AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1361190


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1361190 MtrunA17_Chr8g0383481 93.506 77 4 1 1 76 36 112 2.70e-48 148
Msa1361190 MtrunA17_Chr3g0129411 50.588 85 33 3 1 76 35 119 1.34e-19 75.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 34 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTGTCTGCCTAGAAAATA+TGG 0.191846 tig0017374:+46999 None:intergenic
AAATATTTGTAGCTCCTTCT+AGG 0.236923 tig0017374:+46864 None:intergenic
ACCTCTACTATACGTGTATT+TGG 0.243926 tig0017374:+47077 None:intergenic
AAAATATGGGTATGTGCTAT+TGG 0.285709 tig0017374:+47013 None:intergenic
ATCGGTGGCTTCCTTCTTGC+TGG 0.286574 tig0017374:+46372 None:intergenic
TAAGGTAGATCATATGTTTA+AGG 0.311443 tig0017374:-46445 Msa1361190:CDS
AAATATGGGTATGTGCTATT+GGG 0.333544 tig0017374:+47014 None:intergenic
AATGAGTAATACTCATAATA+AGG 0.356818 tig0017374:-46463 Msa1361190:CDS
GCATTAAACTTCGTGGCAAT+TGG 0.368027 tig0017374:-46904 Msa1361190:five_prime_UTR
ATAGTAGAGGTTGACATTCA+TGG 0.371098 tig0017374:-47065 Msa1361190:five_prime_UTR
AAAAGTCGAATTATTTAAGA+TGG 0.436642 tig0017374:-46737 Msa1361190:exon
CCTCTACTATACGTGTATTT+GGG 0.444033 tig0017374:+47078 None:intergenic
ACAATATTTCAATTGTGAAT+CGG 0.450645 tig0017374:+46354 None:intergenic
TGCATAATACCACAATCATA+TGG 0.494409 tig0017374:-46929 Msa1361190:five_prime_UTR
ATAACTTAATACCTCTAGCT+TGG 0.497100 tig0017374:+46653 None:intergenic
TATGGTTGCATTAAACTTCG+TGG 0.508843 tig0017374:-46911 Msa1361190:five_prime_UTR
TAACTTAATACCTCTAGCTT+GGG 0.523329 tig0017374:+46654 None:intergenic
GAAGGAATAGAACCACTACT+AGG 0.529646 tig0017374:+46692 None:intergenic
CTTGTCTGCCTAGAAAATAT+GGG 0.530731 tig0017374:+47000 None:intergenic
AATATGGGTATGTGCTATTG+GGG 0.541039 tig0017374:+47015 None:intergenic
GGCAAAAGAAGAACATAATG+TGG 0.544421 tig0017374:-46424 Msa1361190:CDS
AAACAAACGTTTCCTAGTAG+TGG 0.554374 tig0017374:-46704 Msa1361190:CDS
TGGGTATGTGCTATTGGGGA+AGG 0.558645 tig0017374:+47019 None:intergenic
TGGTGCAGCACGAACTCTGA+AGG 0.582207 tig0017374:-46502 Msa1361190:intron
GGGTATGTGCTATTGGGGAA+GGG 0.584361 tig0017374:+47020 None:intergenic
ATATTTCAATTGTGAATCGG+TGG 0.587562 tig0017374:+46357 None:intergenic
TTAATGCAACCATATGATTG+TGG 0.591100 tig0017374:+46920 None:intergenic
CCCAAATACACGTATAGTAG+AGG 0.592182 tig0017374:-47078 Msa1361190:five_prime_UTR
TGGATTACACTCCAGCAAGA+AGG 0.596499 tig0017374:-46383 Msa1361190:CDS
GCAAAAGAAGAACATAATGT+GGG 0.604097 tig0017374:-46423 Msa1361190:CDS
GGGTAGATATGAAACAGAGA+AGG 0.633587 tig0017374:+46674 None:intergenic
TTCATATCTACCCAAGCTAG+AGG 0.668712 tig0017374:-46664 Msa1361190:intron
