AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0793760

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0793760 MtrunA17_Chr5g0394621 93.684 190 12 0 1 190 1 190 2.48e-129 361
Msa0793760 MtrunA17_Chr5g0394631 77.222 180 41 0 1 180 1 180 2.36e-96 285
Msa0793760 MtrunA17_Chr5g0394631 73.196 194 42 5 1 190 214 401 1.49e-89 268
Msa0793760 MtrunA17_Chr1g0204951 64.583 192 64 2 1 190 1 190 1.73e-85 250
Msa0793760 MtrunA17_Chr1g0204971 60.417 192 72 2 1 190 1 190 1.87e-79 234
Msa0793760 MtrunA17_Chr7g0273661 40.764 157 90 1 16 172 3 156 1.14e-41 137
Msa0793760 MtrunA17_Chr7g0223361 39.181 171 100 2 17 187 4 170 9.29e-37 125
Msa0793760 MtrunA17_Chr7g0223351 39.286 168 97 3 20 187 7 169 3.16e-35 122
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0793760 AT2G32030.1 51.786 168 74 3 21 187 24 185 1.66e-58 182
Msa0793760 AT2G32020.1 51.190 168 75 2 21 187 19 180 2.46e-54 171
Msa0793760 AT3G22560.1 38.235 170 100 2 20 187 6 172 2.52e-35 122

Find 49 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAATCAATTCTCTCTTCTT+TGG 0.250774 5_3:+5627417 None:intergenic
ATGTTCTAGGCTCTAAATAT+TGG 0.292142 5_3:-5627135 Msa0793760:CDS
TCCTTAGAACTCCCTCCTTT+TGG 0.297796 5_3:+5626975 None:intergenic
GCAGAACTTGGCTATGTTCT+AGG 0.302641 5_3:-5627148 Msa0793760:CDS
TGTTCTAGGCTCTAAATATT+GGG 0.316974 5_3:-5627134 Msa0793760:CDS
GAGTTCCCAAGAGCAGAATT+TGG 0.329740 5_3:+5627318 None:intergenic
GAAGGGCTCGAAGTGTGATT+TGG 0.338927 5_3:+5627392 None:intergenic
GCTCTAAATATTGGGGTAAA+GGG 0.356917 5_3:-5627126 Msa0793760:CDS
AAGTTCTGCACATTTGTTCC+TGG 0.375848 5_3:+5627162 None:intergenic
CTAAACAATTGAATTATAGT+TGG 0.392086 5_3:+5626888 None:intergenic
ATATAGCTACCAAGTTTCTA+TGG 0.402105 5_3:-5627258 Msa0793760:CDS
TGCATCAATGATCGTGCAAT+TGG 0.403589 5_3:-5627223 Msa0793760:CDS
AAGGGCTCGAAGTGTGATTT+GGG 0.403990 5_3:+5627393 None:intergenic
TCCAAAAGGAGGGAGTTCTA+AGG 0.410439 5_3:-5626976 Msa0793760:CDS
GGCTCTAAATATTGGGGTAA+AGG 0.422886 5_3:-5627127 Msa0793760:CDS
AAGTGGCCAAATTCTGCTCT+TGG 0.423997 5_3:-5627324 Msa0793760:CDS
GTTGATGCCATCATCCTTGC+TGG 0.429573 5_3:+5627291 None:intergenic
TGCTGGGTCTCAAAGAGTGC+TGG 0.460731 5_3:-5627011 Msa0793760:CDS
AGTGGCCAAATTCTGCTCTT+GGG 0.474265 5_3:-5627323 Msa0793760:CDS
