AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0067070


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0067070 MtrunA17_Chr1g0170581 86.885 244 32 0 17 260 1 244 2.16e-154 429
Msa0067070 MtrunA17_Chr1g0170571 83.534 249 33 1 17 265 1 241 1.50e-143 402
Msa0067070 MtrunA17_Chr1g0170591 79.116 249 44 1 17 265 1 241 1.53e-142 399
Msa0067070 MtrunA17_Chr7g0256671 57.551 245 97 6 17 257 1 242 6.85e-65 203
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0067070 AT3G56970.1 42.169 249 133 5 17 256 1 247 3.01e-54 176
Msa0067070 AT3G56980.1 39.453 256 139 3 17 258 1 254 2.23e-45 153
Msa0067070 AT2G41240.1 37.247 247 141 5 17 258 1 238 7.97e-42 144
Msa0067070 AT2G41240.2 36.842 247 141 6 17 258 1 237 2.36e-39 137
Msa0067070 AT5G04150.1 42.623 183 97 4 76 253 78 257 4.10e-33 121
Msa0067070 AT5G04150.2 43.558 163 87 2 76 235 78 238 6.19e-33 120

Find 47 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTGACCCTGAAGCTGTTTA+TGG 0.179245 1_2:+31653857 None:intergenic
TGAAGCTGTTTATGGGTTAT+TGG 0.224116 1_2:+31653865 None:intergenic
GAGCTTCTCATTTAGAATTT+CGG 0.255939 1_2:+31652183 None:intergenic
CTTCTATAATTTGCATTTCC+AGG 0.265122 1_2:-31653072 Msa0067070:intron
TTCTGAGATCTTGATATGTT+TGG 0.287728 1_2:-31653153 Msa0067070:CDS
TGAGAAGCTCTTATCAATAA+TGG 0.319674 1_2:-31652170 Msa0067070:CDS
GTTTCTTCATCTCAGACCTT+TGG 0.353556 1_2:-31653104 Msa0067070:CDS
CAGAAGAAATTGAGCATTCC+GGG 0.366600 1_2:-31653416 Msa0067070:CDS
GTAATTCCAGCATGTATTTG+AGG 0.375675 1_2:+31653378 None:intergenic
GCAGAAGAAATTGAGCATTC+CGG 0.378244 1_2:-31653417 Msa0067070:intron
AATAACCCATAAACAGCTTC+AGG 0.395318 1_2:-31653863 Msa0067070:CDS
TCTTCATCTCAGACCTTTGG+AGG 0.399420 1_2:-31653101 Msa0067070:CDS
AGTACCATTTGATCTGAAAC+AGG 0.414053 1_2:+31653646 None:intergenic
GTGACCCTGAAGCTGTTTAT+GGG 0.414301 1_2:+31653858 None:intergenic
ATGGGTTATTGGCTCTTCAA+AGG 0.431180 1_2:+31653876 None:intergenic
GCTCTTATCAATAATGGATA+AGG 0.434619 1_2:-31652164 Msa0067070:CDS
TCTTCCTGTTTCAGATCAAA+TGG 0.439923 1_2:-31653650 Msa0067070:intron
TGGGTTATTGGCTCTTCAAA+GGG 0.480765 1_2:+31653877 None:intergenic
AAGAAACATTAAGTAGCAAA+AGG 0.489430 1_2:+31653120 None:intergenic
CATATCAAGATCTCAGAAAG+TGG 0.493296 1_2:+31653158 None:intergenic
CGAGGGACTAATTAAGAGAA+AGG 0.497408 1_2:-31653345 Msa0067070:CDS
CATGCCAAGGTCACTGCTTG+TGG 0.530365 1_2:+31653753 None:intergenic
AAAAGTCCTCAAATACATGC+TGG 0.531624 1_2:-31653384 Msa0067070:CDS
TTGATATGTTTGGAAAATGA+TGG 0.537710 1_2:-31653143 Msa0067070:CDS
AAGAAACATAGTTACAACTC+TGG 0.547575 1_2:-31653257 Msa0067070:CDS