TGCACAATAAGAGAGAGTAA+TGG 0.674857 tig0017374:+46948 None:intergenic
ATACATATTGATATGATACA+CGG 0.690316 tig0017374:-46211 Msa1361190:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACAAATATTTTTCTATATA+AGG - tig0017374:46423-46442 Msa1361190:CDS 10.0%
!!! ACAAATATTTTTCTATATAA+GGG - tig0017374:46424-46443 Msa1361190:CDS 10.0%
!!! GATTATGATTTTATTAAAAA+AGG + tig0017374:46702-46721 None:intergenic 10.0%
!!! TACAAATATTTTTCTATATA+AGG - tig0017374:46423-46442 Msa1361190:CDS 10.0%
!!! ACAAATATTTTTCTATATAA+GGG - tig0017374:46424-46443 Msa1361190:CDS 10.0%
!!! GATTATGATTTTATTAAAAA+AGG + tig0017374:46702-46721 None:intergenic 10.0%
!! GATTATGTTCTTAATTATAT+TGG - tig0017374:46650-46669 Msa1361190:intron 15.0%
!! TCTAACATGATTTATATATA+TGG - tig0017374:46753-46772 Msa1361190:five_prime_UTR 15.0%
!! GATTATGTTCTTAATTATAT+TGG - tig0017374:46650-46669 Msa1361190:intron 15.0%
!! TCTAACATGATTTATATATA+TGG - tig0017374:46753-46772 Msa1361190:five_prime_UTR 15.0%
!! AAAAGTCGAATTATTTAAGA+TGG - tig0017374:46538-46557 Msa1361190:intron 20.0%
!! AATGAGTAATACTCATAATA+AGG - tig0017374:46812-46831 Msa1361190:five_prime_UTR 20.0%
!! ACAATATTTCAATTGTGAAT+CGG + tig0017374:46924-46943 None:intergenic 20.0%
!! ATACATATTGATATGATACA+CGG - tig0017374:47064-47083 Msa1361190:five_prime_UTR 20.0%
!! AAAAGTCGAATTATTTAAGA+TGG - tig0017374:46538-46557 Msa1361190:intron 20.0%
!! AATGAGTAATACTCATAATA+AGG - tig0017374:46812-46831 Msa1361190:five_prime_UTR 20.0%
!! ACAATATTTCAATTGTGAAT+CGG + tig0017374:46924-46943 None:intergenic 20.0%
!! ATACATATTGATATGATACA+CGG - tig0017374:47064-47083 Msa1361190:five_prime_UTR 20.0%
! TAAGGTAGATCATATGTTTA+AGG - tig0017374:46830-46849 Msa1361190:five_prime_UTR 25.0%
! TAAGGTAGATCATATGTTTA+AGG - tig0017374:46830-46849 Msa1361190:five_prime_UTR 25.0%
! AAATATGGGTATGTGCTATT+GGG + tig0017374:46264-46283 None:intergenic 30.0%
AAAATATGGGTATGTGCTAT+TGG + tig0017374:46265-46284 None:intergenic 30.0%
TGCATAATACCACAATCATA+TGG - tig0017374:46346-46365 Msa1361190:exon 30.0%
TTAATGCAACCATATGATTG+TGG + tig0017374:46358-46377 None:intergenic 30.0%
! CTAGTAATTTTCAACCTAGA+AGG - tig0017374:46397-46416 Msa1361190:CDS 30.0%
AAATATTTGTAGCTCCTTCT+AGG + tig0017374:46414-46433 None:intergenic 30.0%
! TAACTTAATACCTCTAGCTT+GGG + tig0017374:46624-46643 None:intergenic 30.0%
ATAACTTAATACCTCTAGCT+TGG + tig0017374:46625-46644 None:intergenic 30.0%
GCAAAAGAAGAACATAATGT+GGG - tig0017374:46852-46871 Msa1361190:five_prime_UTR 30.0%
ATATTTCAATTGTGAATCGG+TGG + tig0017374:46921-46940 None:intergenic 30.0%
! AAATATGGGTATGTGCTATT+GGG + tig0017374:46264-46283 None:intergenic 30.0%
