AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene034899

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034899.t1 MTR_1g060610 100.000 149 0 0 1 149 1 149 4.81e-109 306
MS.gene034899.t1 MTR_3g080800 44.286 140 75 2 5 144 66 202 1.26e-28 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene034899.t1 AT4G35490 85.315 143 21 0 7 149 13 155 1.15e-91 263
MS.gene034899.t1 AT4G35490 85.315 143 21 0 7 149 13 155 1.15e-91 263
MS.gene034899.t1 AT1G32990 44.286 140 75 2 5 144 72 208 7.44e-28 103

Find 54 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCATTTCTAAATCCATTAT+TGG 0.175466 1.2:-46553844 MS.gene034899:CDS
GTAACAGCCATTGGTGTATC+AGG 0.275383 1.2:+46554069 None:intergenic
CGATACCCGCAGCTTTCTTC+AGG 0.313010 1.2:+46553983 None:intergenic
GCTCCTAGCTGTACCAATAA+TGG 0.322397 1.2:+46553831 None:intergenic
ACAGTCTGATCCTTACTTGC+AGG 0.357839 1.2:-46553881 MS.gene034899:CDS
ACCAATAATGGATTTAGAAA+TGG 0.398795 1.2:+46553843 None:intergenic
GAAAGCTGCGGGTATCGAAT+TGG 0.398936 1.2:-46553977 MS.gene034899:CDS
GGAGGTGGCGGTCACATGAC+CGG 0.412632 1.2:+46553942 None:intergenic
ATTGTCGCTGCTACCACTTT+CGG 0.429301 1.2:+46554216 None:intergenic
AGTGGCATACCCTGCAAGTA+AGG 0.435747 1.2:+46553871 None:intergenic
AACGATGAGCGTTCCGAAAG+TGG 0.442624 1.2:-46554229 None:intergenic
CCTCCTGTGGGACCTGCGCT+AGG 0.444053 1.2:-46554156 MS.gene034899:CDS
CTCCAGCTGGAACTCTCAAC+CGG 0.454096 1.2:+46554193 None:intergenic
TCCAGCTGGAGGAGCACGTC+CGG 0.454983 1.2:-46554181 MS.gene034899:CDS
AGCACGTCCGGCGCCTCCTG+TGG 0.466575 1.2:-46554169 MS.gene034899:CDS
AAAGCTGCGGGTATCGAATT+GGG 0.473529 1.2:-46553976 MS.gene034899:CDS
AGTCTTTGCAGAAAGCCATA+AGG 0.492679 1.2:+46554118 None:intergenic
GCTGTTATTGTAACAGCCAT+TGG 0.492932 1.2:+46554060 None:intergenic
GGCGGTCACATGACCGGGAC+GGG 0.494244 1.2:+46553948 None:intergenic
TCAGTACCGACTGAACCTTA+TGG 0.497875 1.2:-46554133 MS.gene034899:CDS
AAGTGGTAGCAGCGACAATC+CGG 0.509428 1.2:-46554212 MS.gene034899:CDS
GCCGGACGTGCTCCTCCAGC+TGG 0.512277 1.2:+46554180 None:intergenic
GCACGTCCGGCGCCTCCTGT+GGG 0.517535 1.2:-46554168 MS.gene034899:CDS
CATACACGTGCCGAAGTGAC+AGG 0.517596 1.2:+46553920 None:intergenic
GAGGTGGCGGTCACATGACC+GGG 0.519759 1.2:+46553943 None:intergenic
CCGAAGTGACAGGGAGGTGG+CGG 0.522973 1.2:+46553930 None:intergenic
