AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene56810

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene56810.t1 MTR_4g094895 99.588 243 1 0 1 243 1 243 0.0 505
MS.gene56810.t1 MTR_4g485570 53.226 248 101 6 1 242 1 239 1.56e-74 229
MS.gene56810.t1 MTR_4g485560 61.176 170 64 2 74 242 21 189 2.99e-71 219
MS.gene56810.t1 MTR_3g005710 38.693 199 117 4 44 242 51 244 9.76e-44 149
MS.gene56810.t1 MTR_8g080660 34.978 223 136 6 28 246 23 240 2.38e-41 143
MS.gene56810.t1 MTR_3g085270 34.722 216 135 4 34 246 24 236 1.45e-39 138
MS.gene56810.t1 MTR_4g102900 37.059 170 101 4 80 246 85 251 1.08e-28 110
MS.gene56810.t1 MTR_7g029100 28.139 231 143 6 14 242 14 223 3.57e-27 106
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene56810.t1 AT5G67210 69.388 245 69 1 5 243 6 250 1.33e-130 372
MS.gene56810.t1 AT3G50220 67.315 257 70 3 1 243 1 257 1.94e-126 361
MS.gene56810.t1 AT2G15440 54.167 168 75 1 74 241 78 243 6.09e-61 195
MS.gene56810.t1 AT1G71690 39.744 234 125 8 23 244 10 239 1.24e-46 157
MS.gene56810.t1 AT1G33800 39.444 180 104 3 63 242 62 236 1.21e-40 142
MS.gene56810.t1 AT1G09610 35.714 210 129 4 33 242 20 223 1.42e-39 138
MS.gene56810.t1 AT4G09990 37.104 221 125 6 29 241 13 227 2.63e-38 135
MS.gene56810.t1 AT1G67330 34.188 234 139 8 19 244 10 236 6.94e-36 129
MS.gene56810.t1 AT1G27930 34.706 170 105 4 75 242 65 230 8.41e-32 118
MS.gene56810.t1 AT4G24910 39.610 154 78 6 95 239 105 252 6.81e-25 100

Find 45 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGGAAACTCAAATCGATTA+TGG 0.310137 8.2:-25269202 MS.gene56810:CDS
GGTTGATTGGGATGTTATAT+TGG 0.342392 8.2:-25268643 MS.gene56810:CDS
GACATTCTCCCGGGAGCTTC+CGG 0.344971 8.2:+25268597 None:intergenic
AGAAATTATTGCAGTATTTG+TGG 0.362131 8.2:+25269106 None:intergenic
GGGGATTGGCCGGAAGCTCC+CGG 0.374565 8.2:-25268606 MS.gene56810:CDS
TTATTCTCAGATTGTAAACT+TGG 0.376754 8.2:-25268696 MS.gene56810:CDS
TGGAAAGCACTTAACCATAA+TGG 0.380677 8.2:-25268891 MS.gene56810:CDS
TCACACCAGAGACTCTTCTA+TGG 0.388972 8.2:-25268911 MS.gene56810:CDS
TTTCGAAGCACGTCGGAGAT+TGG 0.397431 8.2:+25268969 None:intergenic
ATGTTCAATATACAACAAAA+AGG 0.412243 8.2:-25268791 MS.gene56810:CDS
TGGGATGTTATATTGGTTGA+TGG 0.413519 8.2:-25268636 MS.gene56810:CDS
TTGATGGACCGCGCGGGGAT+TGG 0.417573 8.2:-25268620 MS.gene56810:CDS
TCAACCTCATACACATGGTT+TGG 0.423157 8.2:+25268660 None:intergenic
CAGTGTTCATCGATGAAAAT+CGG 0.433830 8.2:-25268863 MS.gene56810:CDS
ACATCATAAGCATCAATCTC+AGG 0.451907 8.2:+25268810 None:intergenic
GCTGGTAATGGTGCAGAAAC+AGG 0.455046 8.2:+25269068 None:intergenic
AAATATCGCCGACATTCTCC+CGG 0.466806 8.2:+25268587 None:intergenic
ACCATGTGTATGAGGTTGAT+TGG 0.473095 8.2:-25268656 MS.gene56810:CDS
