AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0501220

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0501220 MtrunA17_Chr3g0138401 95.327 107 5 0 2 108 310 416 1.33e-66 206
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 41 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTTGAACCGTCGGATTTC+TGG 0.144469 3_4:-41867937 None:intergenic
ACCAGCTTTGCAGTAGATTT+TGG 0.210010 3_4:-41867263 None:intergenic
CTTATTTCTGATTATTCATT+GGG 0.297519 3_4:+41868057 Msa0501220:three_prime_UTR
TCTTATTTCTGATTATTCAT+TGG 0.313097 3_4:+41868056 Msa0501220:three_prime_UTR
GATGTTATAATGGCTTTAGC+TGG 0.336522 3_4:+41867206 Msa0501220:CDS
GAAGCTGCTTGGCCTGATTA+AGG 0.341954 3_4:-41868254 None:intergenic
CATAGTGGAGAAAATGAAAC+AGG 0.343306 3_4:+41867302 Msa0501220:CDS
CTAAATCAGCCACCTTAATC+AGG 0.358859 3_4:+41868242 Msa0501220:three_prime_UTR
CAGAAATAAGAGAAAGCTCT+TGG 0.383667 3_4:-41868044 None:intergenic
TATGCAGGCTGATGTTATAA+TGG 0.398803 3_4:+41867196 Msa0501220:exon
ACCAAAATCTACTGCAAAGC+TGG 0.409213 3_4:+41867262 Msa0501220:CDS
TCTATTGACCAACATTTGTA+AGG 0.415789 3_4:-41868303 None:intergenic
CATGGGAAGTTGTCTGCTAC+TGG 0.416162 3_4:+41867359 Msa0501220:CDS
GCACGCTCTTTGGTCTATGC+AGG 0.433348 3_4:+41867181 Msa0501220:exon
GCATTCCCACAAGAGCTTCA+TGG 0.467087 3_4:+41867341 Msa0501220:CDS
ATGAGAAAATTTGACAAAAG+AGG 0.468526 3_4:-41868086 None:intergenic
CATTCCCACAAGAGCTTCAT+GGG 0.469855 3_4:+41867342 Msa0501220:CDS
GGAGTAGATACACGATCAAC+AGG 0.476638 3_4:-41867404 None:intergenic
CTGGGTCAAATGGTGGATCT+TGG 0.478685 3_4:+41867225 Msa0501220:CDS
ATGGCTTTAGCTGGGTCAAA+TGG 0.490826 3_4:+41867215 Msa0501220:CDS
AGAAATAAGAGAAAGCTCTT+GGG 0.490918 3_4:-41868043 None:intergenic
AACTTCCCATGAAGCTCTTG+TGG 0.491396 3_4:-41867347 None:intergenic
ACTTCCCATGAAGCTCTTGT+GGG 0.498210 3_4:-41867346 None:intergenic
GGATCTGCTGCTTGAACCGT+CGG 0.509893 3_4:-41867945 None:intergenic
AATAACAACCTTACAAATGT+TGG 0.511804 3_4:+41868295 Msa0501220:three_prime_UTR
ATTATGTGGGGAGCAAGAGT+AGG 0.524042 3_4:+41868138 Msa0501220:three_prime_UTR
AGTAGGATGATTGTTTAAAG+AGG 0.538914 3_4:+41868155 Msa0501220:three_prime_UTR
GGCAGTTCTAGCCGTGCCGT+TGG 0.541164 3_4:+41867380 Msa0501220:CDS
ATGTTATAATGGCTTTAGCT+GGG 0.549931 3_4:+41867207 Msa0501220:CDS
TATCAAGACAAGAAGCTGCT+TGG 0.550491 3_4:-41868265 None:intergenic
GTCAATAGAATCAGAACGAT+AGG 0.578558 3_4:+41868317 Msa0501220:three_prime_UTR
CCGGTTGTAGGGGCGCATCA+AGG 0.580384 3_4:+41867894 Msa0501220:intron
AACGATAGTAACTTGCATAG+TGG 0.584799 3_4:+41867287 Msa0501220:CDS
GCTTTAGCTGGGTCAAATGG+TGG 0.588269 3_4:+41867218 Msa0501220:CDS
GATCGTGTATCTACTCCAGC+CGG 0.597972 3_4:+41867410 Msa0501220:CDS
TACACGATCAACAGGTCCAA+CGG 0.603243 3_4:-41867396 None:intergenic
GATCAACAGGTCCAACGGCA+CGG 0.605689 3_4:-41867391 None:intergenic
GCTGCTTGGCCTGATTAAGG+TGG 0.658928 3_4:-41868251 None:intergenic
