AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0296130

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0296130 MtrunA17_Chr2g0318581 100.000 85 0 0 3 87 159 243 1.55e-54 169
Msa0296130 MtrunA17_Chr4g0048491 73.256 86 22 1 3 87 181 266 6.19e-37 124
Msa0296130 MtrunA17_Chr2g0323731 79.268 82 17 0 3 84 185 266 2.09e-33 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0296130 AT5G54110.1 75.294 85 21 0 3 87 181 265 3.30e-39 130
Msa0296130 AT4G21450.1 74.118 85 22 0 3 87 211 295 1.95e-38 129
Msa0296130 AT4G21450.3 74.118 85 22 0 3 87 230 314 3.57e-38 129
Msa0296130 AT4G05060.1 65.000 80 25 2 3 80 203 281 2.40e-21 85.1

Find 34 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCACGGGACTTGGCCGTTC+TGG 0.241641 2_3:+48994433 None:intergenic
TAATTGCGGCAGGATGTTTC+AGG 0.266270 2_3:-48994618 None:intergenic
TTAGCATTATTTCACAAATA+TGG 0.270986 2_3:+48993844 None:intergenic
TTGTCAAAGTTCTTGTTCTT+TGG 0.278955 2_3:-48993932 Msa0296130:three_prime_UTR
TAGGAAATAAGTTTGGTCTT+TGG 0.283749 2_3:-48994531 Msa0296130:five_prime_UTR
ACGGTGAGCAATTAATTAAT+AGG 0.300694 2_3:-48994550 Msa0296130:five_prime_UTR
AGTTACAGTGGAGCGAATCT+TGG 0.383870 2_3:-48994473 Msa0296130:CDS
TAATTAATAGGAAATAAGTT+TGG 0.414609 2_3:-48994538 Msa0296130:five_prime_UTR
ATGGTAAATCAAGATGTTAT+TGG 0.424631 2_3:-48994017 Msa0296130:three_prime_UTR
TCAAAGTTCTTGTTCTTTGG+AGG 0.435145 2_3:-48993929 Msa0296130:three_prime_UTR
AAAATTTGACTCACGGGACT+TGG 0.453363 2_3:+48994424 None:intergenic
TGAATTGCATCCAAGGTTGA+TGG 0.462903 2_3:+48993981 None:intergenic
CTTGAACTTGCTGCCGAGCC+AGG 0.464176 2_3:+48994097 None:intergenic
CATTATTTCACAAATATGGC+AGG 0.464434 2_3:+48993848 None:intergenic
CGATTTGTCGCCATCAACCT+TGG 0.473613 2_3:-48993991 Msa0296130:three_prime_UTR
AAGAAGCCTGCTGCAGAGAC+AGG 0.477766 2_3:-48994279 Msa0296130:CDS
GTTACAGTGGAGCGAATCTT+GGG 0.480501 2_3:-48994472 Msa0296130:CDS
AATTGCGGCAGGATGTTTCA+GGG 0.503533 2_3:-48994617 None:intergenic
CGAGGACCTGTCTCTGCAGC+AGG 0.506742 2_3:+48994273 None:intergenic
AATGTTTATAGAAAGAAAGA+AGG 0.514218 2_3:-48994128 Msa0296130:intron
GGTCCTCGTGTTGCTGCTGA+AGG 0.516882 2_3:-48994258 Msa0296130:CDS
TATATCTTGAATTGCATCCA+AGG 0.519230 2_3:+48993974 None:intergenic
AAGGTCTTGTCATTGATGAA+TGG 0.524280 2_3:-48994239 Msa0296130:CDS
AGGTCTTGTCATTGATGAAT+GGG 0.532752 2_3:-48994238 Msa0296130:intron
CATGCAGTTTGATGAACAAA+GGG 0.533122 2_3:-48994500 Msa0296130:CDS