GCTTTCCATAGAAGAGTCTC+TGG 0.473937 8.2:+25268906 None:intergenic
TTGATAACTGTTGCTGGTAA+TGG 0.483594 8.2:+25269056 None:intergenic
CCATGTGTATGAGGTTGATT+GGG 0.495004 8.2:-25268655 MS.gene56810:CDS
TGGACCGCGCGGGGATTGGC+CGG 0.499438 8.2:-25268616 MS.gene56810:CDS
GGGATTGGCCGGAAGCTCCC+GGG 0.501763 8.2:-25268605 MS.gene56810:CDS
AGAGTGTTGATAACTGTTGC+TGG 0.504927 8.2:+25269050 None:intergenic
TATTGGTTGATGGACCGCGC+GGG 0.516968 8.2:-25268626 MS.gene56810:CDS
GAGAATAAAAGATTCTGCAC+TGG 0.527711 8.2:+25268711 None:intergenic
TTTATGTAAAGAGAATTTGT+TGG 0.541273 8.2:-25268460 MS.gene56810:intron
GATATTTACCGCCGGTGTGT+TGG 0.542500 8.2:-25268571 MS.gene56810:CDS
TCTTCCAAACCATGTGTATG+AGG 0.545799 8.2:-25268664 MS.gene56810:CDS
ATTGGTTGATGGACCGCGCG+GGG 0.550084 8.2:-25268625 MS.gene56810:CDS
AATATCGCCGACATTCTCCC+GGG 0.567547 8.2:+25268588 None:intergenic
TGTCATGTGGTATGAGTCGT+TGG 0.578039 8.2:+25269007 None:intergenic
GGAAGCTCCCGGGAGAATGT+CGG 0.592858 8.2:-25268595 MS.gene56810:CDS
CCCAATCAACCTCATACACA+TGG 0.608735 8.2:+25268655 None:intergenic
CATCATAAGCATCAATCTCA+GGG 0.612180 8.2:+25268811 None:intergenic
ATAGAAGAGTCTCTGGTGTG+AGG 0.646087 8.2:+25268913 None:intergenic
ATGTCGGCGATATTTACCGC+CGG 0.657606 8.2:-25268579 MS.gene56810:CDS
TTTACTTCTAGCCAACACAC+CGG 0.666056 8.2:+25268560 None:intergenic
TTGTGTAAATGAGTGTTGCA+AGG 0.669621 8.2:+25269144 None:intergenic
ACTTCTAGCCAACACACCGG+CGG 0.671290 8.2:+25268563 None:intergenic
TGAACACTTTCGAAGCACGT+CGG 0.688069 8.2:+25268962 None:intergenic
TAATGGTGCAGAAACAGGAG+TGG 0.701846 8.2:+25269073 None:intergenic
TGAGATCAGAGTATGTCATG+TGG 0.715244 8.2:+25268994 None:intergenic
ATATTGGTTGATGGACCGCG+CGG 0.745881 8.2:-25268627 MS.gene56810:CDS
GCTTCCGGCCAATCCCCGCG+CGG 0.746128 8.2:+25268612 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGTTCAATATACAACAAAA+AGG - chr8.2:25268919-25268938 MS.gene56810:CDS 20.0%
!! TTTATGTAAAGAGAATTTGT+TGG - chr8.2:25269250-25269269 MS.gene56810:CDS 20.0%
! AGAAATTATTGCAGTATTTG+TGG + chr8.2:25268607-25268626 None:intergenic 25.0%
! TTATTCTCAGATTGTAAACT+TGG - chr8.2:25269014-25269033 MS.gene56810:CDS 25.0%
!!! GTTTTTTTGCATGATTTTTC+TGG - chr8.2:25269197-25269216 MS.gene56810:CDS 25.0%
!!! TTTCCTTGTTTTTGGATATA+TGG + chr8.2:25268495-25268514 None:intergenic 25.0%
AAGGAAACTCAAATCGATTA+TGG - chr8.2:25268508-25268527 MS.gene56810:intron 30.0%
CATCCATATATCCAAAAACA+AGG - chr8.2:25268489-25268508 MS.gene56810:intron 30.0%
CCAAAAATAAGCAAGTTACA+TGG + chr8.2:25268777-25268796 None:intergenic 30.0%
GCAAAAAAACATGAGTCTTT+GGG + chr8.2:25269187-25269206 None:intergenic 30.0%
TGCAAAAAAACATGAGTCTT+TGG + chr8.2:25269188-25269207 None:intergenic 30.0%
!! AAGAAGAATGAGTTTTGTGT+TGG + chr8.2:25268469-25268488 None:intergenic 30.0%