CGCTAACATAATGTTGACGC+AGG 0.553009 1_2:+31653933 None:intergenic
AGTGTAACATGAAATCTGAA+TGG 0.555088 1_2:+31653193 None:intergenic
CATCCAATTGTTGAAAACAT+AGG 0.558093 1_2:+31653901 None:intergenic
TTATCAATAATGGATAAGGA+AGG 0.562276 1_2:-31652160 Msa0067070:CDS
CTTCATCTCAGACCTTTGGA+GGG 0.563936 1_2:-31653100 Msa0067070:CDS
ATGATCACCTCATCTACTTG+TGG 0.565875 1_2:+31653299 None:intergenic
TCTCAGAAAGTGGAATCTTG+TGG 0.569417 1_2:+31653168 None:intergenic
ATAACCCATAAACAGCTTCA+GGG 0.574272 1_2:-31653862 Msa0067070:CDS
CCAATTGTTGAAAACATAGG+AGG 0.582074 1_2:+31653904 None:intergenic
ATAGAAGACTCTCCCTCCAA+AGG 0.594272 1_2:+31653088 None:intergenic
GTCACTGCTTGTGGACTGTG+AGG 0.594409 1_2:+31653762 None:intergenic
AGGAAGAAGTGAACGAAGTG+AGG 0.599839 1_2:+31653666 None:intergenic
TATCAATAATGGATAAGGAA+GGG 0.600012 1_2:-31652159 Msa0067070:CDS
CACAAGCAGTGACCTTGGCA+TGG 0.603384 1_2:-31653752 Msa0067070:CDS
CAGTCCACAAGCAGTGACCT+TGG 0.605273 1_2:-31653757 Msa0067070:CDS
GAATTACAGAAGCAAGTCGA+GGG 0.635400 1_2:-31653362 Msa0067070:CDS
ACTTTCTCCACAAGTAGATG+AGG 0.642125 1_2:-31653306 Msa0067070:CDS
GCTAACATAATGTTGACGCA+GGG 0.644780 1_2:+31653934 None:intergenic
TCACTGCTTGTGGACTGTGA+GGG 0.645141 1_2:+31653763 None:intergenic
CAAGCTTCTTGACCATGCCA+AGG 0.656633 1_2:+31653740 None:intergenic
GGAATTACAGAAGCAAGTCG+AGG 0.659886 1_2:-31653363 Msa0067070:CDS
CTAACATAATGTTGACGCAG+GGG 0.723756 1_2:+31653935 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACATAAATATATAGAAATTT+TGG + chr1_2:31653696-31653715 None:intergenic 10.0%
!!! ACAAATTATTGATTTTTTTG+CGG + chr1_2:31652413-31652432 None:intergenic 15.0%
!!! TTTAAAGTAATATCGAAAAA+GGG + chr1_2:31652605-31652624 None:intergenic 15.0%
!!! ATTTAAAGTAATATCGAAAA+AGG + chr1_2:31652606-31652625 None:intergenic 15.0%
!! TTTGTCATTGTAATATTTAT+AGG + chr1_2:31653484-31653503 None:intergenic 15.0%
!! GTGATTAATTATTTGTATAA+TGG + chr1_2:31653577-31653596 None:intergenic 15.0%
!! TTCGATATTACTTTAAATTG+TGG - chr1_2:31652608-31652627 Msa0067070:intron 20.0%
!! AAGACTTTACTCAATAATAT+TGG + chr1_2:31653100-31653119 None:intergenic 20.0%
!! AAATAATGAAACAAAGATGT+AGG - chr1_2:31653519-31653538 Msa0067070:intron 20.0%
!!! AATGAGTATATTTTTTGTAG+TGG + chr1_2:31653839-31653858 None:intergenic 20.0%
! TATAGACAATTAGAAACAGA+AGG + chr1_2:31652495-31652514 None:intergenic 25.0%
! TTGATATGTTTGGAAAATGA+TGG - chr1_2:31652959-31652978 Msa0067070:intron 25.0%
! AAGAAACATTAAGTAGCAAA+AGG + chr1_2:31652985-31653004 None:intergenic 25.0%
!!! AGTATATTTTTTGTAGTGGT+CGG + chr1_2:31653835-31653854 None:intergenic 25.0%