TGTTACAATAACAGCTTACA+AGG 0.549953 1.2:-46554052 MS.gene034899:CDS
TGACCTAGCGCAGGTCCCAC+AGG 0.552959 1.2:+46554153 None:intergenic
GCAGGTCCCACAGGAGGCGC+CGG 0.567732 1.2:+46554162 None:intergenic
ATTGGTACAGCTAGGAGCAT+GGG 0.571876 1.2:-46553826 MS.gene034899:CDS
CCGCCACCTCCCTGTCACTT+CGG 0.584871 1.2:-46553930 MS.gene034899:CDS
TGGTACCTGAAGAAAGCTGC+GGG 0.584881 1.2:-46553988 MS.gene034899:CDS
ATCCGGTTGAGAGTTCCAGC+TGG 0.592293 1.2:-46554195 MS.gene034899:CDS
TATTGGTACAGCTAGGAGCA+TGG 0.593721 1.2:-46553827 MS.gene034899:CDS
CAGTCTGATCCTTACTTGCA+GGG 0.597928 1.2:-46553880 MS.gene034899:CDS
GTGCCGAAGTGACAGGGAGG+TGG 0.602083 1.2:+46553927 None:intergenic
TTAAATCTCCTTCCGTCTCG+TGG 0.602388 1.2:-46554008 MS.gene034899:CDS
TTCAGGTACCACGAGACGGA+AGG 0.605506 1.2:+46554000 None:intergenic
TGGCGGTCACATGACCGGGA+CGG 0.607191 1.2:+46553947 None:intergenic
TTTCTTCAGGTACCACGAGA+CGG 0.610355 1.2:+46553996 None:intergenic
AGTCGGTACTGACCTAGCGC+AGG 0.626095 1.2:+46554144 None:intergenic
GAATTGGGAAGTACCCGTCC+CGG 0.626450 1.2:-46553961 MS.gene034899:CDS
AATCCATTATTGGTACAGCT+AGG 0.638443 1.2:-46553834 MS.gene034899:CDS
CCTAGCGCAGGTCCCACAGG+AGG 0.638505 1.2:+46554156 None:intergenic
ATACACGTGCCGAAGTGACA+GGG 0.645886 1.2:+46553921 None:intergenic
AGAAAGCCATAAGGTTCAGT+CGG 0.648161 1.2:+46554127 None:intergenic
TCTGCAAAGACTTCAACGCA+CGG 0.650245 1.2:-46554107 MS.gene034899:CDS
AGATTTAACAGTGAACTCAA+AGG 0.651355 1.2:+46554023 None:intergenic
GATTTAGAAATGGACTCAAG+TGG 0.655714 1.2:+46553853 None:intergenic
ATTCAAGCCTGATACACCAA+TGG 0.658568 1.2:-46554076 MS.gene034899:CDS
GTGGTACCTGAAGAAAGCTG+CGG 0.662466 1.2:-46553989 MS.gene034899:CDS
CGGTTGAGAGTTCCAGCTGG+AGG 0.663118 1.2:-46554192 MS.gene034899:CDS
GCACGTGTATGAGATCGCTA+AGG 0.664058 1.2:-46553908 MS.gene034899:CDS
CACGTGCCGAAGTGACAGGG+AGG 0.790794 1.2:+46553924 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCCATTTCTAAATCCATTAT+TGG - chr1.2:46554179-46554198 MS.gene034899:CDS 25.0%
!!! ACCAATAATGGATTTAGAAA+TGG + chr1.2:46554183-46554202 None:intergenic 25.0%
AGATTTAACAGTGAACTCAA+AGG + chr1.2:46554003-46554022 None:intergenic 30.0%
TGTTACAATAACAGCTTACA+AGG - chr1.2:46553971-46553990 MS.gene034899:CDS 30.0%
AATCCATTATTGGTACAGCT+AGG - chr1.2:46554189-46554208 MS.gene034899:CDS 35.0%
! GATTTAGAAATGGACTCAAG+TGG + chr1.2:46554173-46554192 None:intergenic 35.0%
