AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0626990


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0626990 MtrunA17_Chr4g0003391 96.063 127 5 0 1 127 1 127 1.07e-77 225
Msa0626990 MtrunA17_Chr2g0333051 52.555 137 48 5 1 123 1 134 4.27e-35 117
Msa0626990 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
Msa0626990 AT1G52565.1 43.571 140 52 5 1 127 4 129 3.42e-18 75.1
Msa0626990 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:-7082754 Msa0626990:three_prime_UTR
GTCATTGATCATCTTAGTTA+TGG 0.371239 4_3:-7082943 Msa0626990:exon
AGAGATAGAGTTCAAAGAAT+GGG 0.376812 4_3:-7082971 Msa0626990:CDS
TACAAAGCAACTCTATTTGC+TGG 0.381833 4_3:+7083007 None:intergenic
TAGAACAAGAAGAAATTAGA+TGG 0.398648 4_3:-7082859 Msa0626990:three_prime_UTR
TTTCTGAATTGGGTGTTTCA+TGG 0.405044 4_3:+7083491 None:intergenic
CTCTTAAAATTGCCAAGAGT+TGG 0.419774 4_3:+7082618 None:intergenic
GCTTGTAGAGGAAAAGAAGA+AGG 0.443148 4_3:-7083164 Msa0626990:intron
TATAAACAAGATCGTAGAAT+AGG 0.444103 4_3:+7083463 None:intergenic
AAAAGGTTGTGAATTTATGA+TGG 0.447654 4_3:-7082725 Msa0626990:three_prime_UTR
AAGAGATAGAGTTCAAAGAA+TGG 0.465347 4_3:-7082972 Msa0626990:CDS
GGTGTTTCATGGAATTGAAA+TGG 0.466904 4_3:+7083502 None:intergenic
AATAGAGTTGCTTTGTACAA+TGG 0.493962 4_3:-7083001 Msa0626990:CDS
GCTTGACTATGTCCAACTCT+TGG 0.517400 4_3:-7082630 Msa0626990:three_prime_UTR
GTGAATTTATGATGGAAGGG+TGG 0.540534 4_3:-7082717 Msa0626990:three_prime_UTR
CATGTTGTGGTTTGAAACAG+AGG 0.556760 4_3:+7083618 None:intergenic
TGAATTTATGATGGAAGGGT+GGG 0.559563 4_3:-7082716 Msa0626990:three_prime_UTR
CTACGATCTTGTTTATACAC+AGG 0.560268 4_3:-7083457 Msa0626990:intron
GGTTGTGAATTTATGATGGA+AGG 0.562242 4_3:-7082721 Msa0626990:three_prime_UTR
AGTTGAAACAACCATGGCTG+TGG 0.569166 4_3:+7083567 None:intergenic
GAGATAGAGTTCAAAGAATG+GGG 0.570523 4_3:-7082970 Msa0626990:CDS
GTGAGATTGAAGTCATGTTG+TGG 0.573467 4_3:+7083605 None:intergenic
AAGGGTGGGTATTCTTGTGA+AGG 0.586206 4_3:-7082702 Msa0626990:three_prime_UTR
TAGTTATGGAAGTTAGAACA+TGG 0.600995 4_3:-7082929 Msa0626990:three_prime_UTR
GTTGTGAATTTATGATGGAA+GGG 0.606258 4_3:-7082720 Msa0626990:three_prime_UTR
TTAGAACATGGTATAGAACA+TGG 0.610591 4_3:-7082887 Msa0626990:three_prime_UTR
AGTTATGGAAGTTAGAACAT+GGG 0.637332 4_3:-7082928 Msa0626990:three_prime_UTR
TAGAACATGGTATAGAACAT+GGG 0.653391 4_3:-7082886 Msa0626990:three_prime_UTR
