AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1430570


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1430570 MtrunA17_Chr3g0115281 75.847 236 15 3 1 195 1 235 5.99e-108 311
Msa1430570 MtrunA17_Chr7g0254481 33.526 173 75 3 63 195 84 256 3.82e-17 77.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1430570 AT1G36390.1 35.922 206 74 5 31 195 31 219 3.15e-25 99.4
Msa1430570 AT1G36390.2 35.922 206 74 5 31 195 31 219 3.15e-25 99.4
Msa1430570 AT5G17710.3 48.750 80 40 1 116 195 176 254 2.63e-12 64.7
Msa1430570 AT5G17710.1 48.750 80 40 1 116 195 176 254 2.63e-12 64.7
Msa1430570 AT5G17710.2 48.750 80 40 1 116 195 178 256 2.71e-12 64.7

Find 36 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAACGAAATTGGGTGGTTT+TGG 0.202923 tig0026696:-63146 None:intergenic
GATAGTGTTGGAGGCGTAAA+AGG 0.207213 tig0026696:-63183 None:intergenic
TACGCCTCCAACACTATCTT+AGG 0.217564 tig0026696:+63188 Msa1430570:CDS
ACAAGATTTACCAAGCTTAT+TGG 0.223350 tig0026696:+63494 Msa1430570:CDS
TAACTTACCAAAGGATTAAA+AGG 0.227686 tig0026696:-63929 None:intergenic
AGATGGAAAATGAACGAAAT+TGG 0.241708 tig0026696:-63156 None:intergenic
CTTTCTTGTATGCTTTAATA+AGG 0.254294 tig0026696:-63518 None:intergenic
TACACTTGAAAAGGAATCTT+TGG 0.266699 tig0026696:-63249 None:intergenic
GAAGCGAAGAGGGAGGAGAT+TGG 0.344456 tig0026696:-63227 None:intergenic
TACAAGAAAGCCTTTCTTAA+CGG 0.370413 tig0026696:+63531 Msa1430570:CDS
TCAGAAAGTATCTAGTTTAT+CGG 0.373978 tig0026696:+63623 Msa1430570:CDS
CTTTCTATCGCCGTTAAGAA+AGG 0.383363 tig0026696:-63541 None:intergenic
TCTCTCGAATCAATCTCTAT+TGG 0.404166 tig0026696:+63079 Msa1430570:CDS
AGCAATTTGTAGAGACTTTG+AGG 0.424003 tig0026696:+63870 Msa1430570:CDS
GATGGAAAATGAACGAAATT+GGG 0.454309 tig0026696:-63155 None:intergenic
GAGGAGATTGGATTGAGAGT+TGG 0.467807 tig0026696:-63215 None:intergenic
GAGAGAGCGTACACTTGAAA+AGG 0.470698 tig0026696:-63258 None:intergenic
ATAGTGTTGGAGGCGTAAAA+GGG 0.478533 tig0026696:-63182 None:intergenic
ACAACAGATTGAAGCGGAAA+CGG 0.508186 tig0026696:+63805 Msa1430570:CDS
ACGCCTCCAACACTATCTTA+GGG 0.513218 tig0026696:+63189 Msa1430570:CDS
TTAATAAGGACCAATAAGCT+TGG 0.526487 tig0026696:-63504 None:intergenic
TACAATCAAAAGCAATTGAA+AGG 0.537877 tig0026696:+63589 Msa1430570:CDS
GGAATCTTTGGAAGCGAAGA+GGG 0.541715 tig0026696:-63237 None:intergenic
ATGATAAAACAGACGAGACT+CGG 0.560686 tig0026696:+63457 Msa1430570:CDS
