AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene34390

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34390.t1 MTR_5g068910 68.511 235 21 2 1 231 1 186 1.55e-102 296
MS.gene34390.t1 MTR_8g464080 84.181 177 24 1 1 173 1 177 2.31e-99 309
MS.gene34390.t1 MTR_8g464080 67.647 68 22 0 166 233 363 430 2.27e-24 102
MS.gene34390.t1 MTR_5g069010 81.967 122 18 1 107 224 29 150 6.15e-67 204
MS.gene34390.t1 MTR_2g098840 31.579 152 90 4 6 157 8 145 2.46e-12 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 69 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATCACCAACTTCTTCATTA+TGG 0.245858 1.2:-76510114 None:intergenic
CATCATTTGGGGTGTGTAGA+TGG 0.322440 1.2:-76510063 None:intergenic
ATCCCCTCTTGTAAGTTGTC+AGG 0.345066 1.2:-76510316 None:intergenic
TCTGTCCTCATCCTCGTTGA+TGG 0.348730 1.2:-76510173 None:intergenic
TATGAGTCGTTGAATCTTGC+AGG 0.354863 1.2:+76509779 MS.gene34390:CDS
CTCTTTCACAAGGACTTGTT+TGG 0.361717 1.2:+76509756 MS.gene34390:CDS
TAGCACGAACAACATCATTT+GGG 0.387685 1.2:-76510075 None:intergenic
TGTCTGGTTGAATCTTTGTT+TGG 0.398035 1.2:-76509691 None:intergenic
CTAGCACGAACAACATCATT+TGG 0.398412 1.2:-76510076 None:intergenic
ATCCTCGTTGATGGCATGTT+GGG 0.417694 1.2:-76510164 None:intergenic
ACCACCCTCTTGGAGTTGTC+TGG 0.426133 1.2:-76509707 None:intergenic
GGAGGTTTATGCAGGTTTGA+TGG 0.427569 1.2:+76509868 MS.gene34390:CDS
AGTCCTTGTGAAAGAGTTGT+AGG 0.428386 1.2:-76509749 None:intergenic
CATGTCCGTTGTAATATACT+TGG 0.437652 1.2:-76509568 None:intergenic
AATGGCAATGCGGTGCATAA+AGG 0.447044 1.2:+76510357 MS.gene34390:CDS
GTTCGTGCTAGTGTTGTTGT+TGG 0.451950 1.2:+76510088 MS.gene34390:CDS
AACAAGATCGACCACCCTCT+TGG 0.456926 1.2:-76509717 None:intergenic
GCAATTCCCTACGAAAGAAA+TGG 0.474242 1.2:+76510339 MS.gene34390:CDS
CATCCTCGTTGATGGCATGT+TGG 0.478370 1.2:-76510165 None:intergenic
TCCCCTCTTGTAAGTTGTCA+GGG 0.479407 1.2:-76510315 None:intergenic
TCGATAAAAGGATACGAACT+TGG 0.480063 1.2:-76509953 None:intergenic
CGCATTGCCATTTCTTTCGT+AGG 0.480173 1.2:-76510346 None:intergenic
TGAGTTGAGGTCAATGTTGT+GGG 0.482158 1.2:-76510035 None:intergenic
TCAACAATGGAGGTTTATGC+AGG 0.496988 1.2:+76509860 MS.gene34390:CDS
TTCATGACATGCAAACATCT+TGG 0.504931 1.2:+76509833 MS.gene34390:CDS
AAAAGGATACGAACTTGGTA+TGG 0.506256 1.2:-76509948 None:intergenic
GAATCTTTGTTTGGATACAT+TGG 0.513491 1.2:-76509682 None:intergenic
GCATTGCCATTTCTTTCGTA+GGG 0.521395 1.2:-76510345 None:intergenic
GTTGAGGTCAATGTTGTGGG+TGG 0.542978 1.2:-76510032 None:intergenic
ATGTTGTGGGTGGGTTCAGA+TGG 0.555389 1.2:-76510022 None:intergenic
TGAGGGTATGAAGAGGGTGT+TGG 0.557805 1.2:-76509923 None:intergenic