!!! TTATCAATAATGGATAAGGA+AGG - chr1_2:31653942-31653961 Msa0067070:CDS 25.0%
!!! TATCAATAATGGATAAGGAA+GGG - chr1_2:31653943-31653962 Msa0067070:CDS 25.0%
GGAAAAAGTTATAAATGGAG+AGG - chr1_2:31652137-31652156 Msa0067070:CDS 30.0%
CATCCAATTGTTGAAAACAT+AGG + chr1_2:31652204-31652223 None:intergenic 30.0%
! CTATGTTTTCAACAATTGGA+TGG - chr1_2:31652202-31652221 Msa0067070:CDS 30.0%
! TCATTTTCAGCATCAATTTG+AGG - chr1_2:31652296-31652315 Msa0067070:intron 30.0%
ACAATTAGAAACAGAAGGAA+GGG + chr1_2:31652490-31652509 None:intergenic 30.0%
AAGAAACATAGTTACAACTC+TGG - chr1_2:31652845-31652864 Msa0067070:intron 30.0%
! GTTTTGTACTTTCAACAAGT+AGG - chr1_2:31652867-31652886 Msa0067070:intron 30.0%
AGTGTAACATGAAATCTGAA+TGG + chr1_2:31652912-31652931 None:intergenic 30.0%
!! TTCTGAGATCTTGATATGTT+TGG - chr1_2:31652949-31652968 Msa0067070:intron 30.0%
! CTTCTATAATTTGCATTTCC+AGG - chr1_2:31653030-31653049 Msa0067070:intron 30.0%
TATATTTATGTACCAGTCCA+AGG - chr1_2:31653705-31653724 Msa0067070:CDS 30.0%
ATATTTATGTACCAGTCCAA+GGG - chr1_2:31653706-31653725 Msa0067070:CDS 30.0%
GACAATGCATAATATATGCA+AGG - chr1_2:31653794-31653813 Msa0067070:CDS 30.0%
!!! TATATTTTTTGTAGTGGTCG+GGG + chr1_2:31653833-31653852 None:intergenic 30.0%
!!! GTATATTTTTTGTAGTGGTC+GGG + chr1_2:31653834-31653853 None:intergenic 30.0%
! GAGCTTCTCATTTAGAATTT+CGG + chr1_2:31653922-31653941 None:intergenic 30.0%
TGAGAAGCTCTTATCAATAA+TGG - chr1_2:31653932-31653951 Msa0067070:CDS 30.0%
!! GCTCTTATCAATAATGGATA+AGG - chr1_2:31653938-31653957 Msa0067070:CDS 30.0%
CCAATTGTTGAAAACATAGG+AGG + chr1_2:31652201-31652220 None:intergenic 35.0%
! CCTCCTATGTTTTCAACAAT+TGG - chr1_2:31652198-31652217 Msa0067070:CDS 35.0%
! TGAAGCTGTTTATGGGTTAT+TGG + chr1_2:31652240-31652259 None:intergenic 35.0%
AATAACCCATAAACAGCTTC+AGG - chr1_2:31652239-31652258 Msa0067070:intron 35.0%
ATAACCCATAAACAGCTTCA+GGG - chr1_2:31652240-31652259 Msa0067070:intron 35.0%
TCTTCCTGTTTCAGATCAAA+TGG - chr1_2:31652452-31652471 Msa0067070:intron 35.0%
! AGTACCATTTGATCTGAAAC+AGG + chr1_2:31652459-31652478 None:intergenic 35.0%
GACAATTAGAAACAGAAGGA+AGG + chr1_2:31652491-31652510 None:intergenic 35.0%
! CTTGAAAACCTTGTGTTTTG+AGG - chr1_2:31652549-31652568 Msa0067070:intron 35.0%
!!! AGGACTTTTGAAATTGTTCC+CGG + chr1_2:31652707-31652726 None:intergenic 35.0%
AAAAGTCCTCAAATACATGC+TGG - chr1_2:31652718-31652737 Msa0067070:intron 35.0%
GTAATTCCAGCATGTATTTG+AGG + chr1_2:31652727-31652746 None:intergenic 35.0%
CATATCAAGATCTCAGAAAG+TGG + chr1_2:31652947-31652966 None:intergenic 35.0%
