AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1386180


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1386180 MtrunA17_Chr7g0266241 94.737 171 6 2 1 168 10 180 8.13e-115 323
Msa1386180 MtrunA17_Chr1g0178641 68.182 66 20 1 96 160 68 133 1.59e-27 100
Msa1386180 MtrunA17_Chr2g0321471 44.286 70 37 1 95 162 70 139 5.39e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1386180 AT3G52740.1 65.753 73 25 0 98 170 64 136 1.36e-31 111
Msa1386180 AT3G44450.1 58.182 55 23 0 99 153 39 93 7.09e-16 70.1

Find 38 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCTTTATCATCATGGTTT+TGG 0.183603 tig0020787:-81032 Msa1386170:three_prime_UTR
TCCTCTTGACCCCATATTTC+AGG 0.201417 tig0020787:-81246 Msa1386170:three_prime_UTR
GAGTTTGGATTCCTGAAATA+TGG 0.212739 tig0020787:+81235 Msa1386180:CDS
GATAGCTCCTGTTTCTTCTA+TGG 0.252691 tig0020787:+81113 Msa1386180:CDS
TTGAAGTAGCTGGAAGAGTT+TGG 0.294041 tig0020787:+81220 Msa1386180:CDS
CACTATGGCACGTGCTGCTT+TGG 0.339934 tig0020787:+81329 Msa1386180:CDS
AGCAAAAGAGTTAACAACTA+TGG 0.376017 tig0020787:+81146 Msa1386180:CDS
CACCTGTTGTGTATAGTTAG+AGG 0.380745 tig0020787:-81381 Msa1386170:intron
CATCTTTATCTTTATCATCA+TGG 0.388480 tig0020787:-81038 Msa1386170:three_prime_UTR
AAGAGGATTTATTGAAGGAT+TGG 0.393645 tig0020787:+81262 Msa1386180:CDS
AGTTTGGATTCCTGAAATAT+GGG 0.425242 tig0020787:+81236 Msa1386180:CDS
AGTTCCAAGCAAGATCACTA+TGG 0.434204 tig0020787:+81314 Msa1386180:CDS
TTCTCCTTGTTGCAAAGAGA+TGG 0.438417 tig0020787:-81072 Msa1386170:three_prime_UTR
ACATCATCCATAGAAGAAAC+AGG 0.460873 tig0020787:-81120 Msa1386170:three_prime_UTR
CTCCTCTAACTATACACAAC+AGG 0.463941 tig0020787:+81379 Msa1386180:CDS
GGGTCAAGAGGATTTATTGA+AGG 0.475977 tig0020787:+81257 Msa1386180:CDS
CAAGATTCCTTCACACCCAT+TGG 0.482903 tig0020787:+80927 Msa1386180:CDS
GTGATCTTGCTTGGAACTAA+AGG 0.483762 tig0020787:-81309 Msa1386170:three_prime_UTR
AGGCATAGAGTTGAAGTAGC+TGG 0.488896 tig0020787:+81210 Msa1386180:CDS
AACAACTATGGATGAAGTAT+TGG 0.489801 tig0020787:+81158 Msa1386180:CDS
CTCATCTAAAGATGTCAACT+TGG 0.490619 tig0020787:+80966 Msa1386180:CDS
TCTCCTTGTTGCAAAGAGAT+GGG 0.506171 tig0020787:-81071 Msa1386170:three_prime_UTR
CATCAGATTCAACAGAGGAT+TGG 0.517512 tig0020787:-80903 Msa1386170:three_prime_UTR
CGTGCCATAGTGATCTTGCT+TGG 0.523167 tig0020787:-81318 Msa1386170:three_prime_UTR
TATAGTTAGAGGAGCAGCAT+TGG 0.530992 tig0020787:-81370 Msa1386170:three_prime_UTR
TTTGAGTCCAATGGGTGTGA+AGG 0.539347 tig0020787:-80934 Msa1386170:three_prime_UTR
GTTGACATCTTTAGATGAGT+GGG 0.544029 tig0020787:-80962 Msa1386170:three_prime_UTR
GTGAAAGAGAGAGGCTGAAG+AGG 0.548904 tig0020787:+81190 Msa1386180:CDS
TCCTGAAATATGGGGTCAAG+AGG 0.551314 tig0020787:+81245 Msa1386180:CDS
TATGGATGAAGTATTGGAAG+AGG 0.560016 tig0020787:+81164 Msa1386180:CDS
AGTTGACATCTTTAGATGAG+TGG 0.576084 tig0020787:-80963 Msa1386170:three_prime_UTR
CGTGCTGCTTTGGTTGAAGA+GGG 0.579273 tig0020787:+81339 Msa1386180:CDS
AAGAGGATAGTGAAAGAGAG+AGG 0.580510 tig0020787:+81181 Msa1386180:CDS
ACGTGCTGCTTTGGTTGAAG+AGG 0.593330 tig0020787:+81338 Msa1386180:CDS
AAACCCATCTCTTTGCAACA+AGG 0.624582 tig0020787:+81068 Msa1386180:CDS
TTGACATCTTTAGATGAGTG+GGG 0.627794 tig0020787:-80961 Msa1386170:three_prime_UTR
GTTTGGATTCCTGAAATATG+GGG 0.638334 tig0020787:+81237 Msa1386180:CDS
CTTGTCATCAGATTCAACAG+AGG 0.696844 tig0020787:-80908 Msa1386170:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATCTTTATCATCATGGTTT+TGG - tig0020787:81035-81054 Msa1386170:three_prime_UTR 25.0%
! CATCTTTATCTTTATCATCA+TGG - tig0020787:81041-81060 Msa1386170:three_prime_UTR 25.0%
TTTGAGTGTTCAAAAAAGGA+GGG - tig0020787:81008-81027 Msa1386170:three_prime_UTR 30.0%
