AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0505620


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0505620 MtrunA17_Chr3g0106861 83.544 158 10 1 1 142 1 158 1.60e-91 262
Msa0505620 MtrunA17_Chr5g0437991 44.737 152 70 2 1 138 25 176 5.37e-34 117
Msa0505620 MtrunA17_Chr7g0244441 45.528 123 50 3 28 135 7 127 5.03e-24 90.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0505620 AT3G56220.1 41.176 153 75 2 1 138 1 153 7.44e-33 114
Msa0505620 AT2G40435.1 40.909 154 75 3 1 139 1 153 4.57e-31 109
Msa0505620 AT3G56220.2 47.154 123 64 1 1 122 1 123 9.82e-30 105
Msa0505620 AT2G40435.2 43.750 128 69 2 1 126 1 127 4.45e-27 98.2
Msa0505620 AT2G40435.3 43.411 129 70 2 1 127 1 128 5.62e-27 98.2

Find 32 sgRNAs with CRISPR-Local

Find 115 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTACAAAGCCCTCTTCTTT+TGG 0.297287 3_4:-51216795 None:intergenic
AGTTGCAACATCAACTAAAA+TGG 0.297879 3_4:+51216505 Msa0505620:CDS
TTGAGTTTCCCTTGTTGTTA+AGG 0.336259 3_4:+51217318 Msa0505620:three_prime_UTR
TAGTAAAACCTCCGTAATAT+TGG 0.370604 3_4:+51216424 Msa0505620:CDS
TGTGAGAGAGAGAGTGAGAA+TGG 0.379871 3_4:+51216184 None:intergenic
TGTCTCAAGCTATTCAAAAC+TGG 0.409559 3_4:+51217208 Msa0505620:CDS
AGGATTGCTAGTGTTCATAT+TGG 0.440392 3_4:+51216845 Msa0505620:CDS
TTCAAGACCCAGCTCTTCAA+TGG 0.441356 3_4:-51216871 None:intergenic
TTGATGTTGCAACTTGTAAC+GGG 0.455870 3_4:-51216496 None:intergenic
GTCTTGAAGTGCTCGAGGCT+AGG 0.471261 3_4:+51216886 Msa0505620:CDS
ATTGGAAGCCATTGAAGAGC+TGG 0.474257 3_4:+51216863 Msa0505620:CDS
TCTTGAAGTGCTCGAGGCTA+GGG 0.480065 3_4:+51216887 Msa0505620:CDS
AGCTGTTCTCTTGTGAACCT+TGG 0.501707 3_4:-51216210 None:intergenic
GTTGATGTTGCAACTTGTAA+CGG 0.518123 3_4:-51216497 None:intergenic
TCAACTAATTGTGCATTCAA+AGG 0.526427 3_4:-51217177 None:intergenic
GAGAGTGAGAATGGTTTCCA+AGG 0.528898 3_4:+51216193 Msa0505620:exon
ATGAGTGAAAAGAGATGTCA+AGG 0.549501 3_4:+51216825 Msa0505620:CDS
TAAAGTTGAACCAAAAGAAG+AGG 0.570672 3_4:+51216785 Msa0505620:CDS
CTCAAGCTATTCAAAACTGG+AGG 0.571158 3_4:+51217211 Msa0505620:CDS
TGACAATGATGCTACGCCTA+AGG 0.573738 3_4:+51216529 Msa0505620:CDS
TGATTGAACGTAGAAGATGT+AGG 0.579806 3_4:-51216244 None:intergenic
GTTCAACATATTCATGACAA+AGG 0.582081 3_4:-51217365 None:intergenic
AAAGTTGAACCAAAAGAAGA+GGG 0.591604 3_4:+51216786 Msa0505620:CDS
TATAAGAATAATCACCGAAG+TGG 0.597896 3_4:-51216273 None:intergenic
TTGGAAGCCATTGAAGAGCT+GGG 0.599149 3_4:+51216864 Msa0505620:CDS
TGCAAAAGTCCTTAACAACA+AGG 0.624345 3_4:-51217327 None:intergenic
AGAAGAGGGCTTTGTAATCG+AGG 0.630502 3_4:+51216800 Msa0505620:CDS
TCAAGCTATTCAAAACTGGA+GGG 0.633417 3_4:+51217212 Msa0505620:CDS
TTCAATCATACACTCCACTT+CGG 0.634345 3_4:+51216259 Msa0505620:CDS
GCTGGGTCTTGAAGTGCTCG+AGG 0.649444 3_4:+51216881 Msa0505620:CDS