TGCATAATATATGCAAGGTC+TGG - chr1_2:31653799-31653818 Msa0067070:CDS 35.0%
GCATAATATATGCAAGGTCT+GGG - chr1_2:31653800-31653819 Msa0067070:CDS 35.0%
CATAATATATGCAAGGTCTG+GGG - chr1_2:31653801-31653820 Msa0067070:CDS 35.0%
!! GTTCCTTTTGTGTTTTTTGC+AGG - chr1_2:31653872-31653891 Msa0067070:CDS 35.0%
CTACCTGCAAAAAACACAAA+AGG + chr1_2:31653878-31653897 None:intergenic 35.0%
CTAACATAATGTTGACGCAG+GGG + chr1_2:31652170-31652189 None:intergenic 40.0%
GCTAACATAATGTTGACGCA+GGG + chr1_2:31652171-31652190 None:intergenic 40.0%
!! TGGGTTATTGGCTCTTCAAA+GGG + chr1_2:31652228-31652247 None:intergenic 40.0%
!! ATGGGTTATTGGCTCTTCAA+AGG + chr1_2:31652229-31652248 None:intergenic 40.0%
!!! ACCTTGTGTTTTGAGGAGTA+TGG - chr1_2:31652556-31652575 Msa0067070:intron 40.0%
ACCATACTCCTCAAAACACA+AGG + chr1_2:31652560-31652579 None:intergenic 40.0%
! GAAAAAGGGCGTACACAATT+AGG + chr1_2:31652591-31652610 None:intergenic 40.0%
GCAGAAGAAATTGAGCATTC+CGG - chr1_2:31652685-31652704 Msa0067070:intron 40.0%
CAGAAGAAATTGAGCATTCC+GGG - chr1_2:31652686-31652705 Msa0067070:intron 40.0%
GAATTACAGAAGCAAGTCGA+GGG - chr1_2:31652740-31652759 Msa0067070:intron 40.0%
CGAGGGACTAATTAAGAGAA+AGG - chr1_2:31652757-31652776 Msa0067070:intron 40.0%
ACTTTCTCCACAAGTAGATG+AGG - chr1_2:31652796-31652815 Msa0067070:intron 40.0%
ATGATCACCTCATCTACTTG+TGG + chr1_2:31652806-31652825 None:intergenic 40.0%
TCTCAGAAAGTGGAATCTTG+TGG + chr1_2:31652937-31652956 None:intergenic 40.0%
GTTTCTTCATCTCAGACCTT+TGG - chr1_2:31652998-31653017 Msa0067070:intron 40.0%
TCCAGGTGTGTTAACTTTAC+AGG - chr1_2:31653047-31653066 Msa0067070:intron 40.0%
TCCTGTAAAGTTAACACACC+TGG + chr1_2:31653051-31653070 None:intergenic 40.0%
TGAGCTTAGCTCAGTTTGTA+TGG - chr1_2:31653772-31653791 Msa0067070:CDS 40.0%
CGCTAACATAATGTTGACGC+AGG + chr1_2:31652172-31652191 None:intergenic 45.0%
GTGACCCTGAAGCTGTTTAT+GGG + chr1_2:31652247-31652266 None:intergenic 45.0%
AGTGACCCTGAAGCTGTTTA+TGG + chr1_2:31652248-31652267 None:intergenic 45.0%
AGGAAGAAGTGAACGAAGTG+AGG + chr1_2:31652439-31652458 None:intergenic 45.0%
GGAATTACAGAAGCAAGTCG+AGG - chr1_2:31652739-31652758 Msa0067070:intron 45.0%
TCTTCATCTCAGACCTTTGG+AGG - chr1_2:31653001-31653020 Msa0067070:intron 45.0%
CTTCATCTCAGACCTTTGGA+GGG - chr1_2:31653002-31653021 Msa0067070:intron 45.0%
ATAGAAGACTCTCCCTCCAA+AGG + chr1_2:31653017-31653036 None:intergenic 45.0%
!! AAAATTAAAAGAAAAAATAT+TGG - chr1_2:31653643-31653662 Msa0067070:intron 5.0%
! TCACTGCTTGTGGACTGTGA+GGG + chr1_2:31652342-31652361 None:intergenic 50.0%
CAAGCTTCTTGACCATGCCA+AGG + chr1_2:31652365-31652384 None:intergenic 50.0%
