AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene05264

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05264.t1 MTR_6g078940 85.507 69 10 0 39 107 57 125 3.55e-36 119
MS.gene05264.t1 MTR_6g077630 50.862 116 27 2 17 103 48 162 5.53e-28 100
MS.gene05264.t1 MTR_6g079130 50.862 116 27 2 17 103 100 214 4.98e-27 99.4
MS.gene05264.t1 MTR_6g477680 58.763 97 13 1 37 106 353 449 2.95e-26 100
MS.gene05264.t1 MTR_6g077680 58.763 97 13 1 37 106 435 531 5.38e-26 100
MS.gene05264.t1 MTR_6g077680 56.962 79 7 1 37 88 435 513 4.04e-19 81.3
MS.gene05264.t1 MTR_6g077630 46.316 95 21 2 17 82 48 141 8.98e-18 73.9
MS.gene05264.t1 MTR_6g078950 64.912 57 18 1 38 94 52 106 3.53e-17 75.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCAAGAAGTTGGTTATTTC+TGG 0.137180 6.2:-78355254 MS.gene05264:CDS
TGAAGAACAGATTGAGATTT+TGG 0.155235 6.2:-78355300 MS.gene05264:CDS
AATGATGATTTAGTTGAAAA+TGG 0.241490 6.2:-78355480 MS.gene05264:intron
AATGTGATTGACTCTATATT+TGG 0.259312 6.2:-78355413 MS.gene05264:intron
CAATTAACACTCGCCTTCTT+TGG 0.276176 6.2:+78354887 None:intergenic
AAGATCTCCCCTCCACATTC+TGG 0.300473 6.2:-78355706 MS.gene05264:CDS
TCCTTCATCATTGGTGGATC+TGG 0.321529 6.2:-78355438 MS.gene05264:CDS
CATCAAGAATGTGTCAGATT+TGG 0.357757 6.2:-78354943 MS.gene05264:CDS
AAGAGGTGTCAGTGCTATAC+AGG 0.404532 6.2:-78355674 MS.gene05264:intron
AACTTCTTGCAAAGCCAGTC+TGG 0.423623 6.2:+78355266 None:intergenic
TGGAAAAGATTGTGCCAGAC+TGG 0.443412 6.2:-78355280 MS.gene05264:CDS
TATAGCACTGACACCTCTTA+AGG 0.443464 6.2:+78355678 None:intergenic
CATTCTGGATACGCCTTAAG+AGG 0.445628 6.2:-78355691 MS.gene05264:CDS
CTCAGCCATGTGACCAAAGA+AGG 0.458754 6.2:-78354900 MS.gene05264:CDS
GATCTTATGTACTGGTGGAT+TGG 0.469560 6.2:+78355723 None:intergenic
GACTGCAAATCCTTCATCAT+TGG 0.473819 6.2:-78355447 MS.gene05264:CDS
AGACTGGCTTTGCAAGAAGT+TGG 0.484693 6.2:-78355264 MS.gene05264:CDS
TGCAAATCCTTCATCATTGG+TGG 0.512374 6.2:-78355444 MS.gene05264:CDS
ACCAGATCCACCAATGATGA+AGG 0.533226 6.2:+78355437 None:intergenic
TTTCTGGAGACACTATGTAC+TGG 0.549724 6.2:-78355238 MS.gene05264:intron
ACTCGCCTTCTTTGGTCACA+TGG 0.572989 6.2:+78354895 None:intergenic
AGTTGAAAATGGATATTCTG+AGG 0.585036 6.2:-78355469 MS.gene05264:CDS
GGGGAGATCTTATGTACTGG+TGG 0.586694 6.2:+78355718 None:intergenic
AGGCGTATCCAGAATGTGGA+GGG 0.589280 6.2:+78355698 None:intergenic
CTTAAGGCGTATCCAGAATG+TGG 0.599320 6.2:+78355694 None:intergenic
GGAGGGGAGATCTTATGTAC+TGG 0.605142 6.2:+78355715 None:intergenic
AAGGCGTATCCAGAATGTGG+AGG 0.651219 6.2:+78355697 None:intergenic
GGCGTATCCAGAATGTGGAG+GGG 0.654858 6.2:+78355699 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATGCTTGTTATTTATTA+TGG - chr6.2:78355494-78355513 MS.gene05264:intron 15.0%
!! AATGATGATTTAGTTGAAAA+TGG - chr6.2:78355143-78355162 MS.gene05264:intron 20.0%
