AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0627350


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0627350 MtrunA17_Chr4g0003391 96.063 127 5 0 1 127 1 127 1.07e-77 225
Msa0627350 MtrunA17_Chr2g0333051 52.555 137 48 5 1 123 1 134 4.27e-35 117
Msa0627350 MtrunA17_Chr4g0063791 40.411 146 59 6 5 126 35 176 4.91e-17 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0627350 AT1G52565.1 43.571 140 52 5 1 127 4 129 3.42e-18 75.1
Msa0627350 AT3G15760.1 40.580 138 60 6 1 123 1 131 4.83e-15 67.0

Find 32 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAATATTTGAAGTCCTAA+TGG 0.333607 4_3:+7408901 Msa0627350:three_prime_UTR
GTCATTGATCATCTTAGTTA+TGG 0.371239 4_3:+7408712 Msa0627350:exon
AGAGATAGAGTTCAAAGAAT+GGG 0.376812 4_3:+7408684 Msa0627350:CDS
TACAAAGCAACTCTATTTGC+TGG 0.381833 4_3:-7408648 None:intergenic
TAGAACAAGAAGAAATTAGA+TGG 0.398648 4_3:+7408796 Msa0627350:three_prime_UTR
TTTCTGAATTGGGTGTTTCA+TGG 0.405044 4_3:-7408164 None:intergenic
CTCTTAAAATTGCCAAGAGT+TGG 0.419774 4_3:-7409037 None:intergenic
GCTTGTAGAGGAAAAGAAGA+AGG 0.443148 4_3:+7408491 Msa0627350:intron
TATAAACAAGATCGTAGAAT+AGG 0.444103 4_3:-7408192 None:intergenic
AAAAGGTTGTGAATTTATGA+TGG 0.447654 4_3:+7408930 Msa0627350:three_prime_UTR
AAGAGATAGAGTTCAAAGAA+TGG 0.465347 4_3:+7408683 Msa0627350:CDS
GGTGTTTCATGGAATTGAAA+TGG 0.466904 4_3:-7408153 None:intergenic
AATAGAGTTGCTTTGTACAA+TGG 0.493962 4_3:+7408654 Msa0627350:CDS
GCTTGACTATGTCCAACTCT+TGG 0.517400 4_3:+7409025 Msa0627350:three_prime_UTR
GTGAATTTATGATGGAAGGG+TGG 0.540534 4_3:+7408938 Msa0627350:three_prime_UTR
CATGTTGTGGTTTGAAACAG+AGG 0.556760 4_3:-7408037 None:intergenic
TGAATTTATGATGGAAGGGT+GGG 0.559563 4_3:+7408939 Msa0627350:three_prime_UTR
CTACGATCTTGTTTATACAC+AGG 0.560268 4_3:+7408198 Msa0627350:CDS
GGTTGTGAATTTATGATGGA+AGG 0.562242 4_3:+7408934 Msa0627350:three_prime_UTR
AGTTGAAACAACCATGGCTG+TGG 0.569166 4_3:-7408088 None:intergenic
GAGATAGAGTTCAAAGAATG+GGG 0.570523 4_3:+7408685 Msa0627350:CDS
GTGAGATTGAAGTCATGTTG+TGG 0.573467 4_3:-7408050 None:intergenic
AAGGGTGGGTATTCTTGTGA+AGG 0.586206 4_3:+7408953 Msa0627350:three_prime_UTR
TAGTTATGGAAGTTAGAACA+TGG 0.600995 4_3:+7408726 Msa0627350:three_prime_UTR
GTTGTGAATTTATGATGGAA+GGG 0.606258 4_3:+7408935 Msa0627350:three_prime_UTR
TTAGAACATGGTATAGAACA+TGG 0.610591 4_3:+7408768 Msa0627350:three_prime_UTR
AGTTATGGAAGTTAGAACAT+GGG 0.637332 4_3:+7408727 Msa0627350:three_prime_UTR