GAGGAGTCATCATGTTTCTG+TGG 0.562710 tig0026696:+63889 Msa1430570:CDS
GTTTCTGTGGTAGCTACAGT+TGG 0.563597 tig0026696:+63902 Msa1430570:CDS
AGGAATCTTTGGAAGCGAAG+AGG 0.565783 tig0026696:-63238 None:intergenic
GAGGCGTAAAAGGGGCGAGA+TGG 0.577768 tig0026696:-63173 None:intergenic
AAACCCTAAGATAGTGTTGG+AGG 0.580015 tig0026696:-63192 None:intergenic
TGGAAACCCTAAGATAGTGT+TGG 0.587421 tig0026696:-63195 None:intergenic
GGAAAATGAACGAAATTGGG+TGG 0.597271 tig0026696:-63152 None:intergenic
AGTTAAACAACAGATTGAAG+CGG 0.621582 tig0026696:+63799 Msa1430570:CDS
ATCTTTGGAAGCGAAGAGGG+AGG 0.628356 tig0026696:-63234 None:intergenic
GAAAGTATCTAGTTTATCGG+CGG 0.637283 tig0026696:+63626 Msa1430570:CDS
TATTTCTTCAATCAACAATG+CGG 0.663325 tig0026696:-63565 None:intergenic
TAGTGTTGGAGGCGTAAAAG+GGG 0.663351 tig0026696:-63181 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CTTTCTTGTATGCTTTAATA+AGG - tig0026696:63521-63540 None:intergenic 25.0%
! TATTTCTTCAATCAACAATG+CGG - tig0026696:63568-63587 None:intergenic 25.0%
! TACAATCAAAAGCAATTGAA+AGG + tig0026696:63589-63608 Msa1430570:CDS 25.0%
!!! TCAGAAAGTATCTAGTTTAT+CGG + tig0026696:63623-63642 Msa1430570:CDS 25.0%
! TCATTAAAAACTTCTGTTGA+TGG + tig0026696:63760-63779 Msa1430570:intron 25.0%
! CTTTCTTGTATGCTTTAATA+AGG - tig0026696:63521-63540 None:intergenic 25.0%
! TATTTCTTCAATCAACAATG+CGG - tig0026696:63568-63587 None:intergenic 25.0%
! TACAATCAAAAGCAATTGAA+AGG + tig0026696:63589-63608 Msa1430570:CDS 25.0%
!!! TCAGAAAGTATCTAGTTTAT+CGG + tig0026696:63623-63642 Msa1430570:CDS 25.0%
! TCATTAAAAACTTCTGTTGA+TGG + tig0026696:63760-63779 Msa1430570:intron 25.0%
GATGGAAAATGAACGAAATT+GGG - tig0026696:63158-63177 None:intergenic 30.0%
AGATGGAAAATGAACGAAAT+TGG - tig0026696:63159-63178 None:intergenic 30.0%
TACACTTGAAAAGGAATCTT+TGG - tig0026696:63252-63271 None:intergenic 30.0%
!! CTTATTTTCATAAGCTCTTG+GGG - tig0026696:63382-63401 None:intergenic 30.0%
!! GCTTATTTTCATAAGCTCTT+GGG - tig0026696:63383-63402 None:intergenic 30.0%
!! AGCTTATTTTCATAAGCTCT+TGG - tig0026696:63384-63403 None:intergenic 30.0%
ACAAGATTTACCAAGCTTAT+TGG + tig0026696:63494-63513 Msa1430570:CDS 30.0%
TTAATAAGGACCAATAAGCT+TGG - tig0026696:63507-63526 None:intergenic 30.0%
TACAAGAAAGCCTTTCTTAA+CGG + tig0026696:63531-63550 Msa1430570:CDS 30.0%
