AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene57244

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene57244.t1 MTR_1g016200 56.311 103 34 3 9 100 2 104 2.03e-24 90.1
MS.gene57244.t1 MTR_1g016170 62.500 48 15 1 56 100 187 234 4.86e-13 64.3
MS.gene57244.t1 MTR_7g112330 42.373 59 34 0 56 114 22 80 2.70e-11 57.0
MS.gene57244.t1 MTR_4g121110 48.276 58 25 2 54 111 28 80 5.24e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene57244.t1 AT5G56860 49.231 65 29 1 25 89 203 263 6.23e-13 64.3
MS.gene57244.t1 AT4G26150 71.875 32 9 0 56 87 199 230 5.75e-11 58.5

Find 27 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCTTTGTGGCTGGAAC+TGG 0.239072 1.4:-6123830 None:intergenic
AGTATTCGCCATTGCCCTTT+TGG 0.253039 1.4:-6123941 None:intergenic
ATGAGTATCAAGACCCTTAT+CGG 0.303482 1.4:-6124230 None:intergenic
ATACAAACACTACTCCTCTT+TGG 0.387924 1.4:+6123993 MS.gene57244:CDS
GGAAGAGGCAAAAGCCGATA+AGG 0.448770 1.4:+6124216 MS.gene57244:CDS
CAATCGAAACAAACCCTAGT+TGG 0.460017 1.4:-6123968 None:intergenic
TCTTGATACTCATAAGGAAA+AGG 0.465163 1.4:+6124240 MS.gene57244:CDS
TTGCCTCTTCCCTTCTTCGT+CGG 0.477939 1.4:-6124204 None:intergenic
CTTGATACTCATAAGGAAAA+GGG 0.489428 1.4:+6124241 MS.gene57244:CDS
TAAGGGTCTTGATACTCATA+AGG 0.492473 1.4:+6124234 MS.gene57244:CDS
ACTGAATACGAATACCCAAA+AGG 0.517161 1.4:+6123926 MS.gene57244:CDS
GAAGAGGCAAAAGCCGATAA+GGG 0.529120 1.4:+6124217 MS.gene57244:CDS
CTGAATACGAATACCCAAAA+GGG 0.529249 1.4:+6123927 MS.gene57244:CDS
ATGTGGACTCCGACGAAGAA+GGG 0.540307 1.4:+6124195 MS.gene57244:CDS
CTTTGGAGGAGTGATCCTAC+AGG 0.546346 1.4:+6124010 MS.gene57244:CDS
GGCGAATACTATATCCAACT+AGG 0.572160 1.4:+6123954 MS.gene57244:CDS
CATGTGGACTCCGACGAAGA+AGG 0.573346 1.4:+6124194 MS.gene57244:CDS
GAGTGATCCTACAGGTTCCA+AGG 0.583772 1.4:+6124018 MS.gene57244:CDS
ACTCCGACGAAGAAGGGAAG+AGG 0.589069 1.4:+6124201 MS.gene57244:CDS
CAAACACTACTCCTCTTTGG+AGG 0.592172 1.4:+6123996 MS.gene57244:CDS
GCGAATACTATATCCAACTA+GGG 0.606852 1.4:+6123955 MS.gene57244:CDS
CAGTCGTTGTGCAATGCATG+TGG 0.610062 1.4:+6124178 MS.gene57244:intron
ACGAATACCCAAAAGGGCAA+TGG 0.610371 1.4:+6123933 MS.gene57244:CDS
ACTCATAAGGAAAAGGGCAA+TGG 0.616678 1.4:+6124247 MS.gene57244:CDS
TGGCGAACGCTCATCATCTG+AGG 0.618644 1.4:+6124267 MS.gene57244:CDS
CTAATTACCTTGGAACCTGT+AGG 0.621221 1.4:-6124025 None:intergenic
GTAGGATCACTCCTCCAAAG+AGG 0.666474 1.4:-6124007 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTTAACAAGAAATATGT+TGG + chr1.4:6124153-6124172 MS.gene57244:intron 20.0%
!!! ACCAGTTTTTATTTTCTTTT+TGG - chr1.4:6123906-6123925 None:intergenic 20.0%
! GCCAAAAAGAAAATAAAAAC+TGG + chr1.4:6123902-6123921 MS.gene57244:CDS 25.0%
! TAGAGATTAACTAATTACCT+TGG - chr1.4:6124038-6124057 None:intergenic 25.0%
CTTGATACTCATAAGGAAAA+GGG + chr1.4:6124241-6124260 MS.gene57244:CDS 30.0%
TCTTGATACTCATAAGGAAA+AGG + chr1.4:6124240-6124259 MS.gene57244:CDS 30.0%
ACTGAATACGAATACCCAAA+AGG + chr1.4:6123926-6123945 MS.gene57244:CDS 35.0%
ATACAAACACTACTCCTCTT+TGG + chr1.4:6123993-6124012 MS.gene57244:CDS 35.0%
ATGAGTATCAAGACCCTTAT+CGG - chr1.4:6124233-6124252 None:intergenic 35.0%
CTGAATACGAATACCCAAAA+GGG + chr1.4:6123927-6123946 MS.gene57244:CDS 35.0%
GCGAATACTATATCCAACTA+GGG + chr1.4:6123955-6123974 MS.gene57244:CDS 35.0%
TAAGGGTCTTGATACTCATA+AGG + chr1.4:6124234-6124253 MS.gene57244:CDS 35.0%
!!! AGCAGCTTTTTTCTTCTTTG+TGG - chr1.4:6123843-6123862 None:intergenic 35.0%
ACTCATAAGGAAAAGGGCAA+TGG + chr1.4:6124247-6124266 MS.gene57244:CDS 40.0%
AGAAGAAAAAAGCTGCTGCT+AGG + chr1.4:6123846-6123865 MS.gene57244:CDS 40.0%
ATGAACCAAGAGTGAAAGCT+GGG - chr1.4:6124066-6124085 None:intergenic 40.0%
CAATCGAAACAAACCCTAGT+TGG - chr1.4:6123971-6123990 None:intergenic 40.0%
CTAATTACCTTGGAACCTGT+AGG - chr1.4:6124028-6124047 None:intergenic 40.0%
GAAGAAAAAAGCTGCTGCTA+GGG + chr1.4:6123847-6123866 MS.gene57244:CDS 40.0%
GGCGAATACTATATCCAACT+AGG + chr1.4:6123954-6123973 MS.gene57244:CDS 40.0%
!!! GCTTTTTTCTTCTTTGTGGC+TGG - chr1.4:6123839-6123858 None:intergenic 40.0%
ACGAATACCCAAAAGGGCAA+TGG + chr1.4:6123933-6123952 MS.gene57244:CDS 45.0%
CAAACACTACTCCTCTTTGG+AGG + chr1.4:6123996-6124015 MS.gene57244:CDS 45.0%
CATGAACCAAGAGTGAAAGC+TGG - chr1.4:6124067-6124086 None:intergenic 45.0%
GAAGAGGCAAAAGCCGATAA+GGG + chr1.4:6124217-6124236 MS.gene57244:CDS 45.0%
TGAACCAAGAGTGAAAGCTG+GGG - chr1.4:6124065-6124084 None:intergenic 45.0%
TTCTTCTTTGTGGCTGGAAC+TGG - chr1.4:6123833-6123852 None:intergenic 45.0%
! AGTATTCGCCATTGCCCTTT+TGG - chr1.4:6123944-6123963 None:intergenic 45.0%
! GTATTCGCCATTGCCCTTTT+GGG - chr1.4:6123943-6123962 None:intergenic 45.0%
ATGTGGACTCCGACGAAGAA+GGG + chr1.4:6124195-6124214 MS.gene57244:CDS 50.0%
CAGTCGTTGTGCAATGCATG+TGG + chr1.4:6124178-6124197 MS.gene57244:intron 50.0%
GAGTGATCCTACAGGTTCCA+AGG + chr1.4:6124018-6124037 MS.gene57244:CDS 50.0%
GGAAGAGGCAAAAGCCGATA+AGG + chr1.4:6124216-6124235 MS.gene57244:CDS 50.0%
GTAGGATCACTCCTCCAAAG+AGG - chr1.4:6124010-6124029 None:intergenic 50.0%
TTCTCCCCAGCTTTCACTCT+TGG + chr1.4:6124058-6124077 MS.gene57244:intron 50.0%
TTGCCTCTTCCCTTCTTCGT+CGG - chr1.4:6124207-6124226 None:intergenic 50.0%
! CTTTGGAGGAGTGATCCTAC+AGG + chr1.4:6124010-6124029 MS.gene57244:CDS 50.0%
ACTCCGACGAAGAAGGGAAG+AGG + chr1.4:6124201-6124220 MS.gene57244:CDS 55.0%
CATGTGGACTCCGACGAAGA+AGG + chr1.4:6124194-6124213 MS.gene57244:CDS 55.0%
TGGCGAACGCTCATCATCTG+AGG + chr1.4:6124267-6124286 MS.gene57244:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 6123809 6124321 6123809 ID=MS.gene57244
chr1.4 mRNA 6123809 6124321 6123809 ID=MS.gene57244.t1;Parent=MS.gene57244
chr1.4 exon 6123809 6124039 6123809 ID=MS.gene57244.t1.exon1;Parent=MS.gene57244.t1
chr1.4 CDS 6123809 6124039 6123809 ID=cds.MS.gene57244.t1;Parent=MS.gene57244.t1
chr1.4 exon 6124181 6124321 6124181 ID=MS.gene57244.t1.exon2;Parent=MS.gene57244.t1
chr1.4 CDS 6124181 6124321 6124181 ID=cds.MS.gene57244.t1;Parent=MS.gene57244.t1
Gene Sequence