TAGAACATGGTATAGAACAT+GGG 0.653391 4_3:+7408769 Msa0627350:three_prime_UTR
AACAGTAGTTGAAACAACCA+TGG 0.660669 4_3:-7408094 None:intergenic
AACATGACTTCAATCTCACA+AGG 0.670440 4_3:+7408054 Msa0627350:exon
AAAGATCTAATGTATTCTTG+TGG 0.676296 4_3:+7408990 Msa0627350:three_prime_UTR
AAACAGAGGAAAGAAAACAG+AGG 0.701650 4_3:-7408023 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATTTTATTTTATTTTTAGA+TGG + chr4_3:7408868-7408887 Msa0627350:three_prime_UTR 10.0%
!!! GATTTTATTTTATTTTTAGA+TGG + chr4_3:7408868-7408887 Msa0627350:three_prime_UTR 10.0%
!!! TTTTTCAGATACTATTCTAT+AGG + chr4_3:7408282-7408301 Msa0627350:intron 20.0%
!! ATGTTTCATACAAAATATTC+AGG - chr4_3:7408440-7408459 None:intergenic 20.0%
!! AAAGAATTTAGAGAAAAACA+GGG + chr4_3:7408564-7408583 Msa0627350:CDS 20.0%
!!! TTTTTCAGATACTATTCTAT+AGG + chr4_3:7408282-7408301 Msa0627350:intron 20.0%
!! ATGTTTCATACAAAATATTC+AGG - chr4_3:7408440-7408459 None:intergenic 20.0%
!! AAAGAATTTAGAGAAAAACA+GGG + chr4_3:7408564-7408583 Msa0627350:CDS 20.0%
!!! ATAGGTTTGTTTTCTGAATT+GGG - chr4_3:7408177-7408196 None:intergenic 25.0%
!!! AATAGGTTTGTTTTCTGAAT+TGG - chr4_3:7408178-7408197 None:intergenic 25.0%
! TATAAACAAGATCGTAGAAT+AGG - chr4_3:7408195-7408214 None:intergenic 25.0%
!! GAAATTTTCAGAAAATGTGA+TGG + chr4_3:7408539-7408558 Msa0627350:CDS 25.0%
! GAAAGAATTTAGAGAAAAAC+AGG + chr4_3:7408563-7408582 Msa0627350:CDS 25.0%
! AAGAATTTAGAGAAAAACAG+GGG + chr4_3:7408565-7408584 Msa0627350:CDS 25.0%
!!! TTTTAAGAGAAGTTAGAACA+TGG + chr4_3:7408756-7408775 Msa0627350:three_prime_UTR 25.0%
! TAGAACAAGAAGAAATTAGA+TGG + chr4_3:7408796-7408815 Msa0627350:three_prime_UTR 25.0%
!! AACAATATTTGAAGTCCTAA+TGG + chr4_3:7408901-7408920 Msa0627350:three_prime_UTR 25.0%
! AAAAGGTTGTGAATTTATGA+TGG + chr4_3:7408930-7408949 Msa0627350:three_prime_UTR 25.0%
! AAAGATCTAATGTATTCTTG+TGG + chr4_3:7408990-7409009 Msa0627350:three_prime_UTR 25.0%
!!! ATAGGTTTGTTTTCTGAATT+GGG - chr4_3:7408177-7408196 None:intergenic 25.0%
!!! AATAGGTTTGTTTTCTGAAT+TGG - chr4_3:7408178-7408197 None:intergenic 25.0%
! TATAAACAAGATCGTAGAAT+AGG - chr4_3:7408195-7408214 None:intergenic 25.0%
!! GAAATTTTCAGAAAATGTGA+TGG + chr4_3:7408539-7408558 Msa0627350:CDS 25.0%
! GAAAGAATTTAGAGAAAAAC+AGG + chr4_3:7408563-7408582 Msa0627350:CDS 25.0%
! AAGAATTTAGAGAAAAACAG+GGG + chr4_3:7408565-7408584 Msa0627350:CDS 25.0%