TAAAGATACCAGAAATCCGA+CGG 0.679270 3_4:+41867929 Msa0501220:CDS
AACAGGGTTAGTGAGTAATG+TGG 0.689431 3_4:+41867319 Msa0501220:CDS
ATAGTGGAGAAAATGAAACA+GGG 0.722474 3_4:+41867303 Msa0501220:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTAAATATATTAGAATAT+TGG + chr3_4:41867712-41867731 Msa0501220:intron 10.0%
!!! CATAATCTTTTTTTTTTTTA+AGG - chr3_4:41868124-41868143 None:intergenic 10.0%
!! TAAAAAAAAAAAAGATTATG+TGG + chr3_4:41868124-41868143 Msa0501220:three_prime_UTR 10.0%
!! AAAAAAAAAAAAGATTATGT+GGG + chr3_4:41868125-41868144 Msa0501220:three_prime_UTR 10.0%
!!! ATAATGAATATAACAATTTT+TGG + chr3_4:41868342-41868361 Msa0501220:three_prime_UTR 10.0%
!! TCTAATATATTTAGAAAGAA+AGG - chr3_4:41867708-41867727 None:intergenic 15.0%
!!! TTTTTATGTTCATATTCAAT+GGG + chr3_4:41868017-41868036 Msa0501220:three_prime_UTR 15.0%
!! AAAAAAAAAAAGATTATGTG+GGG + chr3_4:41868126-41868145 Msa0501220:three_prime_UTR 15.0%
!!! GTTTTTATGTTCATATTCAA+TGG + chr3_4:41868016-41868035 Msa0501220:three_prime_UTR 20.0%
!!! TCTTATTTCTGATTATTCAT+TGG + chr3_4:41868056-41868075 Msa0501220:three_prime_UTR 20.0%
!!! CTTATTTCTGATTATTCATT+GGG + chr3_4:41868057-41868076 Msa0501220:three_prime_UTR 20.0%
!!! GCAATATAAGATGTTTTTTA+CGG - chr3_4:41868217-41868236 None:intergenic 20.0%
!!! ACAATTTTTGGTTTAAAAAG+AGG + chr3_4:41868354-41868373 Msa0501220:three_prime_UTR 20.0%
!! TCTTTTAATCACTACCAATT+TGG - chr3_4:41867499-41867518 None:intergenic 25.0%
! AATTCCCCTTAATATGATAT+CGG + chr3_4:41867559-41867578 Msa0501220:intron 25.0%
! AATCAAGAAAATATTCGAGT+TGG - chr3_4:41867768-41867787 None:intergenic 25.0%
!! AGAAGACAAGAATTTTCATA+TGG - chr3_4:41867807-41867826 None:intergenic 25.0%
! TTGATTGATTGCTAAATATC+CGG + chr3_4:41867875-41867894 Msa0501220:intron 25.0%
! ATGAGAAAATTTGACAAAAG+AGG - chr3_4:41868089-41868108 None:intergenic 25.0%
! AATAACAACCTTACAAATGT+TGG + chr3_4:41868295-41868314 Msa0501220:three_prime_UTR 25.0%
!! ATGTTATAATGGCTTTAGCT+GGG + chr3_4:41867207-41867226 Msa0501220:CDS 30.0%
! ATAGTGGAGAAAATGAAACA+GGG + chr3_4:41867303-41867322 Msa0501220:CDS 30.0%
GCATACTACATAGTTTGATT+TGG + chr3_4:41867443-41867462 Msa0501220:intron 30.0%
GTATTATCATACCTCCAAAT+TGG + chr3_4:41867482-41867501 Msa0501220:intron 30.0%
TTTAATCACTACCAATTTGG+AGG - chr3_4:41867496-41867515 None:intergenic 30.0%
TTGTCCGATATCATATTAAG+GGG - chr3_4:41867566-41867585 None:intergenic 30.0%
GTTGTCCGATATCATATTAA+GGG - chr3_4:41867567-41867586 None:intergenic 30.0%
AGTTGTCCGATATCATATTA+AGG - chr3_4:41867568-41867587 None:intergenic 30.0%
! GGATTGTTGAAAGCTAATTT+TGG - chr3_4:41867605-41867624 None:intergenic 30.0%
AAGAAAAGGATGACACAAAA+AGG - chr3_4:41867674-41867693 None:intergenic 30.0%
!! AGAAAATATTCGAGTTGGTA+CGG - chr3_4:41867763-41867782 None:intergenic 30.0%
AGAAATAAGAGAAAGCTCTT+GGG - chr3_4:41868046-41868065 None:intergenic 30.0%