AACAGTAGTTGAAACAACCA+TGG 0.660669 4_3:+7083561 None:intergenic
AACATGACTTCAATCTCACA+AGG 0.670440 4_3:-7083601 Msa0626990:CDS
AAAGATCTAATGTATTCTTG+TGG 0.676296 4_3:-7082665 Msa0626990:three_prime_UTR
AAACAGAGGAAAGAAAACAG+AGG 0.701650 4_3:+7083632 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATTTTATTTTATTTTTAGA+TGG - chr4_3:7083485-7083504 Msa0626990:CDS 10.0%
!!! GATTTTATTTTATTTTTAGA+TGG - chr4_3:7083485-7083504 Msa0626990:CDS 10.0%
!!! TTTTTCAGATACTATTCTAT+AGG - chr4_3:7082899-7082918 Msa0626990:three_prime_UTR 20.0%
!! ATGTTTCATACAAAATATTC+AGG + chr4_3:7083057-7083076 None:intergenic 20.0%
!! AAAGAATTTAGAGAAAAACA+GGG - chr4_3:7083181-7083200 Msa0626990:intron 20.0%
!!! TTTTTCAGATACTATTCTAT+AGG - chr4_3:7082899-7082918 Msa0626990:three_prime_UTR 20.0%
!! ATGTTTCATACAAAATATTC+AGG + chr4_3:7083057-7083076 None:intergenic 20.0%
!! AAAGAATTTAGAGAAAAACA+GGG - chr4_3:7083181-7083200 Msa0626990:intron 20.0%
!!! ATAGGTTTGTTTTCTGAATT+GGG + chr4_3:7082794-7082813 None:intergenic 25.0%
!!! AATAGGTTTGTTTTCTGAAT+TGG + chr4_3:7082795-7082814 None:intergenic 25.0%
! TATAAACAAGATCGTAGAAT+AGG + chr4_3:7082812-7082831 None:intergenic 25.0%
!! GAAATTTTCAGAAAATGTGA+TGG - chr4_3:7083156-7083175 Msa0626990:CDS 25.0%
! GAAAGAATTTAGAGAAAAAC+AGG - chr4_3:7083180-7083199 Msa0626990:intron 25.0%
! AAGAATTTAGAGAAAAACAG+GGG - chr4_3:7083182-7083201 Msa0626990:intron 25.0%
!!! TTTTAAGAGAAGTTAGAACA+TGG - chr4_3:7083373-7083392 Msa0626990:intron 25.0%
! TAGAACAAGAAGAAATTAGA+TGG - chr4_3:7083413-7083432 Msa0626990:intron 25.0%
!! AACAATATTTGAAGTCCTAA+TGG - chr4_3:7083518-7083537 Msa0626990:CDS 25.0%
! AAAAGGTTGTGAATTTATGA+TGG - chr4_3:7083547-7083566 Msa0626990:CDS 25.0%
! AAAGATCTAATGTATTCTTG+TGG - chr4_3:7083607-7083626 Msa0626990:exon 25.0%
!!! ATAGGTTTGTTTTCTGAATT+GGG + chr4_3:7082794-7082813 None:intergenic 25.0%
!!! AATAGGTTTGTTTTCTGAAT+TGG + chr4_3:7082795-7082814 None:intergenic 25.0%
! TATAAACAAGATCGTAGAAT+AGG + chr4_3:7082812-7082831 None:intergenic 25.0%
!! GAAATTTTCAGAAAATGTGA+TGG - chr4_3:7083156-7083175 Msa0626990:CDS 25.0%
! GAAAGAATTTAGAGAAAAAC+AGG - chr4_3:7083180-7083199 Msa0626990:intron 25.0%
! AAGAATTTAGAGAAAAACAG+GGG - chr4_3:7083182-7083201 Msa0626990:intron 25.0%
!!! TTTTAAGAGAAGTTAGAACA+TGG - chr4_3:7083373-7083392 Msa0626990:intron 25.0%