!!! TTTTAAGAGAAGTTAGAACA+TGG + chr4_3:7408756-7408775 Msa0627350:three_prime_UTR 25.0%
! TAGAACAAGAAGAAATTAGA+TGG + chr4_3:7408796-7408815 Msa0627350:three_prime_UTR 25.0%
!! AACAATATTTGAAGTCCTAA+TGG + chr4_3:7408901-7408920 Msa0627350:three_prime_UTR 25.0%
! AAAAGGTTGTGAATTTATGA+TGG + chr4_3:7408930-7408949 Msa0627350:three_prime_UTR 25.0%
! AAAGATCTAATGTATTCTTG+TGG + chr4_3:7408990-7409009 Msa0627350:three_prime_UTR 25.0%
!!! GTTTTTGTTTTTGCTTGTAG+AGG + chr4_3:7408479-7408498 Msa0627350:intron 30.0%
! AATAGAGTTGCTTTGTACAA+TGG + chr4_3:7408654-7408673 Msa0627350:CDS 30.0%
AAGAGATAGAGTTCAAAGAA+TGG + chr4_3:7408683-7408702 Msa0627350:CDS 30.0%
AGAGATAGAGTTCAAAGAAT+GGG + chr4_3:7408684-7408703 Msa0627350:CDS 30.0%
GTCATTGATCATCTTAGTTA+TGG + chr4_3:7408712-7408731 Msa0627350:exon 30.0%
TAGTTATGGAAGTTAGAACA+TGG + chr4_3:7408726-7408745 Msa0627350:three_prime_UTR 30.0%
AGTTATGGAAGTTAGAACAT+GGG + chr4_3:7408727-7408746 Msa0627350:three_prime_UTR 30.0%
TTAGAACATGGTATAGAACA+TGG + chr4_3:7408768-7408787 Msa0627350:three_prime_UTR 30.0%
TAGAACATGGTATAGAACAT+GGG + chr4_3:7408769-7408788 Msa0627350:three_prime_UTR 30.0%
!!! TTATTTTTAGATGGGTGTGT+TGG + chr4_3:7408877-7408896 Msa0627350:three_prime_UTR 30.0%
! AGTCCTAATGGATCAAAAAA+AGG + chr4_3:7408913-7408932 Msa0627350:three_prime_UTR 30.0%
!!! CAACCTTTTTTTGATCCATT+AGG - chr4_3:7408919-7408938 None:intergenic 30.0%
! GTTGTGAATTTATGATGGAA+GGG + chr4_3:7408935-7408954 Msa0627350:three_prime_UTR 30.0%
!!! GTTTTTGTTTTTGCTTGTAG+AGG + chr4_3:7408479-7408498 Msa0627350:intron 30.0%
! AATAGAGTTGCTTTGTACAA+TGG + chr4_3:7408654-7408673 Msa0627350:CDS 30.0%
AAGAGATAGAGTTCAAAGAA+TGG + chr4_3:7408683-7408702 Msa0627350:CDS 30.0%
AGAGATAGAGTTCAAAGAAT+GGG + chr4_3:7408684-7408703 Msa0627350:CDS 30.0%
GTCATTGATCATCTTAGTTA+TGG + chr4_3:7408712-7408731 Msa0627350:exon 30.0%
TAGTTATGGAAGTTAGAACA+TGG + chr4_3:7408726-7408745 Msa0627350:three_prime_UTR 30.0%
AGTTATGGAAGTTAGAACAT+GGG + chr4_3:7408727-7408746 Msa0627350:three_prime_UTR 30.0%
TTAGAACATGGTATAGAACA+TGG + chr4_3:7408768-7408787 Msa0627350:three_prime_UTR 30.0%
TAGAACATGGTATAGAACAT+GGG + chr4_3:7408769-7408788 Msa0627350:three_prime_UTR 30.0%
!!! TTATTTTTAGATGGGTGTGT+TGG + chr4_3:7408877-7408896 Msa0627350:three_prime_UTR 30.0%
! AGTCCTAATGGATCAAAAAA+AGG + chr4_3:7408913-7408932 Msa0627350:three_prime_UTR 30.0%
!!! CAACCTTTTTTTGATCCATT+AGG - chr4_3:7408919-7408938 None:intergenic 30.0%