AGGAACAAATGTGCAGAACT+TGG 0.475881 5_3:-5627160 Msa0793760:CDS
AGGAAATATTTGTTCATGAA+AGG 0.480337 5_3:-5626956 Msa0793760:CDS
GCTTGAAGCTTTAGTTGATG+TGG 0.488968 5_3:-5627038 Msa0793760:CDS
TGCTTTGCACCATAGAAACT+TGG 0.496119 5_3:+5627249 None:intergenic
TTCTGACCTTGATGATCTCA+TGG 0.505164 5_3:-5627365 Msa0793760:CDS
CATCAAGGTCAGAAAGTTGA+AGG 0.505953 5_3:+5627374 None:intergenic
TGTTGTGAAACAAGTTGTTA+AGG 0.509712 5_3:-5627092 Msa0793760:CDS
TTGTTCCTGGATTTATCACC+AGG 0.514781 5_3:+5627175 None:intergenic
ATTCTGTGAGTTGACTTACT+TGG 0.516104 5_3:-5627065 Msa0793760:CDS
CAAAGAGTGCTGGAGAAAGC+TGG 0.517457 5_3:-5627001 Msa0793760:CDS
TTAGTTGATGTGGAAAATGC+TGG 0.527178 5_3:-5627028 Msa0793760:CDS
GTGAGTTGACTTACTTGGAA+AGG 0.541309 5_3:-5627060 Msa0793760:CDS
GTTCACCTGGTGATAAATCC+AGG 0.542743 5_3:-5627180 Msa0793760:CDS
TCTCTATCCTCAAGTTCACC+TGG 0.545696 5_3:-5627193 Msa0793760:CDS
CTCTACACCAGCAAGGATGA+TGG 0.559987 5_3:-5627298 Msa0793760:CDS
GAAAGCTGGTTTCCAAAAGG+AGG 0.562242 5_3:-5626987 Msa0793760:CDS
CTCTAAATATTGGGGTAAAG+GGG 0.564900 5_3:-5627125 Msa0793760:CDS
GCATCAATGATCGTGCAATT+GGG 0.567462 5_3:-5627222 Msa0793760:CDS
GGAGAAAGCTGGTTTCCAAA+AGG 0.570344 5_3:-5626990 Msa0793760:CDS
TTTATCACCAGGTGAACTTG+AGG 0.573291 5_3:+5627186 None:intergenic
TAGTTGATGTGGAAAATGCT+GGG 0.573363 5_3:-5627027 Msa0793760:CDS
ATTCTCTCTTCTTTGGCACG+TGG 0.591899 5_3:+5627424 None:intergenic
ACCTTGATGATCTCATGGTG+TGG 0.606125 5_3:-5627360 Msa0793760:CDS
AACTTGTTTCACAACACATG+TGG 0.607173 5_3:+5627099 None:intergenic
GTTCTAGGCTCTAAATATTG+GGG 0.619040 5_3:-5627133 Msa0793760:CDS
TCCACACCATGAGATCATCA+AGG 0.646997 5_3:+5627359 None:intergenic
ATCAAGGTCAGAAAGTTGAA+GGG 0.653293 5_3:+5627375 None:intergenic
AAAGCTGGTTTCCAAAAGGA+GGG 0.657724 5_3:-5626986 Msa0793760:CDS
GAGATCAGTAGAAAGAACAC+TGG 0.658551 5_3:+5626910 None:intergenic
TTGGGAACTCTACACCAGCA+AGG 0.679749 5_3:-5627305 Msa0793760:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TAAATCAATTCTCTCTTCTT+TGG + chr5_3:5626938-5626957 None:intergenic 25.0%
! AGGAAATATTTGTTCATGAA+AGG - chr5_3:5627396-5627415 Msa0793760:CDS 25.0%
ATATAGCTACCAAGTTTCTA+TGG - chr5_3:5627094-5627113 Msa0793760:CDS 30.0%
!! ATGTTCTAGGCTCTAAATAT+TGG - chr5_3:5627217-5627236 Msa0793760:CDS 30.0%
!! TGTTCTAGGCTCTAAATATT+GGG - chr5_3:5627218-5627237 Msa0793760:CDS 30.0%