CTGATGCTGCAGTTGAAGCT+CGG 0.544153 2_3:-48994302 Msa0296130:CDS
ATTATTTCACAAATATGGCA+GGG 0.566540 2_3:+48993849 None:intergenic
GAAGGGAAAAGTACCTGGCT+CGG 0.581187 2_3:-48994110 Msa0296130:CDS
AGAAAGAAGGGAAAAGTACC+TGG 0.583055 2_3:-48994115 Msa0296130:CDS
TCATGCAGTTTGATGAACAA+AGG 0.592282 2_3:-48994501 Msa0296130:CDS
TCATCAAACTGCATGACAGA+AGG 0.609165 2_3:+48994508 None:intergenic
ATGTTTATAGAAAGAAAGAA+GGG 0.622615 2_3:-48994127 Msa0296130:intron
ACAAAGGGATCTAGTTACAG+TGG 0.658163 2_3:-48994485 Msa0296130:CDS
AGACCTTCAGCAGCAACACG+AGG 0.693217 2_3:+48994255 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATTAATAGGAAATAAGTT+TGG - chr2_3:48993881-48993900 Msa0296130:three_prime_UTR 15.0%
!! TAATTAATAGGAAATAAGTT+TGG - chr2_3:48993881-48993900 Msa0296130:three_prime_UTR 15.0%
!! GATGTGTAATTATAGAAATT+TGG - chr2_3:48994051-48994070 Msa0296130:three_prime_UTR 20.0%
!! TCTTTCTTTCTATAAACATT+TGG + chr2_3:48994291-48994310 None:intergenic 20.0%
!! AATGTTTATAGAAAGAAAGA+AGG - chr2_3:48994291-48994310 Msa0296130:CDS 20.0%
!! ATGTTTATAGAAAGAAAGAA+GGG - chr2_3:48994292-48994311 Msa0296130:CDS 20.0%
!! TTAGCATTATTTCACAAATA+TGG + chr2_3:48994578-48994597 None:intergenic 20.0%
!! GATGTGTAATTATAGAAATT+TGG - chr2_3:48994051-48994070 Msa0296130:three_prime_UTR 20.0%
!! TCTTTCTTTCTATAAACATT+TGG + chr2_3:48994291-48994310 None:intergenic 20.0%
!! AATGTTTATAGAAAGAAAGA+AGG - chr2_3:48994291-48994310 Msa0296130:CDS 20.0%
!! ATGTTTATAGAAAGAAAGAA+GGG - chr2_3:48994292-48994311 Msa0296130:CDS 20.0%
!! TTAGCATTATTTCACAAATA+TGG + chr2_3:48994578-48994597 None:intergenic 20.0%
!! TGCTATTGACAATATTTTCA+CGG - chr2_3:48993850-48993869 Msa0296130:three_prime_UTR 25.0%
!!! TTGTATTTTTAGATCCAGAA+CGG - chr2_3:48993972-48993991 Msa0296130:three_prime_UTR 25.0%
!!! TATAGAAATTTGGTCGTTTT+AGG - chr2_3:48994061-48994080 Msa0296130:exon 25.0%
! AATGGGTATGTAAAATGTTT+AGG - chr2_3:48994198-48994217 Msa0296130:intron 25.0%
! ATGGGTATGTAAAATGTTTA+GGG - chr2_3:48994199-48994218 Msa0296130:intron 25.0%
! AAACATTTGGAGACAATTTA+GGG + chr2_3:48994278-48994297 None:intergenic 25.0%
! TAAACATTTGGAGACAATTT+AGG + chr2_3:48994279-48994298 None:intergenic 25.0%
! ATGGTAAATCAAGATGTTAT+TGG - chr2_3:48994402-48994421 Msa0296130:intron 25.0%
! ATTATTTCACAAATATGGCA+GGG + chr2_3:48994573-48994592 None:intergenic 25.0%
!!! TCATGACCATATCATTTTTT+AGG - chr2_3:48994611-48994630 Msa0296130:five_prime_UTR 25.0%
!! TGCTATTGACAATATTTTCA+CGG - chr2_3:48993850-48993869 Msa0296130:three_prime_UTR 25.0%