! GTTGTGAATTTATGATGGAA+GGG + chr4_3:7408935-7408954 Msa0627350:three_prime_UTR 30.0%
AAACAGAGGAAAGAAAACAG+AGG - chr4_3:7408026-7408045 None:intergenic 35.0%
AACATGACTTCAATCTCACA+AGG + chr4_3:7408054-7408073 Msa0627350:exon 35.0%
AACAGTAGTTGAAACAACCA+TGG - chr4_3:7408097-7408116 None:intergenic 35.0%
GGTGTTTCATGGAATTGAAA+TGG - chr4_3:7408156-7408175 None:intergenic 35.0%
TTTCTGAATTGGGTGTTTCA+TGG - chr4_3:7408167-7408186 None:intergenic 35.0%
! CTACGATCTTGTTTATACAC+AGG + chr4_3:7408198-7408217 Msa0627350:CDS 35.0%
TACAAAGCAACTCTATTTGC+TGG - chr4_3:7408651-7408670 None:intergenic 35.0%
GAGATAGAGTTCAAAGAATG+GGG + chr4_3:7408685-7408704 Msa0627350:CDS 35.0%
! GGTTGTGAATTTATGATGGA+AGG + chr4_3:7408934-7408953 Msa0627350:three_prime_UTR 35.0%
! TGAATTTATGATGGAAGGGT+GGG + chr4_3:7408939-7408958 Msa0627350:three_prime_UTR 35.0%
CTCTTAAAATTGCCAAGAGT+TGG - chr4_3:7409040-7409059 None:intergenic 35.0%
AAACAGAGGAAAGAAAACAG+AGG - chr4_3:7408026-7408045 None:intergenic 35.0%
AACATGACTTCAATCTCACA+AGG + chr4_3:7408054-7408073 Msa0627350:exon 35.0%
AACAGTAGTTGAAACAACCA+TGG - chr4_3:7408097-7408116 None:intergenic 35.0%
GGTGTTTCATGGAATTGAAA+TGG - chr4_3:7408156-7408175 None:intergenic 35.0%
TTTCTGAATTGGGTGTTTCA+TGG - chr4_3:7408167-7408186 None:intergenic 35.0%
! CTACGATCTTGTTTATACAC+AGG + chr4_3:7408198-7408217 Msa0627350:CDS 35.0%
TACAAAGCAACTCTATTTGC+TGG - chr4_3:7408651-7408670 None:intergenic 35.0%
GAGATAGAGTTCAAAGAATG+GGG + chr4_3:7408685-7408704 Msa0627350:CDS 35.0%
! GGTTGTGAATTTATGATGGA+AGG + chr4_3:7408934-7408953 Msa0627350:three_prime_UTR 35.0%
! TGAATTTATGATGGAAGGGT+GGG + chr4_3:7408939-7408958 Msa0627350:three_prime_UTR 35.0%
CTCTTAAAATTGCCAAGAGT+TGG - chr4_3:7409040-7409059 None:intergenic 35.0%
! CATGTTGTGGTTTGAAACAG+AGG - chr4_3:7408040-7408059 None:intergenic 40.0%
GTGAGATTGAAGTCATGTTG+TGG - chr4_3:7408053-7408072 None:intergenic 40.0%
!!! TCTTGTTTTAACCACAGCCA+TGG + chr4_3:7408077-7408096 Msa0627350:CDS 40.0%
GCTTGTAGAGGAAAAGAAGA+AGG + chr4_3:7408491-7408510 Msa0627350:intron 40.0%
! GTGAATTTATGATGGAAGGG+TGG + chr4_3:7408938-7408957 Msa0627350:three_prime_UTR 40.0%
AACAACGTTGTCTTGTGTTG+TGG - chr4_3:7407986-7408005 None:intergenic 40.0%
! CATGTTGTGGTTTGAAACAG+AGG - chr4_3:7408040-7408059 None:intergenic 40.0%
GTGAGATTGAAGTCATGTTG+TGG - chr4_3:7408053-7408072 None:intergenic 40.0%
!!! TCTTGTTTTAACCACAGCCA+TGG + chr4_3:7408077-7408096 Msa0627350:CDS 40.0%