ACATCTTGGTATTTCAACAA+TGG 0.562241 1.2:+76509847 MS.gene34390:CDS
GTTCACATTACGAAAGTGCA+TGG 0.568947 1.2:-76510218 None:intergenic
GTGAGTTGAGGTCAATGTTG+TGG 0.573756 1.2:-76510036 None:intergenic
TTGAGGTCAATGTTGTGGGT+GGG 0.573792 1.2:-76510031 None:intergenic
ATGTTGTGATGAAGAGGGAA+TGG 0.577041 1.2:-76509996 None:intergenic
ACATGCCATCAACGAGGATG+AGG 0.579477 1.2:+76510168 MS.gene34390:CDS
TCTTGGTATTTCAACAATGG+AGG 0.584361 1.2:+76509850 MS.gene34390:CDS
ATGGAGTGAGGGTATGAAGA+GGG 0.585323 1.2:-76509929 None:intergenic
TTCAACCAGACAACTCCAAG+AGG 0.588574 1.2:+76509702 MS.gene34390:CDS
GTCCTTGTGAAAGAGTTGTA+GGG 0.588682 1.2:-76509748 None:intergenic
TTTGGGGTGTGTAGATGGAA+TGG 0.594174 1.2:-76510058 None:intergenic
GGCCCTGACAACTTACAAGA+GGG 0.594661 1.2:+76510313 MS.gene34390:intron
ACATTACGAAAGTGCATGGG+AGG 0.602406 1.2:-76510214 None:intergenic
GAGGGTGTTGGTTCAATACA+TGG 0.607556 1.2:-76509911 None:intergenic
TACGAACTTGGTATGGAGTG+AGG 0.611430 1.2:-76509941 None:intergenic
GTTGAAAGAACAAACACAGA+AGG 0.621859 1.2:+76509590 MS.gene34390:CDS
ATACATGGTGGTTCATCACA+AGG 0.623860 1.2:-76509896 None:intergenic
GGTGTCCATAATGAAGAAGT+TGG 0.626151 1.2:+76510109 MS.gene34390:CDS
TTCCCTCTTCATCACAACAT+CGG 0.629011 1.2:+76509999 MS.gene34390:CDS
ACGAACTTGGTATGGAGTGA+GGG 0.630924 1.2:-76509940 None:intergenic
TGGCCGATGTTGTGATGAAG+AGG 0.635448 1.2:-76510002 None:intergenic
TTTGTCCAAGTATATTACAA+CGG 0.635915 1.2:+76509563 MS.gene34390:CDS
TTCACATTACGAAAGTGCAT+GGG 0.636527 1.2:-76510217 None:intergenic
TACATGGTGGTTCATCACAA+GGG 0.637590 1.2:-76509895 None:intergenic
AGGCCCTGACAACTTACAAG+AGG 0.646335 1.2:+76510312 MS.gene34390:intron
ACATGGTGGTTCATCACAAG+GGG 0.647051 1.2:-76509894 None:intergenic
TACCCTACAACTCTTTCACA+AGG 0.662981 1.2:+76509746 MS.gene34390:CDS
ACCAGACAACTCCAAGAGGG+TGG 0.677155 1.2:+76509706 MS.gene34390:CDS
AGCACGAACAACATCATTTG+GGG 0.678596 1.2:-76510074 None:intergenic
TCAACCAGACAACTCCAAGA+GGG 0.681416 1.2:+76509703 MS.gene34390:CDS
GCCCTGACAACTTACAAGAG+GGG 0.687893 1.2:+76510314 MS.gene34390:CDS
CATTACGAAAGTGCATGGGA+GGG 0.690922 1.2:-76510213 None:intergenic
TATGGAGTGAGGGTATGAAG+AGG 0.699268 1.2:-76509930 None:intergenic
GTAGATGGAATGGTGAGTTG+AGG 0.712008 1.2:-76510048 None:intergenic
GGTGTTGGTTCAATACATGG+TGG 0.717217 1.2:-76509908 None:intergenic
GGCCGATGTTGTGATGAAGA+GGG 0.717605 1.2:-76510001 None:intergenic
TGCCCAACATGCCATCAACG+AGG 0.721499 1.2:+76510162 MS.gene34390:CDS
CTACGAAAGAAATGGCAATG+CGG 0.757949 1.2:+76510347 MS.gene34390:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGAAAAACATCAAATTGGA+AGG + chr1.2:76509653-76509672 MS.gene34390:CDS 25.0%