!! TGAACACTGTTTTTCCATTA+TGG + chr8.2:25268836-25268855 None:intergenic 30.0%
!!! CCATGTAACTTGCTTATTTT+TGG - chr8.2:25268774-25268793 MS.gene56810:CDS 30.0%
!!! GATTTGAGTTTCCTTGTTTT+TGG + chr8.2:25268503-25268522 None:intergenic 30.0%
ACATCATAAGCATCAATCTC+AGG + chr8.2:25268903-25268922 None:intergenic 35.0%
CAGTGTTCATCGATGAAAAT+CGG - chr8.2:25268847-25268866 MS.gene56810:CDS 35.0%
CATCATAAGCATCAATCTCA+GGG + chr8.2:25268902-25268921 None:intergenic 35.0%
GAGAATAAAAGATTCTGCAC+TGG + chr8.2:25269002-25269021 None:intergenic 35.0%
GGTTGATTGGGATGTTATAT+TGG - chr8.2:25269067-25269086 MS.gene56810:CDS 35.0%
GTGAAGTTGAACAAGTTTGT+GGG - chr8.2:25269219-25269238 MS.gene56810:CDS 35.0%
TTGGCTAGAAGTAAAAAAGG+TGG - chr8.2:25269158-25269177 MS.gene56810:CDS 35.0%
! TGGGATGTTATATTGGTTGA+TGG - chr8.2:25269074-25269093 MS.gene56810:CDS 35.0%
! TTGATAACTGTTGCTGGTAA+TGG + chr8.2:25268657-25268676 None:intergenic 35.0%
! TTGTGTAAATGAGTGTTGCA+AGG + chr8.2:25268569-25268588 None:intergenic 35.0%
!! GTGTTGGCTAGAAGTAAAAA+AGG - chr8.2:25269155-25269174 MS.gene56810:CDS 35.0%
!! TGGAAAGCACTTAACCATAA+TGG - chr8.2:25268819-25268838 MS.gene56810:CDS 35.0%
!!! TGGATTTTGAAGCATAGTGA+AGG + chr8.2:25268686-25268705 None:intergenic 35.0%
GGTGAAGTTGAACAAGTTTG+TGG - chr8.2:25269218-25269237 MS.gene56810:CDS 40.0%
TCAACCTCATACACATGGTT+TGG + chr8.2:25269053-25269072 None:intergenic 40.0%
TCTTCCAAACCATGTGTATG+AGG - chr8.2:25269046-25269065 MS.gene56810:CDS 40.0%
TGAGATCAGAGTATGTCATG+TGG + chr8.2:25268719-25268738 None:intergenic 40.0%
TTTACTTCTAGCCAACACAC+CGG + chr8.2:25269153-25269172 None:intergenic 40.0%
! ACCATGTGTATGAGGTTGAT+TGG - chr8.2:25269054-25269073 MS.gene56810:CDS 40.0%
! CCATGTGTATGAGGTTGATT+GGG - chr8.2:25269055-25269074 MS.gene56810:CDS 40.0%
!! AGAGTGTTGATAACTGTTGC+TGG + chr8.2:25268663-25268682 None:intergenic 40.0%
AAATATCGCCGACATTCTCC+CGG + chr8.2:25269126-25269145 None:intergenic 45.0%
ATAGAAGAGTCTCTGGTGTG+AGG + chr8.2:25268800-25268819 None:intergenic 45.0%
CCCAATCAACCTCATACACA+TGG + chr8.2:25269058-25269077 None:intergenic 45.0%
GCTTTCCATAGAAGAGTCTC+TGG + chr8.2:25268807-25268826 None:intergenic 45.0%
TAATGGTGCAGAAACAGGAG+TGG + chr8.2:25268640-25268659 None:intergenic 45.0%
TCACACCAGAGACTCTTCTA+TGG - chr8.2:25268799-25268818 MS.gene56810:CDS 45.0%
TGAACACTTTCGAAGCACGT+CGG + chr8.2:25268751-25268770 None:intergenic 45.0%
TGTCATGTGGTATGAGTCGT+TGG + chr8.2:25268706-25268725 None:intergenic 45.0%
AATATCGCCGACATTCTCCC+GGG + chr8.2:25269125-25269144 None:intergenic 50.0%
ATGTCGGCGATATTTACCGC+CGG - chr8.2:25269131-25269150 MS.gene56810:CDS 50.0%
GATATTTACCGCCGGTGTGT+TGG - chr8.2:25269139-25269158 MS.gene56810:CDS 50.0%