GCAAAAGTCCTTAACAACAA+GGG 0.659973 3_4:-51217326 None:intergenic
TGTTGCATCCAATATTACGG+AGG 0.660873 3_4:-51216432 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATCAATAAAAACAAAAA+AGG + chr3_4:51216683-51216702 Msa0505620:intron 10.0%
!! AAAATCAATAAAAACAAAAA+AGG + chr3_4:51216683-51216702 Msa0505620:intron 10.0%
!!! ATCTTTGAAACATATTTTTA+AGG + chr3_4:51217097-51217116 Msa0505620:intron 15.0%
!!! ATCTTTGAAACATATTTTTA+AGG + chr3_4:51217097-51217116 Msa0505620:intron 15.0%
!! TAAAACAAGGAAGAAAAAAA+CGG - chr3_4:51216325-51216344 None:intergenic 20.0%
!!! TTTAAGTTTAAGAGATAACA+AGG + chr3_4:51216627-51216646 Msa0505620:intron 20.0%
!! TTAAGTTTAAGAGATAACAA+GGG + chr3_4:51216628-51216647 Msa0505620:intron 20.0%
!!! TTTTGTATTGTGTCAAATAT+TGG - chr3_4:51216659-51216678 None:intergenic 20.0%
!!! GTAATTTTATATATTGTAGC+AGG + chr3_4:51217134-51217153 Msa0505620:intron 20.0%
!! TAAAACAAGGAAGAAAAAAA+CGG - chr3_4:51216325-51216344 None:intergenic 20.0%
!!! TTTAAGTTTAAGAGATAACA+AGG + chr3_4:51216627-51216646 Msa0505620:intron 20.0%
!! TTAAGTTTAAGAGATAACAA+GGG + chr3_4:51216628-51216647 Msa0505620:intron 20.0%
!!! TTTTGTATTGTGTCAAATAT+TGG - chr3_4:51216659-51216678 None:intergenic 20.0%
!!! GTAATTTTATATATTGTAGC+AGG + chr3_4:51217134-51217153 Msa0505620:intron 20.0%
! ACAAAAGATGAGTTAAAACA+AGG - chr3_4:51216338-51216357 None:intergenic 25.0%
! ATGATGCAAAGTAAATATAG+AGG - chr3_4:51216376-51216395 None:intergenic 25.0%
! TCTATATTTACTTTGCATCA+TGG + chr3_4:51216375-51216394 Msa0505620:intron 25.0%
!! TTTTGTTGCATCCAATATTA+CGG - chr3_4:51216438-51216457 None:intergenic 25.0%
! ATTTATGAACATGTTACCTT+AGG - chr3_4:51216548-51216567 None:intergenic 25.0%
! TAAGTTTAAGAGATAACAAG+GGG + chr3_4:51216629-51216648 Msa0505620:intron 25.0%
!! TTTCTTGTTTATGTCCAAAA+AGG - chr3_4:51216723-51216742 None:intergenic 25.0%
!!! TTGCAATTTGAAGGTTTTAT+AGG - chr3_4:51217041-51217060 None:intergenic 25.0%
!!! AGTTCTAAATTGCAATTTGA+AGG - chr3_4:51217050-51217069 None:intergenic 25.0%
! TGTTGAACTTAAAATACTTG+CGG + chr3_4:51217380-51217399 Msa0505620:three_prime_UTR 25.0%
! ACAAAAGATGAGTTAAAACA+AGG - chr3_4:51216338-51216357 None:intergenic 25.0%
! ATGATGCAAAGTAAATATAG+AGG - chr3_4:51216376-51216395 None:intergenic 25.0%
! TCTATATTTACTTTGCATCA+TGG + chr3_4:51216375-51216394 Msa0505620:intron 25.0%
!! TTTTGTTGCATCCAATATTA+CGG - chr3_4:51216438-51216457 None:intergenic 25.0%
! ATTTATGAACATGTTACCTT+AGG - chr3_4:51216548-51216567 None:intergenic 25.0%
! TAAGTTTAAGAGATAACAAG+GGG + chr3_4:51216629-51216648 Msa0505620:intron 25.0%
!! TTTCTTGTTTATGTCCAAAA+AGG - chr3_4:51216723-51216742 None:intergenic 25.0%
!!! TTGCAATTTGAAGGTTTTAT+AGG - chr3_4:51217041-51217060 None:intergenic 25.0%