! TAGAACAAGAAGAAATTAGA+TGG - chr4_3:7083413-7083432 Msa0626990:intron 25.0%
!! AACAATATTTGAAGTCCTAA+TGG - chr4_3:7083518-7083537 Msa0626990:CDS 25.0%
! AAAAGGTTGTGAATTTATGA+TGG - chr4_3:7083547-7083566 Msa0626990:CDS 25.0%
! AAAGATCTAATGTATTCTTG+TGG - chr4_3:7083607-7083626 Msa0626990:exon 25.0%
!!! GTTTTTGTTTTTGCTTGTAG+AGG - chr4_3:7083096-7083115 Msa0626990:CDS 30.0%
! AATAGAGTTGCTTTGTACAA+TGG - chr4_3:7083271-7083290 Msa0626990:intron 30.0%
AAGAGATAGAGTTCAAAGAA+TGG - chr4_3:7083300-7083319 Msa0626990:intron 30.0%
AGAGATAGAGTTCAAAGAAT+GGG - chr4_3:7083301-7083320 Msa0626990:intron 30.0%
GTCATTGATCATCTTAGTTA+TGG - chr4_3:7083329-7083348 Msa0626990:intron 30.0%
TAGTTATGGAAGTTAGAACA+TGG - chr4_3:7083343-7083362 Msa0626990:intron 30.0%
AGTTATGGAAGTTAGAACAT+GGG - chr4_3:7083344-7083363 Msa0626990:intron 30.0%
TTAGAACATGGTATAGAACA+TGG - chr4_3:7083385-7083404 Msa0626990:intron 30.0%
TAGAACATGGTATAGAACAT+GGG - chr4_3:7083386-7083405 Msa0626990:intron 30.0%
!!! TTATTTTTAGATGGGTGTGT+TGG - chr4_3:7083494-7083513 Msa0626990:CDS 30.0%
! AGTCCTAATGGATCAAAAAA+AGG - chr4_3:7083530-7083549 Msa0626990:CDS 30.0%
!!! CAACCTTTTTTTGATCCATT+AGG + chr4_3:7083536-7083555 None:intergenic 30.0%
! GTTGTGAATTTATGATGGAA+GGG - chr4_3:7083552-7083571 Msa0626990:CDS 30.0%
!!! GTTTTTGTTTTTGCTTGTAG+AGG - chr4_3:7083096-7083115 Msa0626990:CDS 30.0%
! AATAGAGTTGCTTTGTACAA+TGG - chr4_3:7083271-7083290 Msa0626990:intron 30.0%
AAGAGATAGAGTTCAAAGAA+TGG - chr4_3:7083300-7083319 Msa0626990:intron 30.0%
AGAGATAGAGTTCAAAGAAT+GGG - chr4_3:7083301-7083320 Msa0626990:intron 30.0%
GTCATTGATCATCTTAGTTA+TGG - chr4_3:7083329-7083348 Msa0626990:intron 30.0%
TAGTTATGGAAGTTAGAACA+TGG - chr4_3:7083343-7083362 Msa0626990:intron 30.0%
AGTTATGGAAGTTAGAACAT+GGG - chr4_3:7083344-7083363 Msa0626990:intron 30.0%
TTAGAACATGGTATAGAACA+TGG - chr4_3:7083385-7083404 Msa0626990:intron 30.0%
TAGAACATGGTATAGAACAT+GGG - chr4_3:7083386-7083405 Msa0626990:intron 30.0%
!!! TTATTTTTAGATGGGTGTGT+TGG - chr4_3:7083494-7083513 Msa0626990:CDS 30.0%
! AGTCCTAATGGATCAAAAAA+AGG - chr4_3:7083530-7083549 Msa0626990:CDS 30.0%
!!! CAACCTTTTTTTGATCCATT+AGG + chr4_3:7083536-7083555 None:intergenic 30.0%
! GTTGTGAATTTATGATGGAA+GGG - chr4_3:7083552-7083571 Msa0626990:CDS 30.0%