AGAAAGCCATAAGGTTCAGT+CGG + chr1.2:46553899-46553918 None:intergenic 40.0%
AGTCTTTGCAGAAAGCCATA+AGG + chr1.2:46553908-46553927 None:intergenic 40.0%
ATTCAAGCCTGATACACCAA+TGG - chr1.2:46553947-46553966 MS.gene034899:CDS 40.0%
GCTGTTATTGTAACAGCCAT+TGG + chr1.2:46553966-46553985 None:intergenic 40.0%
ACAGTCTGATCCTTACTTGC+AGG - chr1.2:46554142-46554161 MS.gene034899:CDS 45.0%
ATTGTCGCTGCTACCACTTT+CGG + chr1.2:46553810-46553829 None:intergenic 45.0%
CAGTCTGATCCTTACTTGCA+GGG - chr1.2:46554143-46554162 MS.gene034899:CDS 45.0%
GCTCCTAGCTGTACCAATAA+TGG + chr1.2:46554195-46554214 None:intergenic 45.0%
GTAACAGCCATTGGTGTATC+AGG + chr1.2:46553957-46553976 None:intergenic 45.0%
TATTGGTACAGCTAGGAGCA+TGG - chr1.2:46554196-46554215 MS.gene034899:CDS 45.0%
TCTGCAAAGACTTCAACGCA+CGG - chr1.2:46553916-46553935 MS.gene034899:CDS 45.0%
TTAAATCTCCTTCCGTCTCG+TGG - chr1.2:46554015-46554034 MS.gene034899:CDS 45.0%
TTTCTTCAGGTACCACGAGA+CGG + chr1.2:46554030-46554049 None:intergenic 45.0%
! ATTGGTACAGCTAGGAGCAT+GGG - chr1.2:46554197-46554216 MS.gene034899:CDS 45.0%
!! AAAGCTGCGGGTATCGAATT+GGG - chr1.2:46554047-46554066 MS.gene034899:CDS 45.0%
!! TCAGTACCGACTGAACCTTA+TGG - chr1.2:46553890-46553909 MS.gene034899:CDS 45.0%
AAGTGGTAGCAGCGACAATC+CGG - chr1.2:46553811-46553830 MS.gene034899:CDS 50.0%
AGTGGCATACCCTGCAAGTA+AGG + chr1.2:46554155-46554174 None:intergenic 50.0%
ATACACGTGCCGAAGTGACA+GGG + chr1.2:46554105-46554124 None:intergenic 50.0%
GCACGTGTATGAGATCGCTA+AGG - chr1.2:46554115-46554134 MS.gene034899:CDS 50.0%
GTGGTACCTGAAGAAAGCTG+CGG - chr1.2:46554034-46554053 MS.gene034899:CDS 50.0%
TGGTACCTGAAGAAAGCTGC+GGG - chr1.2:46554035-46554054 MS.gene034899:CDS 50.0%
!! GAAAGCTGCGGGTATCGAAT+TGG - chr1.2:46554046-46554065 MS.gene034899:CDS 50.0%
ATCCGGTTGAGAGTTCCAGC+TGG - chr1.2:46553828-46553847 MS.gene034899:CDS 55.0%
CATACACGTGCCGAAGTGAC+AGG + chr1.2:46554106-46554125 None:intergenic 55.0%
CGATACCCGCAGCTTTCTTC+AGG + chr1.2:46554043-46554062 None:intergenic 55.0%
CTCCAGCTGGAACTCTCAAC+CGG + chr1.2:46553833-46553852 None:intergenic 55.0%
TTCAGGTACCACGAGACGGA+AGG + chr1.2:46554026-46554045 None:intergenic 55.0%
!! GAATTGGGAAGTACCCGTCC+CGG - chr1.2:46554062-46554081 MS.gene034899:CDS 55.0%
CGGTTGAGAGTTCCAGCTGG+AGG - chr1.2:46553831-46553850 MS.gene034899:CDS 60.0%