!!! AGTTCTAAATTGCAATTTGA+AGG - chr3_4:51217050-51217069 None:intergenic 25.0%
TATAAGAATAATCACCGAAG+TGG - chr3_4:51216276-51216295 None:intergenic 30.0%
GTGATTCGAATTATAGAAAG+AGG - chr3_4:51216301-51216320 None:intergenic 30.0%
TAGTAAAACCTCCGTAATAT+TGG + chr3_4:51216424-51216443 Msa0505620:CDS 30.0%
AGTTGCAACATCAACTAAAA+TGG + chr3_4:51216505-51216524 Msa0505620:CDS 30.0%
ACGAAACAATTCATATGATG+CGG + chr3_4:51216582-51216601 Msa0505620:intron 30.0%
TAAAGTTGAACCAAAAGAAG+AGG + chr3_4:51216785-51216804 Msa0505620:CDS 30.0%
AAAGTTGAACCAAAAGAAGA+GGG + chr3_4:51216786-51216805 Msa0505620:CDS 30.0%
TCAACTAATTGTGCATTCAA+AGG - chr3_4:51217180-51217199 None:intergenic 30.0%
GTTCAACATATTCATGACAA+AGG - chr3_4:51217368-51217387 None:intergenic 30.0%
TATAAGAATAATCACCGAAG+TGG - chr3_4:51216276-51216295 None:intergenic 30.0%
GTGATTCGAATTATAGAAAG+AGG - chr3_4:51216301-51216320 None:intergenic 30.0%
TAGTAAAACCTCCGTAATAT+TGG + chr3_4:51216424-51216443 Msa0505620:CDS 30.0%
AGTTGCAACATCAACTAAAA+TGG + chr3_4:51216505-51216524 Msa0505620:CDS 30.0%
ACGAAACAATTCATATGATG+CGG + chr3_4:51216582-51216601 Msa0505620:intron 30.0%
TAAAGTTGAACCAAAAGAAG+AGG + chr3_4:51216785-51216804 Msa0505620:CDS 30.0%
AAAGTTGAACCAAAAGAAGA+GGG + chr3_4:51216786-51216805 Msa0505620:CDS 30.0%
TCAACTAATTGTGCATTCAA+AGG - chr3_4:51217180-51217199 None:intergenic 30.0%
GTTCAACATATTCATGACAA+AGG - chr3_4:51217368-51217387 None:intergenic 30.0%
TGATTGAACGTAGAAGATGT+AGG - chr3_4:51216247-51216266 None:intergenic 35.0%
TTCAATCATACACTCCACTT+CGG + chr3_4:51216259-51216278 Msa0505620:CDS 35.0%
TTGATGTTGCAACTTGTAAC+GGG - chr3_4:51216499-51216518 None:intergenic 35.0%
GTTGATGTTGCAACTTGTAA+CGG - chr3_4:51216500-51216519 None:intergenic 35.0%
! AAGACATTCCTTGACCTTTT+TGG + chr3_4:51216706-51216725 Msa0505620:intron 35.0%
GTTTATGTCCAAAAAGGTCA+AGG - chr3_4:51216717-51216736 None:intergenic 35.0%
! ATTACAAAGCCCTCTTCTTT+TGG - chr3_4:51216798-51216817 None:intergenic 35.0%
ATGAGTGAAAAGAGATGTCA+AGG + chr3_4:51216825-51216844 Msa0505620:CDS 35.0%
AGGATTGCTAGTGTTCATAT+TGG + chr3_4:51216845-51216864 Msa0505620:CDS 35.0%
!! TGTTGATAACTTCTCCTTAG+AGG + chr3_4:51216917-51216936 Msa0505620:intron 35.0%
TGTCTCAAGCTATTCAAAAC+TGG + chr3_4:51217208-51217227 Msa0505620:CDS 35.0%
TCAAGCTATTCAAAACTGGA+GGG + chr3_4:51217212-51217231 Msa0505620:CDS 35.0%
!! TTGAGTTTCCCTTGTTGTTA+AGG + chr3_4:51217318-51217337 Msa0505620:three_prime_UTR 35.0%
GCAAAAGTCCTTAACAACAA+GGG - chr3_4:51217329-51217348 None:intergenic 35.0%
TGCAAAAGTCCTTAACAACA+AGG - chr3_4:51217330-51217349 None:intergenic 35.0%
! TGTTGTTAAGGACTTTTGCA+TGG + chr3_4:51217330-51217349 Msa0505620:three_prime_UTR 35.0%
TGATTGAACGTAGAAGATGT+AGG - chr3_4:51216247-51216266 None:intergenic 35.0%