CAAACTGAGCTAAGCTCACG+AGG + chr1_2:31653770-31653789 None:intergenic 50.0%
! GTCACTGCTTGTGGACTGTG+AGG + chr1_2:31652343-31652362 None:intergenic 55.0%
CAGTCCACAAGCAGTGACCT+TGG - chr1_2:31652345-31652364 Msa0067070:intron 55.0%
CATGCCAAGGTCACTGCTTG+TGG + chr1_2:31652352-31652371 None:intergenic 55.0%
CACAAGCAGTGACCTTGGCA+TGG - chr1_2:31652350-31652369 Msa0067070:intron 55.0%
ACCAGTCCAAGGGAGAGATG+CGG - chr1_2:31653716-31653735 Msa0067070:CDS 55.0%
AGTACTCCGCATCTCTCCCT+TGG + chr1_2:31653725-31653744 None:intergenic 55.0%
TCCGCATCTCTCCCTTGGAC+TGG + chr1_2:31653720-31653739 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 31652135 31653989 31652135 ID=Msa0067070;Name=Msa0067070
chr1_2 mRNA 31652135 31653989 31652135 ID=Msa0067070-mRNA-1;Parent=Msa0067070;Name=Msa0067070-mRNA-1;_AED=0.11;_eAED=0.11;_QI=0|0|0|0.66|1|1|3|0|265
chr1_2 exon 31653651 31653989 31653651 ID=Msa0067070-mRNA-1:exon:10441;Parent=Msa0067070-mRNA-1
chr1_2 exon 31653073 31653435 31653073 ID=Msa0067070-mRNA-1:exon:10440;Parent=Msa0067070-mRNA-1
chr1_2 exon 31652135 31652230 31652135 ID=Msa0067070-mRNA-1:exon:10439;Parent=Msa0067070-mRNA-1
chr1_2 CDS 31653651 31653989 31653651 ID=Msa0067070-mRNA-1:cds;Parent=Msa0067070-mRNA-1
chr1_2 CDS 31653073 31653435 31653073 ID=Msa0067070-mRNA-1:cds;Parent=Msa0067070-mRNA-1
chr1_2 CDS 31652135 31652230 31652135 ID=Msa0067070-mRNA-1:cds;Parent=Msa0067070-mRNA-1
Gene Sequence

>Msa0067070

ATGGAAAAAGTTATAAATGGAGAGGATCTTGACCCCTGCGTCAACATTATGTTAGCGTTATCTCCTCCTATGTTTTCAACAATTGGATGGCCCTTTGAAGAGCCAATAACCCATAAACAGCTTCAGGGTCACTTCTACAAAGACAGTACTGATCAATTATTTCATTTTCAGCATCAATTTGAGGCAGAAATTAATTCAACAGATCCCTCACAGTCCACAAGCAGTGACCTTGGCATGGTCAAGAAGCTTGTTCATAATGCTAGTGAACGCGATCGCCGCAAAAAAATCAATAATTTGTATTCCTCACTTCGTTCACTTCTTCCTGTTTCAGATCAAATGAAGAAATTGAGCATTCCGGGAACAATTTCAAAAGTCCTCAAATACATGCTGGAATTACAGAAGCAAGTCGAGGGACTAATTAAGAGAAAGGATGAGATCTTATTGAGACTTTCTCCACAAGTAGATGAGGTGATCATGAACAAAGAATCTCAAAAGAAGAAACATAGTTACAACTCTGGTTTTGTACTTTCAACAAGTAGGCTCAATGATAGTGAAATTACCATTCAGATTTCATGTTACACTGTCCACAAGATTCCACTTTCTGAGATCTTGATATGTTTGGAAAATGATGGCCTTTTGCTACTTAATGTTTCTTCATCTCAGACCTTTGGAGGGAGAGTCTTCTATAATTTGCATTTCCAGGTAGATAAAACACAAAGATTAGAATCCGAAATTCTAAATGAGAAGCTCTTATCAATAATGGATAAGGAAGGGATATTTGAAGTCAACAAAGATTAG

Protein sequence

>Msa0067070

MEKVINGEDLDPCVNIMLALSPPMFSTIGWPFEEPITHKQLQGHFYKDSTDQLFHFQHQFEAEINSTDPSQSTSSDLGMVKKLVHNASERDRRKKINNLYSSLRSLLPVSDQMKKLSIPGTISKVLKYMLELQKQVEGLIKRKDEILLRLSPQVDEVIMNKESQKKKHSYNSGFVLSTSRLNDSEITIQISCYTVHKIPLSEILICLENDGLLLLNVSSSQTFGGRVFYNLHFQVDKTQRLESEILNEKLLSIMDKEGIFEVNKD*