!! TTTTGAGTGTTCAAAAAAGG+AGG - tig0020787:81009-81028 Msa1386170:three_prime_UTR 30.0%
!!! TCCTTTTTTGAACACTCAAA+AGG + tig0020787:81008-81027 Msa1386180:CDS 30.0%
!! ACCTTTTGAGTGTTCAAAAA+AGG - tig0020787:81012-81031 Msa1386170:three_prime_UTR 30.0%
AGCAAAAGAGTTAACAACTA+TGG + tig0020787:81146-81165 Msa1386180:CDS 30.0%
AACAACTATGGATGAAGTAT+TGG + tig0020787:81158-81177 Msa1386180:CDS 30.0%
AGTTTGGATTCCTGAAATAT+GGG + tig0020787:81236-81255 Msa1386180:CDS 30.0%
AAGAGGATTTATTGAAGGAT+TGG + tig0020787:81262-81281 Msa1386180:CDS 30.0%
TTGACATCTTTAGATGAGTG+GGG - tig0020787:80964-80983 Msa1386170:three_prime_UTR 35.0%
GTTGACATCTTTAGATGAGT+GGG - tig0020787:80965-80984 Msa1386170:three_prime_UTR 35.0%
AGTTGACATCTTTAGATGAG+TGG - tig0020787:80966-80985 Msa1386170:three_prime_UTR 35.0%
CTCATCTAAAGATGTCAACT+TGG + tig0020787:80966-80985 Msa1386180:CDS 35.0%
ACATCATCCATAGAAGAAAC+AGG - tig0020787:81123-81142 Msa1386170:three_prime_UTR 35.0%
!! TATGGATGAAGTATTGGAAG+AGG + tig0020787:81164-81183 Msa1386180:CDS 35.0%
GAGTTTGGATTCCTGAAATA+TGG + tig0020787:81235-81254 Msa1386180:CDS 35.0%
GTTTGGATTCCTGAAATATG+GGG + tig0020787:81237-81256 Msa1386180:CDS 35.0%
CATCAGATTCAACAGAGGAT+TGG - tig0020787:80906-80925 Msa1386170:three_prime_UTR 40.0%
CTTGTCATCAGATTCAACAG+AGG - tig0020787:80911-80930 Msa1386170:three_prime_UTR 40.0%
!!! GGGGTTTTTTTGAGTCCAAT+GGG - tig0020787:80945-80964 Msa1386170:three_prime_UTR 40.0%
!!! TGGGGTTTTTTTGAGTCCAA+TGG - tig0020787:80946-80965 Msa1386170:three_prime_UTR 40.0%
AAACCCATCTCTTTGCAACA+AGG + tig0020787:81068-81087 Msa1386180:CDS 40.0%
TCTCCTTGTTGCAAAGAGAT+GGG - tig0020787:81074-81093 Msa1386170:three_prime_UTR 40.0%
TTCTCCTTGTTGCAAAGAGA+TGG - tig0020787:81075-81094 Msa1386170:three_prime_UTR 40.0%
! GATAGCTCCTGTTTCTTCTA+TGG + tig0020787:81113-81132 Msa1386180:CDS 40.0%
AAGAGGATAGTGAAAGAGAG+AGG + tig0020787:81181-81200 Msa1386180:CDS 40.0%
TTGAAGTAGCTGGAAGAGTT+TGG + tig0020787:81220-81239 Msa1386180:CDS 40.0%
GGGTCAAGAGGATTTATTGA+AGG + tig0020787:81257-81276 Msa1386180:CDS 40.0%
GTGATCTTGCTTGGAACTAA+AGG - tig0020787:81312-81331 Msa1386170:three_prime_UTR 40.0%
AGTTCCAAGCAAGATCACTA+TGG + tig0020787:81314-81333 Msa1386180:CDS 40.0%
TATAGTTAGAGGAGCAGCAT+TGG - tig0020787:81373-81392 Msa1386170:three_prime_UTR 40.0%
CTCCTCTAACTATACACAAC+AGG + tig0020787:81379-81398 Msa1386180:CDS 40.0%
CACCTGTTGTGTATAGTTAG+AGG - tig0020787:81384-81403 Msa1386170:intron 40.0%
CAAGATTCCTTCACACCCAT+TGG + tig0020787:80927-80946 Msa1386180:CDS 45.0%
TTTGAGTCCAATGGGTGTGA+AGG - tig0020787:80937-80956 Msa1386170:three_prime_UTR 45.0%
AGGCATAGAGTTGAAGTAGC+TGG + tig0020787:81210-81229 Msa1386180:CDS 45.0%
TCCTGAAATATGGGGTCAAG+AGG + tig0020787:81245-81264 Msa1386180:CDS 45.0%
TCCTCTTGACCCCATATTTC+AGG - tig0020787:81249-81268 Msa1386170:three_prime_UTR 45.0%
GTGAAAGAGAGAGGCTGAAG+AGG + tig0020787:81190-81209 Msa1386180:CDS 50.0%
CGTGCCATAGTGATCTTGCT+TGG - tig0020787:81321-81340 Msa1386170:three_prime_UTR 50.0%
!! ACGTGCTGCTTTGGTTGAAG+AGG + tig0020787:81338-81357 Msa1386180:CDS 50.0%
!! CGTGCTGCTTTGGTTGAAGA+GGG + tig0020787:81339-81358 Msa1386180:CDS 50.0%
!! CACTATGGCACGTGCTGCTT+TGG + tig0020787:81329-81348 Msa1386180:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0020787 gene 80895 81407 80895 ID=Msa1386180;Name=Msa1386180
tig0020787 mRNA 80895 81407 80895 ID=Msa1386180-mRNA-1;Parent=Msa1386180;Name=Msa1386180-mRNA-1;_AED=0.37;_eAED=0.38;_QI=0|-1|0|1|-1|1|1|0|170
tig0020787 exon 80895 81407 80895 ID=Msa1386180-mRNA-1:exon:10032;Parent=Msa1386180-mRNA-1
tig0020787 CDS 80895 81407 80895 ID=Msa1386180-mRNA-1:cds;Parent=Msa1386180-mRNA-1
Gene Sequence