!!! TTGTATTTTTAGATCCAGAA+CGG - chr2_3:48993972-48993991 Msa0296130:three_prime_UTR 25.0%
!!! TATAGAAATTTGGTCGTTTT+AGG - chr2_3:48994061-48994080 Msa0296130:exon 25.0%
! AATGGGTATGTAAAATGTTT+AGG - chr2_3:48994198-48994217 Msa0296130:intron 25.0%
! ATGGGTATGTAAAATGTTTA+GGG - chr2_3:48994199-48994218 Msa0296130:intron 25.0%
! AAACATTTGGAGACAATTTA+GGG + chr2_3:48994278-48994297 None:intergenic 25.0%
! TAAACATTTGGAGACAATTT+AGG + chr2_3:48994279-48994298 None:intergenic 25.0%
! ATGGTAAATCAAGATGTTAT+TGG - chr2_3:48994402-48994421 Msa0296130:intron 25.0%
! ATTATTTCACAAATATGGCA+GGG + chr2_3:48994573-48994592 None:intergenic 25.0%
ACGGTGAGCAATTAATTAAT+AGG - chr2_3:48993869-48993888 Msa0296130:three_prime_UTR 30.0%
! TAGGAAATAAGTTTGGTCTT+TGG - chr2_3:48993888-48993907 Msa0296130:three_prime_UTR 30.0%
TTTGCAGAAAATTTGACTCA+CGG + chr2_3:48994005-48994024 None:intergenic 30.0%
TGGGTATGTAAAATGTTTAG+GGG - chr2_3:48994200-48994219 Msa0296130:intron 30.0%
! TAGTGTTTTTCTTCAGAGAA+TGG - chr2_3:48994383-48994402 Msa0296130:intron 30.0%
TATATCTTGAATTGCATCCA+AGG + chr2_3:48994448-48994467 None:intergenic 30.0%
TTGTCAAAGTTCTTGTTCTT+TGG - chr2_3:48994487-48994506 Msa0296130:CDS 30.0%
CATTATTTCACAAATATGGC+AGG + chr2_3:48994574-48994593 None:intergenic 30.0%
ACGGTGAGCAATTAATTAAT+AGG - chr2_3:48993869-48993888 Msa0296130:three_prime_UTR 30.0%
! TAGGAAATAAGTTTGGTCTT+TGG - chr2_3:48993888-48993907 Msa0296130:three_prime_UTR 30.0%
TTTGCAGAAAATTTGACTCA+CGG + chr2_3:48994005-48994024 None:intergenic 30.0%
TGGGTATGTAAAATGTTTAG+GGG - chr2_3:48994200-48994219 Msa0296130:intron 30.0%
! TAGTGTTTTTCTTCAGAGAA+TGG - chr2_3:48994383-48994402 Msa0296130:intron 30.0%
TATATCTTGAATTGCATCCA+AGG + chr2_3:48994448-48994467 None:intergenic 30.0%
TTGTCAAAGTTCTTGTTCTT+TGG - chr2_3:48994487-48994506 Msa0296130:CDS 30.0%
CATTATTTCACAAATATGGC+AGG + chr2_3:48994574-48994593 None:intergenic 30.0%
TCATGCAGTTTGATGAACAA+AGG - chr2_3:48993918-48993937 Msa0296130:three_prime_UTR 35.0%
CATGCAGTTTGATGAACAAA+GGG - chr2_3:48993919-48993938 Msa0296130:three_prime_UTR 35.0%
TTGCAGAAAATTTGACTCAC+GGG + chr2_3:48994004-48994023 None:intergenic 35.0%
!! AATTTGGTCGTTTTAGGCTT+TGG - chr2_3:48994067-48994086 Msa0296130:exon 35.0%
!! AGGCTTTGGAAAAACTGAAA+AGG - chr2_3:48994081-48994100 Msa0296130:CDS 35.0%
! AAGGTCTTGTCATTGATGAA+TGG - chr2_3:48994180-48994199 Msa0296130:intron 35.0%