!! AAGCGGATTTTGATAACTTT+AGG + tig0026696:63685-63704 Msa1430570:intron 30.0%
GGAAAGAATTAGCATTCAAT+CGG + tig0026696:63722-63741 Msa1430570:intron 30.0%
! TTAAAAACTTCTGTTGATGG+TGG + tig0026696:63763-63782 Msa1430570:intron 30.0%
AGTTAAACAACAGATTGAAG+CGG + tig0026696:63799-63818 Msa1430570:CDS 30.0%
GATGGAAAATGAACGAAATT+GGG - tig0026696:63158-63177 None:intergenic 30.0%
AGATGGAAAATGAACGAAAT+TGG - tig0026696:63159-63178 None:intergenic 30.0%
TACACTTGAAAAGGAATCTT+TGG - tig0026696:63252-63271 None:intergenic 30.0%
!! CTTATTTTCATAAGCTCTTG+GGG - tig0026696:63382-63401 None:intergenic 30.0%
!! GCTTATTTTCATAAGCTCTT+GGG - tig0026696:63383-63402 None:intergenic 30.0%
!! AGCTTATTTTCATAAGCTCT+TGG - tig0026696:63384-63403 None:intergenic 30.0%
ACAAGATTTACCAAGCTTAT+TGG + tig0026696:63494-63513 Msa1430570:CDS 30.0%
TTAATAAGGACCAATAAGCT+TGG - tig0026696:63507-63526 None:intergenic 30.0%
TACAAGAAAGCCTTTCTTAA+CGG + tig0026696:63531-63550 Msa1430570:CDS 30.0%
!! AAGCGGATTTTGATAACTTT+AGG + tig0026696:63685-63704 Msa1430570:intron 30.0%
GGAAAGAATTAGCATTCAAT+CGG + tig0026696:63722-63741 Msa1430570:intron 30.0%
! TTAAAAACTTCTGTTGATGG+TGG + tig0026696:63763-63782 Msa1430570:intron 30.0%
AGTTAAACAACAGATTGAAG+CGG + tig0026696:63799-63818 Msa1430570:CDS 30.0%
TCTCTCGAATCAATCTCTAT+TGG + tig0026696:63079-63098 Msa1430570:CDS 35.0%
ATGATAAAACAGACGAGACT+CGG + tig0026696:63457-63476 Msa1430570:CDS 35.0%
!! GAAAGTATCTAGTTTATCGG+CGG + tig0026696:63626-63645 Msa1430570:CDS 35.0%
TATCAAAATCCGCTTGCAAA+CGG - tig0026696:63680-63699 None:intergenic 35.0%
! CTTTAGGAAAAGATGTGAGA+AGG + tig0026696:63701-63720 Msa1430570:intron 35.0%
AGCAATTTGTAGAGACTTTG+AGG + tig0026696:63870-63889 Msa1430570:CDS 35.0%
TCTCTCGAATCAATCTCTAT+TGG + tig0026696:63079-63098 Msa1430570:CDS 35.0%
ATGATAAAACAGACGAGACT+CGG + tig0026696:63457-63476 Msa1430570:CDS 35.0%
!! GAAAGTATCTAGTTTATCGG+CGG + tig0026696:63626-63645 Msa1430570:CDS 35.0%
TATCAAAATCCGCTTGCAAA+CGG - tig0026696:63680-63699 None:intergenic 35.0%
! CTTTAGGAAAAGATGTGAGA+AGG + tig0026696:63701-63720 Msa1430570:intron 35.0%
AGCAATTTGTAGAGACTTTG+AGG + tig0026696:63870-63889 Msa1430570:CDS 35.0%
! TGAACGAAATTGGGTGGTTT+TGG - tig0026696:63149-63168 None:intergenic 40.0%
GGAAAATGAACGAAATTGGG+TGG - tig0026696:63155-63174 None:intergenic 40.0%
! ATAGTGTTGGAGGCGTAAAA+GGG - tig0026696:63185-63204 None:intergenic 40.0%