GCTTGTAGAGGAAAAGAAGA+AGG + chr4_3:7408491-7408510 Msa0627350:intron 40.0%
! GTGAATTTATGATGGAAGGG+TGG + chr4_3:7408938-7408957 Msa0627350:three_prime_UTR 40.0%
AGTTGAAACAACCATGGCTG+TGG - chr4_3:7408091-7408110 None:intergenic 45.0%
!! GCTGGCATTGCTTTTGTTTC+TGG - chr4_3:7408633-7408652 None:intergenic 45.0%
AAGGGTGGGTATTCTTGTGA+AGG + chr4_3:7408953-7408972 Msa0627350:three_prime_UTR 45.0%
GCTTGACTATGTCCAACTCT+TGG + chr4_3:7409025-7409044 Msa0627350:three_prime_UTR 45.0%
AGTTGAAACAACCATGGCTG+TGG - chr4_3:7408091-7408110 None:intergenic 45.0%
!! GCTGGCATTGCTTTTGTTTC+TGG - chr4_3:7408633-7408652 None:intergenic 45.0%
AAGGGTGGGTATTCTTGTGA+AGG + chr4_3:7408953-7408972 Msa0627350:three_prime_UTR 45.0%
GCTTGACTATGTCCAACTCT+TGG + chr4_3:7409025-7409044 Msa0627350:three_prime_UTR 45.0%
!!! ATTTTATTTTATTTTTAGAT+GGG + chr4_3:7408869-7408888 Msa0627350:three_prime_UTR 5.0%
!!! ATTTTATTTTATTTTTAGAT+GGG + chr4_3:7408869-7408888 Msa0627350:three_prime_UTR 5.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 7407984 7409076 7407984 ID=Msa0627350;Name=Msa0627350
chr4_3 mRNA 7407984 7409076 7407984 ID=Msa0627350-mRNA-1;Parent=Msa0627350;Name=Msa0627350-mRNA-1;_AED=0.05;_eAED=0.05;_QI=73|1|1|1|1|1|2|357|127
chr4_3 exon 7407984 7408219 7407984 ID=Msa0627350-mRNA-1:exon:2179;Parent=Msa0627350-mRNA-1
chr4_3 exon 7408499 7409076 7408499 ID=Msa0627350-mRNA-1:exon:2180;Parent=Msa0627350-mRNA-1
chr4_3 five_prime_UTR 7407984 7408056 7407984 ID=Msa0627350-mRNA-1:five_prime_utr;Parent=Msa0627350-mRNA-1
chr4_3 CDS 7408057 7408219 7408057 ID=Msa0627350-mRNA-1:cds;Parent=Msa0627350-mRNA-1
chr4_3 CDS 7408499 7408719 7408499 ID=Msa0627350-mRNA-1:cds;Parent=Msa0627350-mRNA-1
chr4_3 three_prime_UTR 7408720 7409076 7408720 ID=Msa0627350-mRNA-1:three_prime_utr;Parent=Msa0627350-mRNA-1
Gene Sequence

>Msa0627350

ATGACTTCAATCTCACAAGGTCTTGTTTTAACCACAGCCATGGTTGTTTCAACTACTGTTCTTTATCTTACTTTCTGTAAACAAAAAAACTCATCACCATTTCAATTCCATGAAACACCCAATTCAGAAAACAAACCTATTCTACGATCTTGTTTATACACAGAGGAAAAGAAGAAGGAAAAATTAAGAAAGAAGAAGAAAGTGAAATTTTCAGAAAATGTGATGGTGAAAGAATTTAGAGAAAAACAGGGGAAGAAAAACAGAGTATCAATTAATGAATGCAGAAATGAAATTCCAGAAACAAAAGCAATGCCAGCAAATAGAGTTGCTTTGTACAATGGAATTTTAAGAGATAGAGTTCAAAGAATGGGGTGTTGTCATTGA

Protein sequence

>Msa0627350

MTSISQGLVLTTAMVVSTTVLYLTFCKQKNSSPFQFHETPNSENKPILRSCLYTEEKKKEKLRKKKKVKFSENVMVKEFREKQGKKNRVSINECRNEIPETKAMPANRVALYNGILRDRVQRMGCCH*