AAAATATGGGTATGTGCTAT+TGG + tig0017374:46265-46284 None:intergenic 30.0%
TGCATAATACCACAATCATA+TGG - tig0017374:46346-46365 Msa1361190:exon 30.0%
TTAATGCAACCATATGATTG+TGG + tig0017374:46358-46377 None:intergenic 30.0%
! CTAGTAATTTTCAACCTAGA+AGG - tig0017374:46397-46416 Msa1361190:CDS 30.0%
AAATATTTGTAGCTCCTTCT+AGG + tig0017374:46414-46433 None:intergenic 30.0%
! TAACTTAATACCTCTAGCTT+GGG + tig0017374:46624-46643 None:intergenic 30.0%
ATAACTTAATACCTCTAGCT+TGG + tig0017374:46625-46644 None:intergenic 30.0%
GCAAAAGAAGAACATAATGT+GGG - tig0017374:46852-46871 Msa1361190:five_prime_UTR 30.0%
ATATTTCAATTGTGAATCGG+TGG + tig0017374:46921-46940 None:intergenic 30.0%
CCTCTACTATACGTGTATTT+GGG + tig0017374:46200-46219 None:intergenic 35.0%
ACCTCTACTATACGTGTATT+TGG + tig0017374:46201-46220 None:intergenic 35.0%
ATAGTAGAGGTTGACATTCA+TGG - tig0017374:46210-46229 Msa1361190:three_prime_UTR 35.0%
! AATATGGGTATGTGCTATTG+GGG + tig0017374:46263-46282 None:intergenic 35.0%
! AGCACATACCCATATTTTCT+AGG - tig0017374:46267-46286 Msa1361190:three_prime_UTR 35.0%
CTTGTCTGCCTAGAAAATAT+GGG + tig0017374:46278-46297 None:intergenic 35.0%
ACTTGTCTGCCTAGAAAATA+TGG + tig0017374:46279-46298 None:intergenic 35.0%
TGCACAATAAGAGAGAGTAA+TGG + tig0017374:46330-46349 None:intergenic 35.0%
TATGGTTGCATTAAACTTCG+TGG - tig0017374:46364-46383 Msa1361190:CDS 35.0%
AAACAAACGTTTCCTAGTAG+TGG - tig0017374:46571-46590 Msa1361190:intron 35.0%
GGCAAAAGAAGAACATAATG+TGG - tig0017374:46851-46870 Msa1361190:five_prime_UTR 35.0%
!! GGGAGATGAAGTATTTTCAA+TGG - tig0017374:46872-46891 Msa1361190:five_prime_UTR 35.0%
CCTCTACTATACGTGTATTT+GGG + tig0017374:46200-46219 None:intergenic 35.0%
ACCTCTACTATACGTGTATT+TGG + tig0017374:46201-46220 None:intergenic 35.0%
ATAGTAGAGGTTGACATTCA+TGG - tig0017374:46210-46229 Msa1361190:three_prime_UTR 35.0%
! AATATGGGTATGTGCTATTG+GGG + tig0017374:46263-46282 None:intergenic 35.0%
! AGCACATACCCATATTTTCT+AGG - tig0017374:46267-46286 Msa1361190:three_prime_UTR 35.0%
CTTGTCTGCCTAGAAAATAT+GGG + tig0017374:46278-46297 None:intergenic 35.0%
ACTTGTCTGCCTAGAAAATA+TGG + tig0017374:46279-46298 None:intergenic 35.0%
TGCACAATAAGAGAGAGTAA+TGG + tig0017374:46330-46349 None:intergenic 35.0%
TATGGTTGCATTAAACTTCG+TGG - tig0017374:46364-46383 Msa1361190:CDS 35.0%
AAACAAACGTTTCCTAGTAG+TGG - tig0017374:46571-46590 Msa1361190:intron 35.0%
GGCAAAAGAAGAACATAATG+TGG - tig0017374:46851-46870 Msa1361190:five_prime_UTR 35.0%
!! GGGAGATGAAGTATTTTCAA+TGG - tig0017374:46872-46891 Msa1361190:five_prime_UTR 35.0%
CCCAAATACACGTATAGTAG+AGG - tig0017374:46197-46216 Msa1361190:three_prime_UTR 40.0%