AGTAGGATGATTGTTTAAAG+AGG + chr3_4:41868155-41868174 Msa0501220:three_prime_UTR 30.0%
TCTATTGACCAACATTTGTA+AGG - chr3_4:41868306-41868325 None:intergenic 30.0%
TATGCAGGCTGATGTTATAA+TGG + chr3_4:41867196-41867215 Msa0501220:exon 35.0%
!! GATGTTATAATGGCTTTAGC+TGG + chr3_4:41867206-41867225 Msa0501220:CDS 35.0%
! AACGATAGTAACTTGCATAG+TGG + chr3_4:41867287-41867306 Msa0501220:CDS 35.0%
! CATAGTGGAGAAAATGAAAC+AGG + chr3_4:41867302-41867321 Msa0501220:CDS 35.0%
CAAACTATGTAGTATGCTTG+AGG - chr3_4:41867440-41867459 None:intergenic 35.0%
! ACAAAAAGGATCAGTGGATT+TGG - chr3_4:41867660-41867679 None:intergenic 35.0%
! CATCCTTTTCTTTACCTTAC+TGG + chr3_4:41867682-41867701 Msa0501220:intron 35.0%
TTTAGAAAGAAAGGCCAGTA+AGG - chr3_4:41867699-41867718 None:intergenic 35.0%
!! GAAAATATTCGAGTTGGTAC+GGG - chr3_4:41867762-41867781 None:intergenic 35.0%
ATTGCTAAATATCCGGTTGT+AGG + chr3_4:41867882-41867901 Msa0501220:intron 35.0%
TTGCTAAATATCCGGTTGTA+GGG + chr3_4:41867883-41867902 Msa0501220:intron 35.0%
TAAAGATACCAGAAATCCGA+CGG + chr3_4:41867929-41867948 Msa0501220:CDS 35.0%
CAGAAATAAGAGAAAGCTCT+TGG - chr3_4:41868047-41868066 None:intergenic 35.0%
GTCAATAGAATCAGAACGAT+AGG + chr3_4:41868317-41868336 Msa0501220:three_prime_UTR 35.0%
ACCAAAATCTACTGCAAAGC+TGG + chr3_4:41867262-41867281 Msa0501220:CDS 40.0%
! ACCAGCTTTGCAGTAGATTT+TGG - chr3_4:41867266-41867285 None:intergenic 40.0%
! AACAGGGTTAGTGAGTAATG+TGG + chr3_4:41867319-41867338 Msa0501220:CDS 40.0%
GTAGTATGCTTGAGGATTAC+CGG - chr3_4:41867432-41867451 None:intergenic 40.0%
TACTGCAGACGATATGTTTG+GGG - chr3_4:41867537-41867556 None:intergenic 40.0%
CTACTGCAGACGATATGTTT+GGG - chr3_4:41867538-41867557 None:intergenic 40.0%
ACTACTGCAGACGATATGTT+TGG - chr3_4:41867539-41867558 None:intergenic 40.0%
GATGACACAAAAAGGATCAG+TGG - chr3_4:41867666-41867685 None:intergenic 40.0%
AGGCCAGTAAGGTAAAGAAA+AGG - chr3_4:41867688-41867707 None:intergenic 40.0%
TGCTAAATATCCGGTTGTAG+GGG + chr3_4:41867884-41867903 Msa0501220:intron 40.0%
CTAAATCAGCCACCTTAATC+AGG + chr3_4:41868242-41868261 Msa0501220:three_prime_UTR 40.0%
TATCAAGACAAGAAGCTGCT+TGG - chr3_4:41868268-41868287 None:intergenic 40.0%
! CATGACTTTTGCACGCTCTT+TGG + chr3_4:41867171-41867190 Msa0501220:five_prime_UTR 45.0%
!! ATGGCTTTAGCTGGGTCAAA+TGG + chr3_4:41867215-41867234 Msa0501220:CDS 45.0%
CATTCCCACAAGAGCTTCAT+GGG + chr3_4:41867342-41867361 Msa0501220:CDS 45.0%
ACTTCCCATGAAGCTCTTGT+GGG - chr3_4:41867349-41867368 None:intergenic 45.0%
AACTTCCCATGAAGCTCTTG+TGG - chr3_4:41867350-41867369 None:intergenic 45.0%
TACACGATCAACAGGTCCAA+CGG - chr3_4:41867399-41867418 None:intergenic 45.0%
GGAGTAGATACACGATCAAC+AGG - chr3_4:41867407-41867426 None:intergenic 45.0%
! GCTCTTTTGTCTTCGGAACT+GGG - chr3_4:41867969-41867988 None:intergenic 45.0%
! TCACTGCGCTCTTTTGTCTT+CGG - chr3_4:41867976-41867995 None:intergenic 45.0%