! AGTGAAGAAAAACATCAAAT+TGG + chr1.2:76509649-76509668 MS.gene34390:CDS 25.0%
! TTTGTCCAAGTATATTACAA+CGG + chr1.2:76509563-76509582 MS.gene34390:CDS 25.0%
!! GTTTTTCTTCACTTTAAACA+AGG - chr1.2:76509642-76509661 None:intergenic 25.0%
AATCACCAACTTCTTCATTA+TGG - chr1.2:76510117-76510136 None:intergenic 30.0%
ACATCTTGGTATTTCAACAA+TGG + chr1.2:76509847-76509866 MS.gene34390:CDS 30.0%
ACTTGGACAAAAAACTCTAT+TGG - chr1.2:76509554-76509573 None:intergenic 30.0%
TTCAACATATTCAGTATCGT+TGG - chr1.2:76510245-76510264 None:intergenic 30.0%
! CTGTTTTGTGTTTCGATAAA+AGG - chr1.2:76509968-76509987 None:intergenic 30.0%
! GAATCTTTGTTTGGATACAT+TGG - chr1.2:76509685-76509704 None:intergenic 30.0%
!! AACAAGATAAGATTGGTTTC+GGG - chr1.2:76510290-76510309 None:intergenic 30.0%
!! GAACAAGATAAGATTGGTTT+CGG - chr1.2:76510291-76510310 None:intergenic 30.0%
AAAAGGATACGAACTTGGTA+TGG - chr1.2:76509951-76509970 None:intergenic 35.0%
AACCAATCTTATCTTGTTCC+AGG + chr1.2:76510292-76510311 MS.gene34390:intron 35.0%
CATGTCCGTTGTAATATACT+TGG - chr1.2:76509571-76509590 None:intergenic 35.0%
GTTGAAAGAACAAACACAGA+AGG + chr1.2:76509590-76509609 MS.gene34390:CDS 35.0%
TAGCACGAACAACATCATTT+GGG - chr1.2:76510078-76510097 None:intergenic 35.0%
TCGATAAAAGGATACGAACT+TGG - chr1.2:76509956-76509975 None:intergenic 35.0%
TCTTGGTATTTCAACAATGG+AGG + chr1.2:76509850-76509869 MS.gene34390:CDS 35.0%
TGGACAAAAAACTCTATTGG+AGG - chr1.2:76509551-76509570 None:intergenic 35.0%
TGTCTGGTTGAATCTTTGTT+TGG - chr1.2:76509694-76509713 None:intergenic 35.0%
TTCATGACATGCAAACATCT+TGG + chr1.2:76509833-76509852 MS.gene34390:CDS 35.0%
! TTCACATTACGAAAGTGCAT+GGG - chr1.2:76510220-76510239 None:intergenic 35.0%
AGCACGAACAACATCATTTG+GGG - chr1.2:76510077-76510096 None:intergenic 40.0%
AGTCCTTGTGAAAGAGTTGT+AGG - chr1.2:76509752-76509771 None:intergenic 40.0%
ATACATGGTGGTTCATCACA+AGG - chr1.2:76509899-76509918 None:intergenic 40.0%
ATGTTGTGATGAAGAGGGAA+TGG - chr1.2:76509999-76510018 None:intergenic 40.0%
CTACGAAAGAAATGGCAATG+CGG + chr1.2:76510347-76510366 MS.gene34390:CDS 40.0%
CTAGCACGAACAACATCATT+TGG - chr1.2:76510079-76510098 None:intergenic 40.0%
GCAATTCCCTACGAAAGAAA+TGG + chr1.2:76510339-76510358 MS.gene34390:CDS 40.0%
GGTGTCCATAATGAAGAAGT+TGG + chr1.2:76510109-76510128 MS.gene34390:CDS 40.0%
GTCCTTGTGAAAGAGTTGTA+GGG - chr1.2:76509751-76509770 None:intergenic 40.0%
TACATGGTGGTTCATCACAA+GGG - chr1.2:76509898-76509917 None:intergenic 40.0%
TACCCTACAACTCTTTCACA+AGG + chr1.2:76509746-76509765 MS.gene34390:CDS 40.0%