>Msa1386180

ATGTCTTACCAATCCTCTGTTGAATCTGATGACAAGATTCCTTCACACCCATTGGACTCAAAAAAACCCCACTCATCTAAAGATGTCAACTTGGAGACAAAACAAGATGACCCTCCTTTTTTGAACACTCAAAAGGTCCAAAACCATGATGATAAAGATAAAGATGCAACACAAAACCCATCTCTTTGCAACAAGGAGAAAATGACACTATTGCAAGAGATAGCTCCTGTTTCTTCTATGGATGATGTTGAAGCAAAAGAGTTAACAACTATGGATGAAGTATTGGAAGAGGATAGTGAAAGAGAGAGGCTGAAGAGGCATAGAGTTGAAGTAGCTGGAAGAGTTTGGATTCCTGAAATATGGGGTCAAGAGGATTTATTGAAGGATTGGATAGATTGCACTGCATTTGATGCTCCTTTAGTTCCAAGCAAGATCACTATGGCACGTGCTGCTTTGGTTGAAGAGGGTACTAAAACCAATGCTGCTCCTCTAACTATACACAACAGGTGTTAG

Protein sequence

>Msa1386180

MSYQSSVESDDKIPSHPLDSKKPHSSKDVNLETKQDDPPFLNTQKVQNHDDKDKDATQNPSLCNKEKMTLLQEIAPVSSMDDVEAKELTTMDEVLEEDSERERLKRHRVEVAGRVWIPEIWGQEDLLKDWIDCTAFDAPLVPSKITMARAALVEEGTKTNAAPLTIHNRC*