>MS.gene57244

ATGAGAGTAAGTAACGATGATCCAGTTCCAGCCACAAAGAAGAAAAAAGCTGCTGCTAGGGCTACAAAAAAGAAGAAAACAGCTGCTAGTGCTGCCAAAAAGAAAATAAAAACTGGTACTGAATACGAATACCCAAAAGGGCAATGGCGAATACTATATCCAACTAGGGTTTGTTTCGATTGCAATACAAACACTACTCCTCTTTGGAGGAGTGATCCTACAGGTTCCAAGGTAATTAGTTAATCTCTATTCTCCCCAGCTTTCACTCTTGGTTCATGCAAAAGTGTTATTCTATACTTATACAATGATTAATAATTTGAATATCTAGTTATATATATATATATATAGTTAACAAGAAATATGTTGGTGCAGTCGTTGTGCAATGCATGTGGACTCCGACGAAGAAGGGAAGAGGCAAAAGCCGATAAGGGTCTTGATACTCATAAGGAAAAGGGCAATGGCGAACGCTCATCATCTGAGGATGTGAAGATTAATGTTTTAATGTTCATCTGA
Protein sequence

>MS.gene57244.t1

MRVSNDDPVPATKKKKAAARATKKKKTAASAAKKKIKTGTEYEYPKGQWRILYPTRVCFDCNTNTTPLWRSDPTGSKSLCNACGLRRRREEAKADKGLDTHKEKGNGERSSSEDVKINVLMFI