AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0568920


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0568920 MtrunA17_Chr8g0383861 76.652 227 9 2 1 183 1 227 1.76e-104 299
Msa0568920 MtrunA17_Chr8g0383881 64.889 225 25 4 1 181 1 215 5.48e-84 247
Msa0568920 MtrunA17_Chr8g0383941 61.674 227 34 4 1 182 1 219 6.02e-83 244
Msa0568920 MtrunA17_Chr8g0383901 61.947 226 33 3 1 182 1 217 6.77e-79 234
Msa0568920 MtrunA17_Chr8g0383871 60.619 226 44 3 1 182 1 225 6.33e-76 226
Msa0568920 MtrunA17_Chr8g0383931 60.088 228 46 3 1 183 1 228 4.83e-65 199
Msa0568920 MtrunA17_Chr8g0383921 57.746 213 42 4 1 168 1 210 1.49e-63 195
Msa0568920 MtrunA17_Chr3g0129671 46.121 232 72 4 1 183 1 228 8.29e-57 178
Msa0568920 MtrunA17_Chr7g0244851 37.931 87 49 1 42 128 15 96 4.38e-14 67.0
Msa0568920 MtrunA17_Chr3g0128771 40.449 89 48 1 53 141 36 119 9.08e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0568920 AT1G49230.1 38.532 218 71 5 11 180 17 219 1.49e-35 124
Msa0568920 AT1G49220.1 42.188 128 56 4 21 143 23 137 7.43e-24 94.7
Msa0568920 AT1G49210.1 32.093 215 82 5 21 183 23 225 1.03e-23 93.6
Msa0568920 AT1G49200.1 31.163 215 84 5 21 183 24 226 4.72e-23 92.0
Msa0568920 AT3G18773.1 30.263 228 94 8 6 183 8 220 1.16e-16 75.1
Msa0568920 AT5G05280.1 41.237 97 52 1 46 142 26 117 1.93e-14 68.2
Msa0568920 AT3G10910.1 41.111 90 48 2 57 143 29 116 1.58e-12 63.2
Msa0568920 AT1G20823.1 36.364 110 57 3 23 130 3 101 6.31e-11 59.3