! AGGTCTTGTCATTGATGAAT+GGG - chr2_3:48994181-48994200 Msa0296130:intron 35.0%
TCAAAGTTCTTGTTCTTTGG+AGG - chr2_3:48994490-48994509 Msa0296130:CDS 35.0%
TCATGCAGTTTGATGAACAA+AGG - chr2_3:48993918-48993937 Msa0296130:three_prime_UTR 35.0%
CATGCAGTTTGATGAACAAA+GGG - chr2_3:48993919-48993938 Msa0296130:three_prime_UTR 35.0%
TTGCAGAAAATTTGACTCAC+GGG + chr2_3:48994004-48994023 None:intergenic 35.0%
!! AATTTGGTCGTTTTAGGCTT+TGG - chr2_3:48994067-48994086 Msa0296130:exon 35.0%
!! AGGCTTTGGAAAAACTGAAA+AGG - chr2_3:48994081-48994100 Msa0296130:CDS 35.0%
! AAGGTCTTGTCATTGATGAA+TGG - chr2_3:48994180-48994199 Msa0296130:intron 35.0%
! AGGTCTTGTCATTGATGAAT+GGG - chr2_3:48994181-48994200 Msa0296130:intron 35.0%
TCAAAGTTCTTGTTCTTTGG+AGG - chr2_3:48994490-48994509 Msa0296130:CDS 35.0%
TCATCAAACTGCATGACAGA+AGG + chr2_3:48993914-48993933 None:intergenic 40.0%
ACAAAGGGATCTAGTTACAG+TGG - chr2_3:48993934-48993953 Msa0296130:three_prime_UTR 40.0%
AAAATTTGACTCACGGGACT+TGG + chr2_3:48993998-48994017 None:intergenic 40.0%
GGAAAAACTGAAAAGGCAGT+TGG - chr2_3:48994088-48994107 Msa0296130:CDS 40.0%
!! AGAAAGAAGGGAAAAGTACC+TGG - chr2_3:48994304-48994323 Msa0296130:CDS 40.0%
TGAATTGCATCCAAGGTTGA+TGG + chr2_3:48994441-48994460 None:intergenic 40.0%
TCATCAAACTGCATGACAGA+AGG + chr2_3:48993914-48993933 None:intergenic 40.0%
ACAAAGGGATCTAGTTACAG+TGG - chr2_3:48993934-48993953 Msa0296130:three_prime_UTR 40.0%
AAAATTTGACTCACGGGACT+TGG + chr2_3:48993998-48994017 None:intergenic 40.0%
GGAAAAACTGAAAAGGCAGT+TGG - chr2_3:48994088-48994107 Msa0296130:CDS 40.0%
!! AGAAAGAAGGGAAAAGTACC+TGG - chr2_3:48994304-48994323 Msa0296130:CDS 40.0%
TGAATTGCATCCAAGGTTGA+TGG + chr2_3:48994441-48994460 None:intergenic 40.0%
AGTTACAGTGGAGCGAATCT+TGG - chr2_3:48993946-48993965 Msa0296130:three_prime_UTR 45.0%
GTTACAGTGGAGCGAATCTT+GGG - chr2_3:48993947-48993966 Msa0296130:three_prime_UTR 45.0%
AGTTACAGTGGAGCGAATCT+TGG - chr2_3:48993946-48993965 Msa0296130:three_prime_UTR 45.0%
GTTACAGTGGAGCGAATCTT+GGG - chr2_3:48993947-48993966 Msa0296130:three_prime_UTR 45.0%
CTGATGCTGCAGTTGAAGCT+CGG - chr2_3:48994117-48994136 Msa0296130:CDS 50.0%
!! GAAGGGAAAAGTACCTGGCT+CGG - chr2_3:48994309-48994328 Msa0296130:CDS 50.0%
CGATTTGTCGCCATCAACCT+TGG - chr2_3:48994428-48994447 Msa0296130:intron 50.0%
CTGATGCTGCAGTTGAAGCT+CGG - chr2_3:48994117-48994136 Msa0296130:CDS 50.0%
!! GAAGGGAAAAGTACCTGGCT+CGG - chr2_3:48994309-48994328 Msa0296130:CDS 50.0%