GCATTAAACTTCGTGGCAAT+TGG - tig0017374:46371-46390 Msa1361190:CDS 40.0%
GAAGGAATAGAACCACTACT+AGG + tig0017374:46586-46605 None:intergenic 40.0%
GGGTAGATATGAAACAGAGA+AGG + tig0017374:46604-46623 None:intergenic 40.0%
TTCATATCTACCCAAGCTAG+AGG - tig0017374:46611-46630 Msa1361190:intron 40.0%
CCCAAATACACGTATAGTAG+AGG - tig0017374:46197-46216 Msa1361190:three_prime_UTR 40.0%
GCATTAAACTTCGTGGCAAT+TGG - tig0017374:46371-46390 Msa1361190:CDS 40.0%
GAAGGAATAGAACCACTACT+AGG + tig0017374:46586-46605 None:intergenic 40.0%
GGGTAGATATGAAACAGAGA+AGG + tig0017374:46604-46623 None:intergenic 40.0%
TTCATATCTACCCAAGCTAG+AGG - tig0017374:46611-46630 Msa1361190:intron 40.0%
TGGATTACACTCCAGCAAGA+AGG - tig0017374:46892-46911 Msa1361190:five_prime_UTR 45.0%
TGGATTACACTCCAGCAAGA+AGG - tig0017374:46892-46911 Msa1361190:five_prime_UTR 45.0%
! GGGTATGTGCTATTGGGGAA+GGG + tig0017374:46258-46277 None:intergenic 50.0%
! TGGGTATGTGCTATTGGGGA+AGG + tig0017374:46259-46278 None:intergenic 50.0%
! GGGTATGTGCTATTGGGGAA+GGG + tig0017374:46258-46277 None:intergenic 50.0%
! TGGGTATGTGCTATTGGGGA+AGG + tig0017374:46259-46278 None:intergenic 50.0%
TGGTGCAGCACGAACTCTGA+AGG - tig0017374:46773-46792 Msa1361190:five_prime_UTR 55.0%
ATCGGTGGCTTCCTTCTTGC+TGG + tig0017374:46906-46925 None:intergenic 55.0%
TGGTGCAGCACGAACTCTGA+AGG - tig0017374:46773-46792 Msa1361190:five_prime_UTR 55.0%
ATCGGTGGCTTCCTTCTTGC+TGG + tig0017374:46906-46925 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0017374 gene 46178 47119 46178 ID=Msa1361190;Name=Msa1361190
tig0017374 mRNA 46178 47119 46178 ID=Msa1361190-mRNA-1;Parent=Msa1361190;Name=Msa1361190-mRNA-1;_AED=0.03;_eAED=0.03;_QI=379|1|1|1|1|1|2|184|76
tig0017374 exon 46178 46516 46178 ID=Msa1361190-mRNA-1:exon:12302;Parent=Msa1361190-mRNA-1
tig0017374 exon 46665 47119 46665 ID=Msa1361190-mRNA-1:exon:12301;Parent=Msa1361190-mRNA-1
tig0017374 five_prime_UTR 46741 47119 46741 ID=Msa1361190-mRNA-1:five_prime_utr;Parent=Msa1361190-mRNA-1
tig0017374 CDS 46665 46740 46665 ID=Msa1361190-mRNA-1:cds;Parent=Msa1361190-mRNA-1
tig0017374 CDS 46362 46516 46362 ID=Msa1361190-mRNA-1:cds;Parent=Msa1361190-mRNA-1
tig0017374 three_prime_UTR 46178 46361 46178 ID=Msa1361190-mRNA-1:three_prime_utr;Parent=Msa1361190-mRNA-1
Gene Sequence

>Msa1361190

ATGGCTATTGCACAAAACAAACGTTTCCTAGTAGTGGTTCTATTCCTTCTCTGTTTCATATCTACCCAAGCTAGAGCACGAACTCTGAAGGAAAAAAGCAATGATGTAATGAGTAATACTCATAATAAGGTAGATCATATGTTTAAGGCAAAAGAAGAACATAATGTGGGAGATGAAGTATTTTCAATGGATTACACTCCAGCAAGAAGGAAGCCACCGATTCACAATTGA

Protein sequence

>Msa1361190

MAIAQNKRFLVVVLFLLCFISTQARARTLKEKSNDVMSNTHNKVDHMFKAKEEHNVGDEVFSMDYTPARRKPPIHN*