TTTCGAAGCACGTCGGAGAT+TGG + chr8.2:25268744-25268763 None:intergenic 50.0%
!! ATATTGGTTGATGGACCGCG+CGG - chr8.2:25269083-25269102 MS.gene56810:CDS 50.0%
!! GCTGGTAATGGTGCAGAAAC+AGG + chr8.2:25268645-25268664 None:intergenic 50.0%
ACTTCTAGCCAACACACCGG+CGG + chr8.2:25269150-25269169 None:intergenic 55.0%
!! TATTGGTTGATGGACCGCGC+GGG - chr8.2:25269084-25269103 MS.gene56810:CDS 55.0%
GACATTCTCCCGGGAGCTTC+CGG + chr8.2:25269116-25269135 None:intergenic 60.0%
GGAAGCTCCCGGGAGAATGT+CGG - chr8.2:25269115-25269134 MS.gene56810:CDS 60.0%
!! ATTGGTTGATGGACCGCGCG+GGG - chr8.2:25269085-25269104 MS.gene56810:CDS 60.0%
! TTGATGGACCGCGCGGGGAT+TGG - chr8.2:25269090-25269109 MS.gene56810:CDS 65.0%
!! GGGATTGGCCGGAAGCTCCC+GGG - chr8.2:25269105-25269124 MS.gene56810:CDS 70.0%
!! GGGGATTGGCCGGAAGCTCC+CGG - chr8.2:25269104-25269123 MS.gene56810:CDS 70.0%
GCTTCCGGCCAATCCCCGCG+CGG + chr8.2:25269101-25269120 None:intergenic 75.0%
! TGGACCGCGCGGGGATTGGC+CGG - chr8.2:25269094-25269113 MS.gene56810:CDS 75.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 25268450 25269282 25268450 ID=MS.gene56810
chr8.2 mRNA 25268450 25269282 25268450 ID=MS.gene56810.t1;Parent=MS.gene56810
chr8.2 exon 25268553 25269282 25268553 ID=MS.gene56810.t1.exon1;Parent=MS.gene56810.t1
chr8.2 CDS 25268553 25269282 25268553 ID=cds.MS.gene56810.t1;Parent=MS.gene56810.t1
chr8.2 exon 25268450 25268469 25268450 ID=MS.gene56810.t1.exon2;Parent=MS.gene56810.t1
chr8.2 CDS 25268450 25268469 25268450 ID=cds.MS.gene56810.t1;Parent=MS.gene56810.t1
Gene Sequence

>MS.gene56810

ATGAAGAACACAAACACCAACACAAAACTCATTCTTCTTCATCCATATATCCAAAAACAAGGAAACTCAAATCGATTATGGCTTCTAGCATTCATATCAATTCTCACTTTAGCATTCCTTGCAACACTCATTTACACAAGAGACAGAGAATCAACCACAAATACTGCAATAATTTCTTCTGTTATTACCACTCCTGTTTCTGCACCATTACCAGCAACAGTTATCAACACTCTCCTTCACTATGCTTCAAAATCCAACGACTCATACCACATGACATACTCTGATCTCAAACCAATCTCCGACGTGCTTCGAAAGTGTTCATCTCCATGTAACTTGCTTATTTTTGGCCTCACACCAGAGACTCTTCTATGGAAAGCACTTAACCATAATGGAAAAACAGTGTTCATCGATGAAAATCGGTATTATGCAGCATATATAGAAGAAAAACACCCTGAGATTGATGCTTATGATGTTCAATATACAACAAAAAGGAGTGAGATGAAAGAGTTAATAGCTTCAGCTAAAGAACATGTAGCAAATGAGTGCAAGCCAGTGCAGAATCTTTTATTCTCAGATTGTAAACTTGGAATTAATGATCTTCCAAACCATGTGTATGAGGTTGATTGGGATGTTATATTGGTTGATGGACCGCGCGGGGATTGGCCGGAAGCTCCCGGGAGAATGTCGGCGATATTTACCGCCGGTGTGTTGGCTAGAAGTAAAAAAGGTGGTAACCCAAAGACTCATGTTTTTTTGCATGATTTTTCTGGTGAAGTTGAACAAGTTTGTGGGAATGAGTTTTTATGTAAAGAGAATTTGTTGGAAGCAAGTGA
Protein sequence

>MS.gene56810.t1

MKNTNTNTKLILLHPYIQKQGNSNRLWLLAFISILTLAFLATLIYTRDRESTTNTAIISSVITTPVSAPLPATVINTLLHYASKSNDSYHMTYSDLKPISDVLRKCSSPCNLLIFGLTPETLLWKALNHNGKTVFIDENRYYAAYIEEKHPEIDAYDVQYTTKRSEMKELIASAKEHVANECKPVQNLLFSDCKLGINDLPNHVYEVDWDVILVDGPRGDWPEAPGRMSAIFTAGVLARSKKGEFVGSK