CGATTTGTCGCCATCAACCT+TGG - chr2_3:48994428-48994447 Msa0296130:intron 50.0%
AAGAAGCCTGCTGCAGAGAC+AGG - chr2_3:48994140-48994159 Msa0296130:intron 55.0%
AGACCTTCAGCAGCAACACG+AGG + chr2_3:48994167-48994186 None:intergenic 55.0%
AAGAAGCCTGCTGCAGAGAC+AGG - chr2_3:48994140-48994159 Msa0296130:intron 55.0%
AGACCTTCAGCAGCAACACG+AGG + chr2_3:48994167-48994186 None:intergenic 55.0%
! GGTCCTCGTGTTGCTGCTGA+AGG - chr2_3:48994161-48994180 Msa0296130:intron 60.0%
!! CTTGAACTTGCTGCCGAGCC+AGG + chr2_3:48994325-48994344 None:intergenic 60.0%
! GGTCCTCGTGTTGCTGCTGA+AGG - chr2_3:48994161-48994180 Msa0296130:intron 60.0%
!! CTTGAACTTGCTGCCGAGCC+AGG + chr2_3:48994325-48994344 None:intergenic 60.0%
CTCACGGGACTTGGCCGTTC+TGG + chr2_3:48993989-48994008 None:intergenic 65.0%
CGAGGACCTGTCTCTGCAGC+AGG + chr2_3:48994149-48994168 None:intergenic 65.0%
CTCACGGGACTTGGCCGTTC+TGG + chr2_3:48993989-48994008 None:intergenic 65.0%
CGAGGACCTGTCTCTGCAGC+AGG + chr2_3:48994149-48994168 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 48993811 48994630 48993811 ID=Msa0296130;Name=Msa0296130
chr2_3 mRNA 48993811 48994630 48993811 ID=Msa0296130-mRNA-1;Parent=Msa0296130;Name=Msa0296130-mRNA-1;_AED=0.17;_eAED=0.17;_QI=109|1|1|1|0.5|0.66|3|269|87
chr2_3 exon 48993811 48994139 48993811 ID=Msa0296130-mRNA-1:exon:15511;Parent=Msa0296130-mRNA-1
chr2_3 exon 48994239 48994358 48994239 ID=Msa0296130-mRNA-1:exon:15510;Parent=Msa0296130-mRNA-1
chr2_3 exon 48994438 48994630 48994438 ID=Msa0296130-mRNA-1:exon:15509;Parent=Msa0296130-mRNA-1
chr2_3 five_prime_UTR 48994522 48994630 48994522 ID=Msa0296130-mRNA-1:five_prime_utr;Parent=Msa0296130-mRNA-1
chr2_3 CDS 48994438 48994521 48994438 ID=Msa0296130-mRNA-1:cds;Parent=Msa0296130-mRNA-1
chr2_3 CDS 48994239 48994358 48994239 ID=Msa0296130-mRNA-1:cds;Parent=Msa0296130-mRNA-1
chr2_3 CDS 48994080 48994139 48994080 ID=Msa0296130-mRNA-1:cds;Parent=Msa0296130-mRNA-1
chr2_3 three_prime_UTR 48993811 48994079 48993811 ID=Msa0296130-mRNA-1:three_prime_utr;Parent=Msa0296130-mRNA-1
Gene Sequence

>Msa0296130

ATGCAGTTTGATGAACAAAGGGATCTAGTTACAGTGGAGCGAATCTTGGGAGTTGTATTTTTAGATCCAGAACGGCCAAGTCCCGCTTTGGAAAAACTGAAAAGGCAGTTGGCTGAAGCTGATGCTGCAGTTGAAGCTCGGAAGAAGCCTGCTGCAGAGACAGGTCCTCGTGTTGCTGCTGAAGGTCTTGTCATTGATGAATGGAAAGAAAGAAGGGAAAAGTACCTGGCTCGGCAGCAAGTTCAAGCAGTAGATACAGTGTAA
Protein sequence

>Msa0296130

MQFDEQRDLVTVERILGVVFLDPERPSPALEKLKRQLAEADAAVEARKKPAAETGPRVAAEGLVIDEWKERREKYLARQQVQAVDTV*