TTCAATCATACACTCCACTT+CGG + chr3_4:51216259-51216278 Msa0505620:CDS 35.0%
TTGATGTTGCAACTTGTAAC+GGG - chr3_4:51216499-51216518 None:intergenic 35.0%
GTTGATGTTGCAACTTGTAA+CGG - chr3_4:51216500-51216519 None:intergenic 35.0%
! AAGACATTCCTTGACCTTTT+TGG + chr3_4:51216706-51216725 Msa0505620:intron 35.0%
GTTTATGTCCAAAAAGGTCA+AGG - chr3_4:51216717-51216736 None:intergenic 35.0%
! ATTACAAAGCCCTCTTCTTT+TGG - chr3_4:51216798-51216817 None:intergenic 35.0%
ATGAGTGAAAAGAGATGTCA+AGG + chr3_4:51216825-51216844 Msa0505620:CDS 35.0%
AGGATTGCTAGTGTTCATAT+TGG + chr3_4:51216845-51216864 Msa0505620:CDS 35.0%
!! TGTTGATAACTTCTCCTTAG+AGG + chr3_4:51216917-51216936 Msa0505620:intron 35.0%
TGTCTCAAGCTATTCAAAAC+TGG + chr3_4:51217208-51217227 Msa0505620:CDS 35.0%
TCAAGCTATTCAAAACTGGA+GGG + chr3_4:51217212-51217231 Msa0505620:CDS 35.0%
!! TTGAGTTTCCCTTGTTGTTA+AGG + chr3_4:51217318-51217337 Msa0505620:three_prime_UTR 35.0%
GCAAAAGTCCTTAACAACAA+GGG - chr3_4:51217329-51217348 None:intergenic 35.0%
TGCAAAAGTCCTTAACAACA+AGG - chr3_4:51217330-51217349 None:intergenic 35.0%
! TGTTGTTAAGGACTTTTGCA+TGG + chr3_4:51217330-51217349 Msa0505620:three_prime_UTR 35.0%
TGTTGCATCCAATATTACGG+AGG - chr3_4:51216435-51216454 None:intergenic 40.0%
!!! TTTTAAGGTATCACTGACGC+AGG + chr3_4:51217112-51217131 Msa0505620:intron 40.0%
CTCAAGCTATTCAAAACTGG+AGG + chr3_4:51217211-51217230 Msa0505620:CDS 40.0%
TGTTGCATCCAATATTACGG+AGG - chr3_4:51216435-51216454 None:intergenic 40.0%
!!! TTTTAAGGTATCACTGACGC+AGG + chr3_4:51217112-51217131 Msa0505620:intron 40.0%
CTCAAGCTATTCAAAACTGG+AGG + chr3_4:51217211-51217230 Msa0505620:CDS 40.0%
GAGAGTGAGAATGGTTTCCA+AGG + chr3_4:51216193-51216212 Msa0505620:exon 45.0%
AGCTGTTCTCTTGTGAACCT+TGG - chr3_4:51216213-51216232 None:intergenic 45.0%
TGACAATGATGCTACGCCTA+AGG + chr3_4:51216529-51216548 Msa0505620:CDS 45.0%
! AGAAGAGGGCTTTGTAATCG+AGG + chr3_4:51216800-51216819 Msa0505620:CDS 45.0%
ATTGGAAGCCATTGAAGAGC+TGG + chr3_4:51216863-51216882 Msa0505620:CDS 45.0%
TTGGAAGCCATTGAAGAGCT+GGG + chr3_4:51216864-51216883 Msa0505620:CDS 45.0%
TTCAAGACCCAGCTCTTCAA+TGG - chr3_4:51216874-51216893 None:intergenic 45.0%
AACTTCTCCTTAGAGGCTGT+TGG + chr3_4:51216924-51216943 Msa0505620:intron 45.0%
ACTTCTCCTTAGAGGCTGTT+GGG + chr3_4:51216925-51216944 Msa0505620:intron 45.0%
TTTGTTCCCAACAGCCTCTA+AGG - chr3_4:51216934-51216953 None:intergenic 45.0%
GAGAGTGAGAATGGTTTCCA+AGG + chr3_4:51216193-51216212 Msa0505620:exon 45.0%
AGCTGTTCTCTTGTGAACCT+TGG - chr3_4:51216213-51216232 None:intergenic 45.0%
TGACAATGATGCTACGCCTA+AGG + chr3_4:51216529-51216548 Msa0505620:CDS 45.0%
! AGAAGAGGGCTTTGTAATCG+AGG + chr3_4:51216800-51216819 Msa0505620:CDS 45.0%
ATTGGAAGCCATTGAAGAGC+TGG + chr3_4:51216863-51216882 Msa0505620:CDS 45.0%