TGTTGTGAAACAAGTTGTTA+AGG - chr5_3:5627260-5627279 Msa0793760:CDS 30.0%
ATCAAGGTCAGAAAGTTGAA+GGG + chr5_3:5626980-5626999 None:intergenic 35.0%
!! GTTCTAGGCTCTAAATATTG+GGG - chr5_3:5627219-5627238 Msa0793760:CDS 35.0%
! GCTCTAAATATTGGGGTAAA+GGG - chr5_3:5627226-5627245 Msa0793760:CDS 35.0%
CTCTAAATATTGGGGTAAAG+GGG - chr5_3:5627227-5627246 Msa0793760:CDS 35.0%
! AACTTGTTTCACAACACATG+TGG + chr5_3:5627256-5627275 None:intergenic 35.0%
! ATTCTGTGAGTTGACTTACT+TGG - chr5_3:5627287-5627306 Msa0793760:CDS 35.0%
! TTAGTTGATGTGGAAAATGC+TGG - chr5_3:5627324-5627343 Msa0793760:CDS 35.0%
! TAGTTGATGTGGAAAATGCT+GGG - chr5_3:5627325-5627344 Msa0793760:CDS 35.0%
CATCAAGGTCAGAAAGTTGA+AGG + chr5_3:5626981-5627000 None:intergenic 40.0%
! TTCTGACCTTGATGATCTCA+TGG - chr5_3:5626987-5627006 Msa0793760:CDS 40.0%
GTGGACAACTGATGAAAAAG+TGG - chr5_3:5627011-5627030 Msa0793760:CDS 40.0%
TGCTTTGCACCATAGAAACT+TGG + chr5_3:5627106-5627125 None:intergenic 40.0%
TGCATCAATGATCGTGCAAT+TGG - chr5_3:5627129-5627148 Msa0793760:CDS 40.0%
GCATCAATGATCGTGCAATT+GGG - chr5_3:5627130-5627149 Msa0793760:CDS 40.0%
TTTATCACCAGGTGAACTTG+AGG + chr5_3:5627169-5627188 None:intergenic 40.0%
TTGTTCCTGGATTTATCACC+AGG + chr5_3:5627180-5627199 None:intergenic 40.0%
AAGTTCTGCACATTTGTTCC+TGG + chr5_3:5627193-5627212 None:intergenic 40.0%
AGGAACAAATGTGCAGAACT+TGG - chr5_3:5627192-5627211 Msa0793760:CDS 40.0%
!! GGCTCTAAATATTGGGGTAA+AGG - chr5_3:5627225-5627244 Msa0793760:CDS 40.0%
! GTGAGTTGACTTACTTGGAA+AGG - chr5_3:5627292-5627311 Msa0793760:CDS 40.0%
! GCTTGAAGCTTTAGTTGATG+TGG - chr5_3:5627314-5627333 Msa0793760:CDS 40.0%
! AAAGCTGGTTTCCAAAAGGA+GGG - chr5_3:5627366-5627385 Msa0793760:CDS 40.0%
GAGATCAGTAGAAAGAACAC+TGG + chr5_3:5627445-5627464 None:intergenic 40.0%
ATTCTCTCTTCTTTGGCACG+TGG + chr5_3:5626931-5626950 None:intergenic 45.0%
AAGGGCTCGAAGTGTGATTT+GGG + chr5_3:5626962-5626981 None:intergenic 45.0%
! ACCTTGATGATCTCATGGTG+TGG - chr5_3:5626992-5627011 Msa0793760:CDS 45.0%
TCCACACCATGAGATCATCA+AGG + chr5_3:5626996-5627015 None:intergenic 45.0%
AAGTGGCCAAATTCTGCTCT+TGG - chr5_3:5627028-5627047 Msa0793760:CDS 45.0%
AGTGGCCAAATTCTGCTCTT+GGG - chr5_3:5627029-5627048 Msa0793760:CDS 45.0%