ATTATGTGGGGAGCAAGAGT+AGG + chr3_4:41868138-41868157 Msa0501220:three_prime_UTR 45.0%
GCTTTAGCTGGGTCAAATGG+TGG + chr3_4:41867218-41867237 Msa0501220:CDS 50.0%
!! CTGGGTCAAATGGTGGATCT+TGG + chr3_4:41867225-41867244 Msa0501220:CDS 50.0%
GCATTCCCACAAGAGCTTCA+TGG + chr3_4:41867341-41867360 Msa0501220:CDS 50.0%
CATGGGAAGTTGTCTGCTAC+TGG + chr3_4:41867359-41867378 Msa0501220:CDS 50.0%
GATCGTGTATCTACTCCAGC+CGG + chr3_4:41867410-41867429 Msa0501220:CDS 50.0%
TATGCTTGAGGATTACCGGC+TGG - chr3_4:41867428-41867447 None:intergenic 50.0%
! CGCGCAGTTTTCGATCTCAA+CGG - chr3_4:41867626-41867645 None:intergenic 50.0%
TTGGTACGGGCAAGGTCTAA+AGG - chr3_4:41867749-41867768 None:intergenic 50.0%
!! TATTCGAGTTGGTACGGGCA+AGG - chr3_4:41867757-41867776 None:intergenic 50.0%
TGCTTGAACCGTCGGATTTC+TGG - chr3_4:41867940-41867959 None:intergenic 50.0%
! CGCTCTTTTGTCTTCGGAAC+TGG - chr3_4:41867970-41867989 None:intergenic 50.0%
GAAGCTGCTTGGCCTGATTA+AGG - chr3_4:41868257-41868276 None:intergenic 50.0%
GCACGCTCTTTGGTCTATGC+AGG + chr3_4:41867181-41867200 Msa0501220:exon 55.0%
GATCAACAGGTCCAACGGCA+CGG - chr3_4:41867394-41867413 None:intergenic 55.0%
! GGATCTGCTGCTTGAACCGT+CGG - chr3_4:41867948-41867967 None:intergenic 55.0%
GCTGCTTGGCCTGATTAAGG+TGG - chr3_4:41868254-41868273 None:intergenic 55.0%
CCTTGATGCGCCCCTACAAC+CGG - chr3_4:41867897-41867916 None:intergenic 60.0%
! GGCAGTTCTAGCCGTGCCGT+TGG + chr3_4:41867380-41867399 Msa0501220:CDS 65.0%
! CCGGTTGTAGGGGCGCATCA+AGG + chr3_4:41867894-41867913 Msa0501220:intron 65.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 41867153 41868384 41867153 ID=Msa0501220;Name=Msa0501220
chr3_4 mRNA 41867153 41868384 41867153 ID=Msa0501220-mRNA-1;Parent=Msa0501220;Name=Msa0501220-mRNA-1;_AED=0.00;_eAED=0.00;_QI=44|1|1|1|1|1|2|389|108
chr3_4 exon 41867153 41867431 41867153 ID=Msa0501220-mRNA-1:exon:8810;Parent=Msa0501220-mRNA-1
chr3_4 exon 41867904 41868384 41867904 ID=Msa0501220-mRNA-1:exon:8811;Parent=Msa0501220-mRNA-1
chr3_4 five_prime_UTR 41867153 41867196 41867153 ID=Msa0501220-mRNA-1:five_prime_utr;Parent=Msa0501220-mRNA-1
chr3_4 CDS 41867197 41867431 41867197 ID=Msa0501220-mRNA-1:cds;Parent=Msa0501220-mRNA-1
chr3_4 CDS 41867904 41867995 41867904 ID=Msa0501220-mRNA-1:cds;Parent=Msa0501220-mRNA-1
chr3_4 three_prime_UTR 41867996 41868384 41867996 ID=Msa0501220-mRNA-1:three_prime_utr;Parent=Msa0501220-mRNA-1
Gene Sequence

>Msa0501220

ATGCAGGCTGATGTTATAATGGCTTTAGCTGGGTCAAATGGTGGATCTTGGTCGACAGCATTCTCACCAAAATCTACTGCAAAGCTGGTCAACGATAGTAACTTGCATAGTGGAGAAAATGAAACAGGGTTAGTGAGTAATGTGGCATTCCCACAAGAGCTTCATGGGAAGTTGTCTGCTACTGGCAGTTCTAGCCGTGCCGTTGGACCTGTTGATCGTGTATCTACTCCAGCCGGGGCGCATCAAGGAAGCATTTTTGCTAAAGATACCAGAAATCCGACGGTTCAAGCAGCAGATCCCAGTTCCGAAGACAAAAGAGCGCAGTGA
Protein sequence

>Msa0501220

MQADVIMALAGSNGGSWSTAFSPKSTAKLVNDSNLHSGENETGLVSNVAFPQELHGKLSATGSSSRAVGPVDRVSTPAGAHQGSIFAKDTRNPTVQAADPSSEDKRAQ*