AAACAGAGGAAAGAAAACAG+AGG + chr4_3:7082643-7082662 None:intergenic 35.0%
AACATGACTTCAATCTCACA+AGG - chr4_3:7082671-7082690 Msa0626990:three_prime_UTR 35.0%
AACAGTAGTTGAAACAACCA+TGG + chr4_3:7082714-7082733 None:intergenic 35.0%
GGTGTTTCATGGAATTGAAA+TGG + chr4_3:7082773-7082792 None:intergenic 35.0%
TTTCTGAATTGGGTGTTTCA+TGG + chr4_3:7082784-7082803 None:intergenic 35.0%
! CTACGATCTTGTTTATACAC+AGG - chr4_3:7082815-7082834 Msa0626990:three_prime_UTR 35.0%
TACAAAGCAACTCTATTTGC+TGG + chr4_3:7083268-7083287 None:intergenic 35.0%
GAGATAGAGTTCAAAGAATG+GGG - chr4_3:7083302-7083321 Msa0626990:intron 35.0%
! GGTTGTGAATTTATGATGGA+AGG - chr4_3:7083551-7083570 Msa0626990:CDS 35.0%
! TGAATTTATGATGGAAGGGT+GGG - chr4_3:7083556-7083575 Msa0626990:CDS 35.0%
CTCTTAAAATTGCCAAGAGT+TGG + chr4_3:7083657-7083676 None:intergenic 35.0%
AAACAGAGGAAAGAAAACAG+AGG + chr4_3:7082643-7082662 None:intergenic 35.0%
AACATGACTTCAATCTCACA+AGG - chr4_3:7082671-7082690 Msa0626990:three_prime_UTR 35.0%
AACAGTAGTTGAAACAACCA+TGG + chr4_3:7082714-7082733 None:intergenic 35.0%
GGTGTTTCATGGAATTGAAA+TGG + chr4_3:7082773-7082792 None:intergenic 35.0%
TTTCTGAATTGGGTGTTTCA+TGG + chr4_3:7082784-7082803 None:intergenic 35.0%
! CTACGATCTTGTTTATACAC+AGG - chr4_3:7082815-7082834 Msa0626990:three_prime_UTR 35.0%
TACAAAGCAACTCTATTTGC+TGG + chr4_3:7083268-7083287 None:intergenic 35.0%
GAGATAGAGTTCAAAGAATG+GGG - chr4_3:7083302-7083321 Msa0626990:intron 35.0%
! GGTTGTGAATTTATGATGGA+AGG - chr4_3:7083551-7083570 Msa0626990:CDS 35.0%
! TGAATTTATGATGGAAGGGT+GGG - chr4_3:7083556-7083575 Msa0626990:CDS 35.0%
CTCTTAAAATTGCCAAGAGT+TGG + chr4_3:7083657-7083676 None:intergenic 35.0%
! CATGTTGTGGTTTGAAACAG+AGG + chr4_3:7082657-7082676 None:intergenic 40.0%
GTGAGATTGAAGTCATGTTG+TGG + chr4_3:7082670-7082689 None:intergenic 40.0%
!!! TCTTGTTTTAACCACAGCCA+TGG - chr4_3:7082694-7082713 Msa0626990:three_prime_UTR 40.0%
GCTTGTAGAGGAAAAGAAGA+AGG - chr4_3:7083108-7083127 Msa0626990:CDS 40.0%
! GTGAATTTATGATGGAAGGG+TGG - chr4_3:7083555-7083574 Msa0626990:CDS 40.0%
AACAACGTTGTCTTGTGTTG+TGG + chr4_3:7082603-7082622 None:intergenic 40.0%
! CATGTTGTGGTTTGAAACAG+AGG + chr4_3:7082657-7082676 None:intergenic 40.0%
GTGAGATTGAAGTCATGTTG+TGG + chr4_3:7082670-7082689 None:intergenic 40.0%
!!! TCTTGTTTTAACCACAGCCA+TGG - chr4_3:7082694-7082713 Msa0626990:three_prime_UTR 40.0%