! AAACCCTAAGATAGTGTTGG+AGG - tig0026696:63195-63214 None:intergenic 40.0%
TGGAAACCCTAAGATAGTGT+TGG - tig0026696:63198-63217 None:intergenic 40.0%
TGCAAAAACAAGACAGAGAG+AGG - tig0026696:63430-63449 None:intergenic 40.0%
CTTTCTATCGCCGTTAAGAA+AGG - tig0026696:63544-63563 None:intergenic 40.0%
ACAACAGATTGAAGCGGAAA+CGG + tig0026696:63805-63824 Msa1430570:CDS 40.0%
! TGAACGAAATTGGGTGGTTT+TGG - tig0026696:63149-63168 None:intergenic 40.0%
GGAAAATGAACGAAATTGGG+TGG - tig0026696:63155-63174 None:intergenic 40.0%
! ATAGTGTTGGAGGCGTAAAA+GGG - tig0026696:63185-63204 None:intergenic 40.0%
! AAACCCTAAGATAGTGTTGG+AGG - tig0026696:63195-63214 None:intergenic 40.0%
TGGAAACCCTAAGATAGTGT+TGG - tig0026696:63198-63217 None:intergenic 40.0%
TGCAAAAACAAGACAGAGAG+AGG - tig0026696:63430-63449 None:intergenic 40.0%
CTTTCTATCGCCGTTAAGAA+AGG - tig0026696:63544-63563 None:intergenic 40.0%
ACAACAGATTGAAGCGGAAA+CGG + tig0026696:63805-63824 Msa1430570:CDS 40.0%
! TAGTGTTGGAGGCGTAAAAG+GGG - tig0026696:63184-63203 None:intergenic 45.0%
! GATAGTGTTGGAGGCGTAAA+AGG - tig0026696:63186-63205 None:intergenic 45.0%
TACGCCTCCAACACTATCTT+AGG + tig0026696:63188-63207 Msa1430570:CDS 45.0%
ACGCCTCCAACACTATCTTA+GGG + tig0026696:63189-63208 Msa1430570:CDS 45.0%
GAGGAGATTGGATTGAGAGT+TGG - tig0026696:63218-63237 None:intergenic 45.0%
! GGAATCTTTGGAAGCGAAGA+GGG - tig0026696:63240-63259 None:intergenic 45.0%
! AGGAATCTTTGGAAGCGAAG+AGG - tig0026696:63241-63260 None:intergenic 45.0%
! GAGAGAGCGTACACTTGAAA+AGG - tig0026696:63261-63280 None:intergenic 45.0%
GCAATATCTCCGTTTGCAAG+CGG + tig0026696:63668-63687 Msa1430570:intron 45.0%
! GAGGAGTCATCATGTTTCTG+TGG + tig0026696:63889-63908 Msa1430570:CDS 45.0%
GTTTCTGTGGTAGCTACAGT+TGG + tig0026696:63902-63921 Msa1430570:CDS 45.0%
! TAGTGTTGGAGGCGTAAAAG+GGG - tig0026696:63184-63203 None:intergenic 45.0%
! GATAGTGTTGGAGGCGTAAA+AGG - tig0026696:63186-63205 None:intergenic 45.0%
TACGCCTCCAACACTATCTT+AGG + tig0026696:63188-63207 Msa1430570:CDS 45.0%
ACGCCTCCAACACTATCTTA+GGG + tig0026696:63189-63208 Msa1430570:CDS 45.0%
GAGGAGATTGGATTGAGAGT+TGG - tig0026696:63218-63237 None:intergenic 45.0%
! GGAATCTTTGGAAGCGAAGA+GGG - tig0026696:63240-63259 None:intergenic 45.0%
! AGGAATCTTTGGAAGCGAAG+AGG - tig0026696:63241-63260 None:intergenic 45.0%