Find 42 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATCATAAGGTGCGCTTTA+AGG 0.098073 4_1:-70564105 Msa0568920:CDS
AATTCAACCAACTCATATTT+TGG 0.106711 4_1:-70564208 Msa0568920:CDS
TGAGTTGAAACTACCAAATT+TGG 0.175122 4_1:-70563957 Msa0568920:CDS
ATTGATAATCAATTGGATTT+TGG 0.213343 4_1:+70564266 None:intergenic
GCACCTTATGATGGAGTTTA+AGG 0.230395 4_1:+70564114 None:intergenic
CGGTGCCAGAAACTATTATT+AGG 0.257137 4_1:-70563737 Msa0568920:CDS
CGAAGAAGAGCCGTTGTTTA+GGG 0.291613 4_1:+70564069 None:intergenic
TCGAAGAAGAGCCGTTGTTT+AGG 0.297762 4_1:+70564068 None:intergenic
ACACACTCTGTATCCAAATT+TGG 0.302122 4_1:+70563944 None:intergenic
TGAATCCTAATAATAGTTTC+TGG 0.307133 4_1:+70563732 None:intergenic
AATATGAGTTGGTTGAATTA+TGG 0.317058 4_1:+70564212 None:intergenic
CAACAACTCTTCACCTCAAT+TGG 0.382798 4_1:-70564038 Msa0568920:CDS
GAGACTTGTCGAAAGATTGT+TGG 0.413029 4_1:-70563783 Msa0568920:CDS
GTTGGTGATTGATAATCAAT+TGG 0.420758 4_1:+70564259 None:intergenic
GGAAGCACCACCTATGTTGC+CGG 0.443914 4_1:-70563757 Msa0568920:CDS
ATAGTTACGTTCAAAAGCTT+CGG 0.462496 4_1:+70563698 None:intergenic
TTATGGTTGTGTGTGAGAAC+AGG 0.463446 4_1:+70564229 None:intergenic
AGCAAATAAGAGCACACAAT+AGG 0.463910 4_1:+70564143 None:intergenic
TCAGTTGAATAACTTACTGT+TGG 0.468597 4_1:+70563977 None:intergenic
ATTCCTTTGTTAGCCAATTG+AGG 0.468663 4_1:+70564025 None:intergenic
TTGTCGAAAGATTGTTGGAT+TGG 0.474737 4_1:-70563778 Msa0568920:CDS
CCTTAAAGCGCACCTTATGA+TGG 0.477521 4_1:+70564105 None:intergenic
CAGTTGAATAACTTACTGTT+GGG 0.481542 4_1:+70563978 None:intergenic
GTGTGTGAGAACAGGGGAGC+TGG 0.495001 4_1:+70564237 None:intergenic
ACGAATTCCAAAATATGAGT+TGG 0.498815 4_1:+70564201 None:intergenic
TTGTAGAATCTCACACAAGA+AGG 0.511006 4_1:-70564297 Msa0568920:CDS
TTGCCTTAAACTCCATCATA+AGG 0.515596 4_1:-70564117 Msa0568920:CDS
ATGGAAGAGTGGTGAAGTAA+AGG 0.523047 4_1:+70564327 None:intergenic
CTAATAATAGTTTCTGGCAC+CGG 0.527248 4_1:+70563738 None:intergenic
GTTTCTGGCACCGGCAACAT+AGG 0.529637 4_1:+70563747 None:intergenic
TATGGTTGTGTGTGAGAACA+GGG 0.557986 4_1:+70564230 None:intergenic
TAACAAAGGAATCAAGAAGA+AGG 0.567789 4_1:-70564014 Msa0568920:CDS
GAGATTCTACAAGAAGCTCA+TGG 0.595637 4_1:+70564308 None:intergenic
CAATCTTTCGACAAGTCTCA+AGG 0.597223 4_1:+70563787 None:intergenic
TCACCTCAATTGGCTAACAA+AGG 0.606400 4_1:-70564028 Msa0568920:CDS
TCAAAAGCTTCGGCGTCTAG+CGG 0.624371 4_1:+70563708 None:intergenic
ACAAGAAGCTCATGGAAGAG+TGG 0.629363 4_1:+70564316 None:intergenic
TCTGGCACCGGCAACATAGG+TGG 0.632227 4_1:+70563750 None:intergenic
GTGAGAACAGGGGAGCTGGT+TGG 0.655380 4_1:+70564241 None:intergenic
TCGAACGTAGCCCTAAACAA+CGG 0.719891 4_1:-70564079 Msa0568920:CDS
ATGGTTGTGTGTGAGAACAG+GGG 0.776032 4_1:+70564231 None:intergenic
TCTTTCGACAAGTCTCAAGG+AGG 0.776052 4_1:+70563790 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTGATAATCAATTGGATTT+TGG + chr4_1:70563763-70563782 None:intergenic 20.0%
!!! AATATGAGTTGGTTGAATTA+TGG + chr4_1:70563817-70563836 None:intergenic 25.0%
!! AATTCAACCAACTCATATTT+TGG - chr4_1:70563818-70563837 Msa0568920:intron 25.0%
! TTTACCTAAATGCAATCATA+TGG - chr4_1:70564147-70564166 Msa0568920:CDS 25.0%
! TGAATCCTAATAATAGTTTC+TGG + chr4_1:70564297-70564316 None:intergenic 25.0%
!! GTTGGTGATTGATAATCAAT+TGG + chr4_1:70563770-70563789 None:intergenic 30.0%
ACGAATTCCAAAATATGAGT+TGG + chr4_1:70563828-70563847 None:intergenic 30.0%
TAACAAAGGAATCAAGAAGA+AGG - chr4_1:70564012-70564031 Msa0568920:CDS 30.0%
CAGTTGAATAACTTACTGTT+GGG + chr4_1:70564051-70564070 None:intergenic 30.0%
TCAGTTGAATAACTTACTGT+TGG + chr4_1:70564052-70564071 None:intergenic 30.0%