GAGTTCCCAAGAGCAGAATT+TGG + chr5_3:5627037-5627056 None:intergenic 45.0%
TCTCTATCCTCAAGTTCACC+TGG - chr5_3:5627159-5627178 Msa0793760:CDS 45.0%
GTTCACCTGGTGATAAATCC+AGG - chr5_3:5627172-5627191 Msa0793760:CDS 45.0%
GCAGAACTTGGCTATGTTCT+AGG - chr5_3:5627204-5627223 Msa0793760:CDS 45.0%
! GGAGAAAGCTGGTTTCCAAA+AGG - chr5_3:5627362-5627381 Msa0793760:CDS 45.0%
! GAAAGCTGGTTTCCAAAAGG+AGG - chr5_3:5627365-5627384 Msa0793760:CDS 45.0%
TCCAAAAGGAGGGAGTTCTA+AGG - chr5_3:5627376-5627395 Msa0793760:CDS 45.0%
! TCCTTAGAACTCCCTCCTTT+TGG + chr5_3:5627380-5627399 None:intergenic 45.0%
GAAGGGCTCGAAGTGTGATT+TGG + chr5_3:5626963-5626982 None:intergenic 50.0%
TTGGGAACTCTACACCAGCA+AGG - chr5_3:5627047-5627066 Msa0793760:CDS 50.0%
CTCTACACCAGCAAGGATGA+TGG - chr5_3:5627054-5627073 Msa0793760:CDS 50.0%
GTTGATGCCATCATCCTTGC+TGG + chr5_3:5627064-5627083 None:intergenic 50.0%
!! CAAAGAGTGCTGGAGAAAGC+TGG - chr5_3:5627351-5627370 Msa0793760:CDS 50.0%
! TGCTGGGTCTCAAAGAGTGC+TGG - chr5_3:5627341-5627360 Msa0793760:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 5626901 5627473 5626901 ID=Msa0793760;Name=Msa0793760
chr5_3 mRNA 5626901 5627473 5626901 ID=Msa0793760-mRNA-1;Parent=Msa0793760;Name=Msa0793760-mRNA-1;_AED=0.43;_eAED=0.43;_QI=0|-1|0|1|-1|1|1|0|190
chr5_3 exon 5626901 5627473 5626901 ID=Msa0793760-mRNA-1:exon:2256;Parent=Msa0793760-mRNA-1
chr5_3 CDS 5626901 5627473 5626901 ID=Msa0793760-mRNA-1:cds;Parent=Msa0793760-mRNA-1
Gene Sequence

>Msa0793760

ATGGAGAGAACTTCTATTTCTTTCGAACCACGTGCCAAAGAAGAGAGAATTGATTTAACCCAAATCACACTTCGAGCCCTTCAACTTTCTGACCTTGATGATCTCATGGTGTGGACAACTGATGAAAAAGTGGCCAAATTCTGCTCTTGGGAACTCTACACCAGCAAGGATGATGGCATCAACTTCATTGAAAATATAGCTACCAAGTTTCTATGGTGCAAAGCAATATGCATCAATGATCGTGCAATTGGGTGTGTTTCTCTATCCTCAAGTTCACCTGGTGATAAATCCAGGAACAAATGTGCAGAACTTGGCTATGTTCTAGGCTCTAAATATTGGGGTAAAGGGGTTGCCACATGTGTTGTGAAACAAGTTGTTAAGGTTGCATTCTGTGAGTTGACTTACTTGGAAAGGCTTGAAGCTTTAGTTGATGTGGAAAATGCTGGGTCTCAAAGAGTGCTGGAGAAAGCTGGTTTCCAAAAGGAGGGAGTTCTAAGGAAATATTTGTTCATGAAAGGAAAAAGTAGAGATATGATCATGTCCAGTGTTCTTTCTACTGATCTCCAACTATAA
Protein sequence

>Msa0793760

MERTSISFEPRAKEERIDLTQITLRALQLSDLDDLMVWTTDEKVAKFCSWELYTSKDDGINFIENIATKFLWCKAICINDRAIGCVSLSSSSPGDKSRNKCAELGYVLGSKYWGKGVATCVVKQVVKVAFCELTYLERLEALVDVENAGSQRVLEKAGFQKEGVLRKYLFMKGKSRDMIMSSVLSTDLQL*