! GAGAGAGCGTACACTTGAAA+AGG - tig0026696:63261-63280 None:intergenic 45.0%
GCAATATCTCCGTTTGCAAG+CGG + tig0026696:63668-63687 Msa1430570:intron 45.0%
! GAGGAGTCATCATGTTTCTG+TGG + tig0026696:63889-63908 Msa1430570:CDS 45.0%
GTTTCTGTGGTAGCTACAGT+TGG + tig0026696:63902-63921 Msa1430570:CDS 45.0%
! ATCTTTGGAAGCGAAGAGGG+AGG - tig0026696:63237-63256 None:intergenic 50.0%
! ATCTTTGGAAGCGAAGAGGG+AGG - tig0026696:63237-63256 None:intergenic 50.0%
GAAGCGAAGAGGGAGGAGAT+TGG - tig0026696:63230-63249 None:intergenic 55.0%
GAAGCGAAGAGGGAGGAGAT+TGG - tig0026696:63230-63249 None:intergenic 55.0%
GAGGCGTAAAAGGGGCGAGA+TGG - tig0026696:63176-63195 None:intergenic 60.0%
GAGGCGTAAAAGGGGCGAGA+TGG - tig0026696:63176-63195 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0026696 gene 63068 63943 63068 ID=Msa1430570;Name=Msa1430570
tig0026696 mRNA 63068 63943 63068 ID=Msa1430570-mRNA-1;Parent=Msa1430570;Name=Msa1430570-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0|0|1|1|1|3|0|195
tig0026696 exon 63068 63268 63068 ID=Msa1430570-mRNA-1:exon:7051;Parent=Msa1430570-mRNA-1
tig0026696 exon 63453 63682 63453 ID=Msa1430570-mRNA-1:exon:7052;Parent=Msa1430570-mRNA-1
tig0026696 exon 63790 63943 63790 ID=Msa1430570-mRNA-1:exon:7053;Parent=Msa1430570-mRNA-1
tig0026696 CDS 63068 63268 63068 ID=Msa1430570-mRNA-1:cds;Parent=Msa1430570-mRNA-1
tig0026696 CDS 63453 63682 63453 ID=Msa1430570-mRNA-1:cds;Parent=Msa1430570-mRNA-1
tig0026696 CDS 63790 63943 63790 ID=Msa1430570-mRNA-1:cds;Parent=Msa1430570-mRNA-1
Gene Sequence

>Msa1430570

ATGGCTACTTCTCTCTCGAATCAATCTCTATTGGCTTGTTCTTCTTCATCATCTTCTTCTTCATTCTCTTCAAAATCTCCAAAACCACCCAATTTCGTTCATTTTCCATCTCGCCCCTTTTACGCCTCCAACACTATCTTAGGGTTTCCAACTCTCAATCCAATCTCCTCCCTCTTCGCTTCCAAAGATTCCTTTTCAAGTACAAATGATAAAACAGACGAGACTCGGAATGATGAAGATAAACAAGATTTACCAAGCTTATTGGTCCTTATTAAAGCATACAAGAAAGCCTTTCTTAACGGCGATAGAAAGACCGCATTGTTGATTGAAGAAATAATACAATCAAAAGCAATTGAAAGGAATAAATTGATTCAGAAAGTATCTAGTTTATCGGCGGATAAAGTTTCTTGTAAAGAGCAATATCTCCGTTTTTTTGAGAGAGTTAAACAACAGATTGAAGCGGAAACGGAGAAAGAGAAGAAGATTGATGCGAGCTATCAAAGTCTTTACAAGCAATTTGTAGAGACTTTGAGGAGTCATCATGTTTCTGTGGTAGCTACAGTTGGCAAGCCTTTTAATCCTTTG

Protein sequence

>Msa1430570

MATSLSNQSLLACSSSSSSSSFSSKSPKPPNFVHFPSRPFYASNTILGFPTLNPISSLFASKDSFSSTNDKTDETRNDEDKQDLPSLLVLIKAYKKAFLNGDRKTALLIEEIIQSKAIERNKLIQKVSSLSADKVSCKEQYLRFFERVKQQIEAETEKEKKIDASYQSLYKQFVETLRSHHVSVVATVGKPFNPL