! TGAGTTGAAACTACCAAATT+TGG - chr4_1:70564069-70564088 Msa0568920:CDS 30.0%
GAAACCATATGATTGCATTT+AGG + chr4_1:70564154-70564173 None:intergenic 30.0%
ATAGTTACGTTCAAAAGCTT+CGG + chr4_1:70564331-70564350 None:intergenic 30.0%
TTGTAGAATCTCACACAAGA+AGG - chr4_1:70563729-70563748 Msa0568920:CDS 35.0%
! AGCAAATAAGAGCACACAAT+AGG + chr4_1:70563886-70563905 None:intergenic 35.0%
TTGCCTTAAACTCCATCATA+AGG - chr4_1:70563909-70563928 Msa0568920:intron 35.0%
ATTCCTTTGTTAGCCAATTG+AGG + chr4_1:70564004-70564023 None:intergenic 35.0%
ACACACTCTGTATCCAAATT+TGG + chr4_1:70564085-70564104 None:intergenic 35.0%
TTGTCGAAAGATTGTTGGAT+TGG - chr4_1:70564248-70564267 Msa0568920:CDS 35.0%
!! CTAATAATAGTTTCTGGCAC+CGG + chr4_1:70564291-70564310 None:intergenic 35.0%
ATGGAAGAGTGGTGAAGTAA+AGG + chr4_1:70563702-70563721 None:intergenic 40.0%
GAGATTCTACAAGAAGCTCA+TGG + chr4_1:70563721-70563740 None:intergenic 40.0%
TATGGTTGTGTGTGAGAACA+GGG + chr4_1:70563799-70563818 None:intergenic 40.0%
TTATGGTTGTGTGTGAGAAC+AGG + chr4_1:70563800-70563819 None:intergenic 40.0%
! GCACCTTATGATGGAGTTTA+AGG + chr4_1:70563915-70563934 None:intergenic 40.0%
CAACAACTCTTCACCTCAAT+TGG - chr4_1:70563988-70564007 Msa0568920:CDS 40.0%
TCACCTCAATTGGCTAACAA+AGG - chr4_1:70563998-70564017 Msa0568920:CDS 40.0%
TGTCTCTCAGAGTTCACAAA+AGG - chr4_1:70564109-70564128 Msa0568920:CDS 40.0%
ATTTGTCGATGCAACGAACA+TGG + chr4_1:70564176-70564195 None:intergenic 40.0%
! ATGTTCGTTGCATCGACAAA+TGG - chr4_1:70564175-70564194 Msa0568920:CDS 40.0%
CAATCTTTCGACAAGTCTCA+AGG + chr4_1:70564242-70564261 None:intergenic 40.0%
GAGACTTGTCGAAAGATTGT+TGG - chr4_1:70564243-70564262 Msa0568920:CDS 40.0%
! CGGTGCCAGAAACTATTATT+AGG - chr4_1:70564289-70564308 Msa0568920:CDS 40.0%
ACAAGAAGCTCATGGAAGAG+TGG + chr4_1:70563713-70563732 None:intergenic 45.0%
ATGGTTGTGTGTGAGAACAG+GGG + chr4_1:70563798-70563817 None:intergenic 45.0%
CCTTAAAGCGCACCTTATGA+TGG + chr4_1:70563924-70563943 None:intergenic 45.0%
CCATCATAAGGTGCGCTTTA+AGG - chr4_1:70563921-70563940 Msa0568920:intron 45.0%
TCGAACGTAGCCCTAAACAA+CGG - chr4_1:70563947-70563966 Msa0568920:intron 45.0%
CGAAGAAGAGCCGTTGTTTA+GGG + chr4_1:70563960-70563979 None:intergenic 45.0%
TCGAAGAAGAGCCGTTGTTT+AGG + chr4_1:70563961-70563980 None:intergenic 45.0%
TCTTTCGACAAGTCTCAAGG+AGG + chr4_1:70564239-70564258 None:intergenic 45.0%
TCAAAAGCTTCGGCGTCTAG+CGG + chr4_1:70564321-70564340 None:intergenic 50.0%
!! AGGAGGCACTGTCTGCACTT+AGG + chr4_1:70564222-70564241 None:intergenic 55.0%
!! GGAAGCACCACCTATGTTGC+CGG - chr4_1:70564269-70564288 Msa0568920:CDS 55.0%
!! GTTTCTGGCACCGGCAACAT+AGG + chr4_1:70564282-70564301 None:intergenic 55.0%
GTGAGAACAGGGGAGCTGGT+TGG + chr4_1:70563788-70563807 None:intergenic 60.0%
GTGTGTGAGAACAGGGGAGC+TGG + chr4_1:70563792-70563811 None:intergenic 60.0%
!! TCTGGCACCGGCAACATAGG+TGG + chr4_1:70564279-70564298 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 70563683 70564365 70563683 ID=Msa0568920;Name=Msa0568920
chr4_1 mRNA 70563683 70564365 70563683 ID=Msa0568920-mRNA-1;Parent=Msa0568920;Name=Msa0568920-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|0|0|1|1|1|2|0|183
chr4_1 exon 70563950 70564365 70563950 ID=Msa0568920-mRNA-1:exon:23823;Parent=Msa0568920-mRNA-1
chr4_1 exon 70563683 70563818 70563683 ID=Msa0568920-mRNA-1:exon:23822;Parent=Msa0568920-mRNA-1
chr4_1 CDS 70563950 70564365 70563950 ID=Msa0568920-mRNA-1:cds;Parent=Msa0568920-mRNA-1
chr4_1 CDS 70563683 70563818 70563683 ID=Msa0568920-mRNA-1:cds;Parent=Msa0568920-mRNA-1
Gene Sequence