GCTTGTAGAGGAAAAGAAGA+AGG - chr4_3:7083108-7083127 Msa0626990:CDS 40.0%
! GTGAATTTATGATGGAAGGG+TGG - chr4_3:7083555-7083574 Msa0626990:CDS 40.0%
AGTTGAAACAACCATGGCTG+TGG + chr4_3:7082708-7082727 None:intergenic 45.0%
!! GCTGGCATTGCTTTTGTTTC+TGG + chr4_3:7083250-7083269 None:intergenic 45.0%
AAGGGTGGGTATTCTTGTGA+AGG - chr4_3:7083570-7083589 Msa0626990:CDS 45.0%
GCTTGACTATGTCCAACTCT+TGG - chr4_3:7083642-7083661 Msa0626990:five_prime_UTR 45.0%
AGTTGAAACAACCATGGCTG+TGG + chr4_3:7082708-7082727 None:intergenic 45.0%
!! GCTGGCATTGCTTTTGTTTC+TGG + chr4_3:7083250-7083269 None:intergenic 45.0%
AAGGGTGGGTATTCTTGTGA+AGG - chr4_3:7083570-7083589 Msa0626990:CDS 45.0%
GCTTGACTATGTCCAACTCT+TGG - chr4_3:7083642-7083661 Msa0626990:five_prime_UTR 45.0%
!!! ATTTTATTTTATTTTTAGAT+GGG - chr4_3:7083486-7083505 Msa0626990:CDS 5.0%
!!! ATTTTATTTTATTTTTAGAT+GGG - chr4_3:7083486-7083505 Msa0626990:CDS 5.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 7082601 7083693 7082601 ID=Msa0626990;Name=Msa0626990
chr4_3 mRNA 7082601 7083693 7082601 ID=Msa0626990-mRNA-1;Parent=Msa0626990;Name=Msa0626990-mRNA-1;_AED=0.05;_eAED=0.05;_QI=73|1|1|1|1|1|2|357|127
chr4_3 exon 7082601 7083178 7082601 ID=Msa0626990-mRNA-1:exon:2047;Parent=Msa0626990-mRNA-1
chr4_3 exon 7083458 7083693 7083458 ID=Msa0626990-mRNA-1:exon:2046;Parent=Msa0626990-mRNA-1
chr4_3 five_prime_UTR 7083621 7083693 7083621 ID=Msa0626990-mRNA-1:five_prime_utr;Parent=Msa0626990-mRNA-1
chr4_3 CDS 7083458 7083620 7083458 ID=Msa0626990-mRNA-1:cds;Parent=Msa0626990-mRNA-1
chr4_3 CDS 7082958 7083178 7082958 ID=Msa0626990-mRNA-1:cds;Parent=Msa0626990-mRNA-1
chr4_3 three_prime_UTR 7082601 7082957 7082601 ID=Msa0626990-mRNA-1:three_prime_utr;Parent=Msa0626990-mRNA-1
Gene Sequence

>Msa0626990

ATGACTTCAATCTCACAAGGTCTTGTTTTAACCACAGCCATGGTTGTTTCAACTACTGTTCTTTATCTTACTTTCTGTAAACAAAAAAACTCATCACCATTTCAATTCCATGAAACACCCAATTCAGAAAACAAACCTATTCTACGATCTTGTTTATACACAGAGGAAAAGAAGAAGGAAAAATTAAGAAAGAAGAAGAAAGTGAAATTTTCAGAAAATGTGATGGTGAAAGAATTTAGAGAAAAACAGGGGAAGAAAAACAGAGTATCAATTAATGAATGCAGAAATGAAATTCCAGAAACAAAAGCAATGCCAGCAAATAGAGTTGCTTTGTACAATGGAATTTTAAGAGATAGAGTTCAAAGAATGGGGTGTTGTCATTGA

Protein sequence

>Msa0626990

MTSISQGLVLTTAMVVSTTVLYLTFCKQKNSSPFQFHETPNSENKPILRSCLYTEEKKKEKLRKKKKVKFSENVMVKEFREKQGKKNRVSINECRNEIPETKAMPANRVALYNGILRDRVQRMGCCH*