TATGAGTCGTTGAATCTTGC+AGG + chr1.2:76509779-76509798 MS.gene34390:CDS 40.0%
TCAACAATGGAGGTTTATGC+AGG + chr1.2:76509860-76509879 MS.gene34390:CDS 40.0%
TTCCCTCTTCATCACAACAT+CGG + chr1.2:76509999-76510018 MS.gene34390:CDS 40.0%
! CTCTTTCACAAGGACTTGTT+TGG + chr1.2:76509756-76509775 MS.gene34390:CDS 40.0%
! GCATTGCCATTTCTTTCGTA+GGG - chr1.2:76510348-76510367 None:intergenic 40.0%
! GTTCACATTACGAAAGTGCA+TGG - chr1.2:76510221-76510240 None:intergenic 40.0%
! TGAGTTGAGGTCAATGTTGT+GGG - chr1.2:76510038-76510057 None:intergenic 40.0%
ACATGGTGGTTCATCACAAG+GGG - chr1.2:76509897-76509916 None:intergenic 45.0%
ACGAACTTGGTATGGAGTGA+GGG - chr1.2:76509943-76509962 None:intergenic 45.0%
ATCCCCTCTTGTAAGTTGTC+AGG - chr1.2:76510319-76510338 None:intergenic 45.0%
GGAGGTTTATGCAGGTTTGA+TGG + chr1.2:76509868-76509887 MS.gene34390:CDS 45.0%
GGCCTGGAACAAGATAAGAT+TGG - chr1.2:76510297-76510316 None:intergenic 45.0%
GTAGATGGAATGGTGAGTTG+AGG - chr1.2:76510051-76510070 None:intergenic 45.0%
TACGAACTTGGTATGGAGTG+AGG - chr1.2:76509944-76509963 None:intergenic 45.0%
TCAACCAGACAACTCCAAGA+GGG + chr1.2:76509703-76509722 MS.gene34390:CDS 45.0%
TCCCCTCTTGTAAGTTGTCA+GGG - chr1.2:76510318-76510337 None:intergenic 45.0%
TTCAACCAGACAACTCCAAG+AGG + chr1.2:76509702-76509721 MS.gene34390:CDS 45.0%
TTGAGGTCAATGTTGTGGGT+GGG - chr1.2:76510034-76510053 None:intergenic 45.0%
! ACATTACGAAAGTGCATGGG+AGG - chr1.2:76510217-76510236 None:intergenic 45.0%
! ATGGAGTGAGGGTATGAAGA+GGG - chr1.2:76509932-76509951 None:intergenic 45.0%
! CATCATTTGGGGTGTGTAGA+TGG - chr1.2:76510066-76510085 None:intergenic 45.0%
! CATTACGAAAGTGCATGGGA+GGG - chr1.2:76510216-76510235 None:intergenic 45.0%
! CGCATTGCCATTTCTTTCGT+AGG - chr1.2:76510349-76510368 None:intergenic 45.0%
! GTGAGTTGAGGTCAATGTTG+TGG - chr1.2:76510039-76510058 None:intergenic 45.0%
! GTTCGTGCTAGTGTTGTTGT+TGG + chr1.2:76510088-76510107 MS.gene34390:CDS 45.0%
! TATGGAGTGAGGGTATGAAG+AGG - chr1.2:76509933-76509952 None:intergenic 45.0%
! TTTGGGGTGTGTAGATGGAA+TGG - chr1.2:76510061-76510080 None:intergenic 45.0%
!! ATCCTCGTTGATGGCATGTT+GGG - chr1.2:76510167-76510186 None:intergenic 45.0%
!! GAGGGTGTTGGTTCAATACA+TGG - chr1.2:76509914-76509933 None:intergenic 45.0%
!! GGTGTTGGTTCAATACATGG+TGG - chr1.2:76509911-76509930 None:intergenic 45.0%
AACAAGATCGACCACCCTCT+TGG - chr1.2:76509720-76509739 None:intergenic 50.0%
ACATGCCATCAACGAGGATG+AGG + chr1.2:76510168-76510187 MS.gene34390:CDS 50.0%
AGGCCCTGACAACTTACAAG+AGG + chr1.2:76510312-76510331 MS.gene34390:intron 50.0%
GCCCTGACAACTTACAAGAG+GGG + chr1.2:76510314-76510333 MS.gene34390:CDS 50.0%