>Msa0568920

ATGTATGCTTCTACTTCCTTTACTTCACCACTCTTCCATGAGCTTCTTGTAGAATCTCACACAAGAAGGTTGCTCTTCCAAAATCCAATTGATTATCAATCACCAACCAGCTCCCCTGTTCTCACACACAACCATAATTCAACCAACTCATATTTTGGAATTCGTGAATTTGATGCAAATGTTGTGATGATACTTGCAGTCCTATTGTGTGCTCTTATTTGCTCACTTGCCTTAAACTCCATCATAAGGTGCGCTTTAAGGTTTTCGAACGTAGCCCTAAACAACGGCTCTTCTTCGAGTTTGAGCAACAACTCTTCACCTCAATTGGCTAACAAAGGAATCAAGAAGAAGGCTCTCAAGACATTCCCAACAGTAAGTTATTCAACTGAGTTGAAACTACCAAATTTGGATACAGAACAGTGCCTCCTTGAGACTTGTCGAAAGATTGTTGGATTGGAAGCACCACCTATGTTGCCGGTGCCAGAAACTATTATTAGGATTCAACCGCTAGACGCCGAAGCTTTTGAACGTAACTATAGAGAATTAAGCTGA

Protein sequence

>Msa0568920

MYASTSFTSPLFHELLVESHTRRLLFQNPIDYQSPTSSPVLTHNHNSTNSYFGIREFDANVVMILAVLLCALICSLALNSIIRCALRFSNVALNNGSSSSLSNNSSPQLANKGIKKKALKTFPTVSYSTELKLPNLDTEQCLLETCRKIVGLEAPPMLPVPETIIRIQPLDAEAFERNYRELS*