTGATCGCCGCAAGAAGATGAATAATTTGTATTCCTCTCTTCGTTCACTTCTTCCTGTTTCAGATCAAATGAAGAAGTTAAGTATTCCAGCAACAATTTCAAGAGTACTCAAATACATACCAGAAATACAGAAACATGTGGAAGGACTAATTAAGAGAAAAGAAGAGATCTTATTGAGACTATCTCCACAAGTAAATGAAGTTATTATAAGCAAAGAATCTCAAAAGAAGAAACATAGTTACAACTCTGGTTTTGTAGTTTCAACAAGTAGGCTCAATGATAGTGAAATTACCATTCAGATTTCATGTTACACTGTCCACAAGATTCCACTACCTGAGATTTTGTTATGTTTCGAAAATGATGGCCTTTTGTTGCTAAATGTTTCTTCATCTCAAACCTTTGGAGGGAGGGTCTTCTACAATTTGCATTTTCAGGTGGATAAAACACAAAGATTAGAATCCGATTTTTTAAACGAGAAGTTGTTATCAATAATGGAAAAGGAAGGAGAGTTTTCAAAACAATAA

Protein sequence

>Msa0158450

MLAISPPMFSTIGWPFEEPISHNHHQNPFYKDTIDQLFHFDDQVEAEINSTDPSQSTSSDLCMVKKLVHNASERDRRKKMNNLYSSLRSLLPVSDQMKKLSIPATISRVLKYIPEIQKHVEGLIKRKEEILLRLSPQVNEVIISKESQKKKHSYNSGFVVSTSRLNDSEITIQISCYTVHKIPLPEILLCFENDGLLLLNVSSSQTFGGRVFYNLHFQVDKTQRLESDFLNEKLLSIMEKEGEFSKQ*