!! AGTCGGTACTGACCTAGCGC+AGG + chr1.2:46553882-46553901 None:intergenic 60.0%
CACGTGCCGAAGTGACAGGG+AGG + chr1.2:46554102-46554121 None:intergenic 65.0%
CCGAAGTGACAGGGAGGTGG+CGG + chr1.2:46554096-46554115 None:intergenic 65.0%
GTGCCGAAGTGACAGGGAGG+TGG + chr1.2:46554099-46554118 None:intergenic 65.0%
TGACCTAGCGCAGGTCCCAC+AGG + chr1.2:46553873-46553892 None:intergenic 65.0%
TGGCGGTCACATGACCGGGA+CGG + chr1.2:46554079-46554098 None:intergenic 65.0%
! CCGCCACCTCCCTGTCACTT+CGG - chr1.2:46554093-46554112 MS.gene034899:CDS 65.0%
! GAGGTGGCGGTCACATGACC+GGG + chr1.2:46554083-46554102 None:intergenic 65.0%
! GGAGGTGGCGGTCACATGAC+CGG + chr1.2:46554084-46554103 None:intergenic 65.0%
! TCCAGCTGGAGGAGCACGTC+CGG - chr1.2:46553842-46553861 MS.gene034899:CDS 65.0%
CCTAGCGCAGGTCCCACAGG+AGG + chr1.2:46553870-46553889 None:intergenic 70.0%
CCTCCTGTGGGACCTGCGCT+AGG - chr1.2:46553867-46553886 MS.gene034899:CDS 70.0%
GGCGGTCACATGACCGGGAC+GGG + chr1.2:46554078-46554097 None:intergenic 70.0%
AGCACGTCCGGCGCCTCCTG+TGG - chr1.2:46553854-46553873 MS.gene034899:CDS 75.0%
GCACGTCCGGCGCCTCCTGT+GGG - chr1.2:46553855-46553874 MS.gene034899:CDS 75.0%
GCCGGACGTGCTCCTCCAGC+TGG + chr1.2:46553846-46553865 None:intergenic 75.0%
! GCAGGTCCCACAGGAGGCGC+CGG + chr1.2:46553864-46553883 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 46553798 46554247 46553798 ID=MS.gene034899
chr1.2 mRNA 46553798 46554247 46553798 ID=MS.gene034899.t1;Parent=MS.gene034899
chr1.2 exon 46553798 46554247 46553798 ID=MS.gene034899.t1.exon1;Parent=MS.gene034899.t1
chr1.2 CDS 46553798 46554247 46553798 ID=cds.MS.gene034899.t1;Parent=MS.gene034899.t1
Gene Sequence

>MS.gene034899

ATGAGCGTTCCGAAAGTGGTAGCAGCGACAATCCGGTTGAGAGTTCCAGCTGGAGGAGCACGTCCGGCGCCTCCTGTGGGACCTGCGCTAGGTCAGTACCGACTGAACCTTATGGCTTTCTGCAAAGACTTCAACGCACGGACTCAGAAATTCAAGCCTGATACACCAATGGCTGTTACAATAACAGCTTACAAGGACAACACCTTTGAGTTCACTGTTAAATCTCCTTCCGTCTCGTGGTACCTGAAGAAAGCTGCGGGTATCGAATTGGGAAGTACCCGTCCCGGTCATGTGACCGCCACCTCCCTGTCACTTCGGCACGTGTATGAGATCGCTAAGGTGAAACAGTCTGATCCTTACTTGCAGGGTATGCCACTTGAGTCCATTTCTAAATCCATTATTGGTACAGCTAGGAGCATGGGAATCAAAATTGTCAAAGATCTTGAATGA
Protein sequence

>MS.gene034899.t1

MSVPKVVAATIRLRVPAGGARPAPPVGPALGQYRLNLMAFCKDFNARTQKFKPDTPMAVTITAYKDNTFEFTVKSPSVSWYLKKAAGIELGSTRPGHVTATSLSLRHVYEIAKVKQSDPYLQGMPLESISKSIIGTARSMGIKIVKDLE