TTGGAAGCCATTGAAGAGCT+GGG + chr3_4:51216864-51216883 Msa0505620:CDS 45.0%
TTCAAGACCCAGCTCTTCAA+TGG - chr3_4:51216874-51216893 None:intergenic 45.0%
AACTTCTCCTTAGAGGCTGT+TGG + chr3_4:51216924-51216943 Msa0505620:intron 45.0%
ACTTCTCCTTAGAGGCTGTT+GGG + chr3_4:51216925-51216944 Msa0505620:intron 45.0%
TTTGTTCCCAACAGCCTCTA+AGG - chr3_4:51216934-51216953 None:intergenic 45.0%
! TCTTGAAGTGCTCGAGGCTA+GGG + chr3_4:51216887-51216906 Msa0505620:CDS 50.0%
! TCTTGAAGTGCTCGAGGCTA+GGG + chr3_4:51216887-51216906 Msa0505620:CDS 50.0%
! GTCTTGAAGTGCTCGAGGCT+AGG + chr3_4:51216886-51216905 Msa0505620:CDS 55.0%
! GTCTTGAAGTGCTCGAGGCT+AGG + chr3_4:51216886-51216905 Msa0505620:CDS 55.0%
! GCTGGGTCTTGAAGTGCTCG+AGG + chr3_4:51216881-51216900 Msa0505620:CDS 60.0%
! GCTGGGTCTTGAAGTGCTCG+AGG + chr3_4:51216881-51216900 Msa0505620:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 51216187 51217401 51216187 ID=Msa0505620;Name=Msa0505620
chr3_4 mRNA 51216187 51217401 51216187 ID=Msa0505620-mRNA-1;Parent=Msa0505620;Name=Msa0505620-mRNA-1;_AED=0.12;_eAED=0.12;_QI=16|0.66|0.5|1|0.66|0.75|4|150|142
chr3_4 exon 51216187 51216280 51216187 ID=Msa0505620-mRNA-1:exon:11187;Parent=Msa0505620-mRNA-1
chr3_4 exon 51216422 51216550 51216422 ID=Msa0505620-mRNA-1:exon:11188;Parent=Msa0505620-mRNA-1
chr3_4 exon 51216783 51216908 51216783 ID=Msa0505620-mRNA-1:exon:11189;Parent=Msa0505620-mRNA-1
chr3_4 exon 51217156 51217401 51217156 ID=Msa0505620-mRNA-1:exon:11190;Parent=Msa0505620-mRNA-1
chr3_4 five_prime_UTR 51216187 51216202 51216187 ID=Msa0505620-mRNA-1:five_prime_utr;Parent=Msa0505620-mRNA-1
chr3_4 CDS 51216203 51216280 51216203 ID=Msa0505620-mRNA-1:cds;Parent=Msa0505620-mRNA-1
chr3_4 CDS 51216422 51216550 51216422 ID=Msa0505620-mRNA-1:cds;Parent=Msa0505620-mRNA-1
chr3_4 CDS 51216783 51216908 51216783 ID=Msa0505620-mRNA-1:cds;Parent=Msa0505620-mRNA-1
chr3_4 CDS 51217156 51217251 51217156 ID=Msa0505620-mRNA-1:cds;Parent=Msa0505620-mRNA-1
chr3_4 three_prime_UTR 51217252 51217401 51217252 ID=Msa0505620-mRNA-1:three_prime_utr;Parent=Msa0505620-mRNA-1
Gene Sequence

>Msa0505620

ATGGTTTCCAAGGTTCACAAGAGAACAGCTATGTACAGAAACCTACATCTTCTACGTTCAATCATACACTCCACTTCGCATAGTAAAACCTCCGTAATATTGGATGCAACAAAATATATACGAGATTTAAAGCAAAAACTTGAAGAACTAAACCCGTTACAAGTTGCAACATCAACTAAAATGGTTGACAATGATGCTACGCCTAAGATTAAAGTTGAACCAAAAGAAGAGGGCTTTGTAATCGAGGTGATGAGTGAAAAGAGATGTCAAGGATTGCTAGTGTTCATATTGGAAGCCATTGAAGAGCTGGGTCTTGAAGTGCTCGAGGCTAGGGAGAAGAATGAAGATACTTGTCCTTTGAATGCACAATTAGTTGAACAAGTAGTGTCTCAAGCTATTCAAAACTGGAGGGAAGTTACACAACAATGA

Protein sequence

>Msa0505620

MVSKVHKRTAMYRNLHLLRSIIHSTSHSKTSVILDATKYIRDLKQKLEELNPLQVATSTKMVDNDATPKIKVEPKEEGFVIEVMSEKRCQGLLVFILEAIEELGLEVLEAREKNEDTCPLNAQLVEQVVSQAIQNWREVTQQ*