GGCCCTGACAACTTACAAGA+GGG + chr1.2:76510313-76510332 MS.gene34390:intron 50.0%
GGCCGATGTTGTGATGAAGA+GGG - chr1.2:76510004-76510023 None:intergenic 50.0%
GTTGAGGTCAATGTTGTGGG+TGG - chr1.2:76510035-76510054 None:intergenic 50.0%
TCTGTCCTCATCCTCGTTGA+TGG - chr1.2:76510176-76510195 None:intergenic 50.0%
TCTTGTAAGTTGTCAGGGCC+TGG - chr1.2:76510313-76510332 None:intergenic 50.0%
TGGCCGATGTTGTGATGAAG+AGG - chr1.2:76510005-76510024 None:intergenic 50.0%
! ATGTTGTGGGTGGGTTCAGA+TGG - chr1.2:76510025-76510044 None:intergenic 50.0%
! TGAGGGTATGAAGAGGGTGT+TGG - chr1.2:76509926-76509945 None:intergenic 50.0%
!! CATCCTCGTTGATGGCATGT+TGG - chr1.2:76510168-76510187 None:intergenic 50.0%
ACCACCCTCTTGGAGTTGTC+TGG - chr1.2:76509710-76509729 None:intergenic 55.0%
ACCAGACAACTCCAAGAGGG+TGG + chr1.2:76509706-76509725 MS.gene34390:CDS 55.0%
TGCCCAACATGCCATCAACG+AGG + chr1.2:76510162-76510181 MS.gene34390:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 76509545 76510376 76509545 ID=MS.gene34390
chr1.2 mRNA 76509545 76510376 76509545 ID=MS.gene34390.t1;Parent=MS.gene34390
chr1.2 exon 76509545 76510234 76509545 ID=MS.gene34390.t1.exon1;Parent=MS.gene34390.t1
chr1.2 CDS 76509545 76510234 76509545 ID=cds.MS.gene34390.t1;Parent=MS.gene34390.t1
chr1.2 exon 76510314 76510376 76510314 ID=MS.gene34390.t1.exon2;Parent=MS.gene34390.t1
chr1.2 CDS 76510314 76510376 76510314 ID=cds.MS.gene34390.t1;Parent=MS.gene34390.t1
Gene Sequence

>MS.gene34390

ATGCCTCCAATAGAGTTTTTTGTCCAAGTATATTACAACGGACATGTTGAAAGAACAAACACAGAAGGTGTTGTATTTTCATGCAATAATTCATCCTTGTTTAAAGTGAAGAAAAACATCAAATTGGAAGGACTTATCCAATGTATCCAAACAAAGATTCAACCAGACAACTCCAAGAGGGTGGTCGATCTTGTTTATCGATACCCTACAACTCTTTCACAAGGACTTGTTTGGTATGAGTCGTTGAATCTTGCAGGAGATGACGACGTTCAGATGATGTTTGACATGTTCATGACATGCAAACATCTTGGTATTTCAACAATGGAGGTTTATGCAGGTTTGATGGATGCCCCTTGTGATGAACCACCATGTATTGAACCAACACCCTCTTCATACCCTCACTCCATACCAAGTTCGTATCCTTTTATCGAAACACAAAACAGTCATCACTCCATTCCCTCTTCATCACAACATCGGCCATCTGAACCCACCCACAACATTGACCTCAACTCACCATTCCATCTACACACCCCAAATGATGTTGTTCGTGCTAGTGTTGTTGTTGGTGTCCATAATGAAGAAGTTGGTGATTTTAGTGAAAATGAAGATGACATTCTTGCCCAACATGCCATCAACGAGGATGAGGACAGAGACATGTGTTTTTATGACCCTCCCATGCACTTTCGTAATGTGAACTCCAACGATACTGAATATGTTGAAGATGAGTTTGTACACTCTATGTCCCGAAACCAATCTTATCTTGTTCCAGGCCCTGACAACTTACAAGAGGGGATGCAATTCCCTACGAAAGAAATGGCAATGCGGTGCATAA
Protein sequence

>MS.gene34390.t1

MPPIEFFVQVYYNGHVERTNTEGVVFSCNNSSLFKVKKNIKLEGLIQCIQTKIQPDNSKRVVDLVYRYPTTLSQGLVWYESLNLAGDDDVQMMFDMFMTCKHLGISTMEVYAGLMDAPCDEPPCIEPTPSSYPHSIPSSYPFIETQNSHHSIPSSSQHRPSEPTHNIDLNSPFHLHTPNDVVRASVVVGVHNEEVGDFSENEDDILAQHAINEDEDRDMCFYDPPMHFRNALTTYKRGCNSLRKKWQCGA