!! TTTCTTAGTAATAAACATTC+TGG - chr6.2:78355268-78355287 MS.gene05264:CDS 20.0%
! TTTGAAAATTGTCTCTTGTA+TGG - chr6.2:78354972-78354991 MS.gene05264:intron 25.0%
!! AATGTGATTGACTCTATATT+TGG - chr6.2:78355210-78355229 MS.gene05264:intron 25.0%
!! TAGAATATCAGAACTTTTGA+TGG - chr6.2:78355540-78355559 MS.gene05264:intron 25.0%
!!! TTTAGAGTATCAGTCTTTTA+GGG - chr6.2:78355442-78355461 MS.gene05264:CDS 25.0%
!!! TTTTAGAGTATCAGTCTTTT+AGG - chr6.2:78355441-78355460 MS.gene05264:CDS 25.0%
AGTTGAAAATGGATATTCTG+AGG - chr6.2:78355154-78355173 MS.gene05264:intron 30.0%
! CTGATACTCTAAAAGAACAA+AGG + chr6.2:78355435-78355454 None:intergenic 30.0%
! TGAAGAACAGATTGAGATTT+TGG - chr6.2:78355323-78355342 MS.gene05264:intron 30.0%
!! TACTTTTAAGTAAATGCCAG+AGG + chr6.2:78355594-78355613 None:intergenic 30.0%
!!! AAGTTGAGCAATCTTTTTTG+AGG + chr6.2:78355107-78355126 None:intergenic 30.0%
CATCAAGAATGTGTCAGATT+TGG - chr6.2:78355680-78355699 MS.gene05264:CDS 35.0%
GGGTCACAAATCACTAAATA+AGG + chr6.2:78355566-78355585 None:intergenic 35.0%
TGATATTCTACCAAACTGCT+AGG + chr6.2:78355530-78355549 None:intergenic 35.0%
! AACACTGAGAGATTGTTGTT+CGG - chr6.2:78355030-78355049 MS.gene05264:intron 35.0%
! AAGTAAATGCCAGAGGATTT+TGG + chr6.2:78355587-78355606 None:intergenic 35.0%
! AGTAAATGCCAGAGGATTTT+GGG + chr6.2:78355586-78355605 None:intergenic 35.0%
! GCTTAAAACACCAGACTTTT+GGG + chr6.2:78355085-78355104 None:intergenic 35.0%
! TGCAAGAAGTTGGTTATTTC+TGG - chr6.2:78355369-78355388 MS.gene05264:intron 35.0%
AAAATGACTGCCCAAAAGTC+TGG - chr6.2:78355072-78355091 MS.gene05264:intron 40.0%
AATAGCAGAACCTAGCAGTT+TGG - chr6.2:78355517-78355536 MS.gene05264:intron 40.0%
ACTAATCCTGTCCTCTCAAT+AGG - chr6.2:78355294-78355313 MS.gene05264:CDS 40.0%
ATTTGTGACCCAAAATCCTC+TGG - chr6.2:78355575-78355594 MS.gene05264:intron 40.0%
GACTGCAAATCCTTCATCAT+TGG - chr6.2:78355176-78355195 MS.gene05264:intron 40.0%
TGCAAATCCTTCATCATTGG+TGG - chr6.2:78355179-78355198 MS.gene05264:intron 40.0%
! GATCTTATGTACTGGTGGAT+TGG + chr6.2:78354903-78354922 None:intergenic 40.0%
! GGCTTAAAACACCAGACTTT+TGG + chr6.2:78355086-78355105 None:intergenic 40.0%
! TTTCTGGAGACACTATGTAC+TGG - chr6.2:78355385-78355404 MS.gene05264:intron 40.0%
!! TATAGCACTGACACCTCTTA+AGG + chr6.2:78354948-78354967 None:intergenic 40.0%
!! TTTTGGGCAGTCATTTTCTG+AGG + chr6.2:78355069-78355088 None:intergenic 40.0%
AACTTCTTGCAAAGCCAGTC+TGG + chr6.2:78355360-78355379 None:intergenic 45.0%
ACCAGATCCACCAATGATGA+AGG + chr6.2:78355189-78355208 None:intergenic 45.0%
CATTCTGGATACGCCTTAAG+AGG - chr6.2:78354932-78354951 MS.gene05264:CDS 45.0%
CTTAAGGCGTATCCAGAATG+TGG + chr6.2:78354932-78354951 None:intergenic 45.0%
CTTCAGCTTCTCCTATTGAG+AGG + chr6.2:78355308-78355327 None:intergenic 45.0%
TGGAAAAGATTGTGCCAGAC+TGG - chr6.2:78355343-78355362 MS.gene05264:intron 45.0%
! TCCTTCATCATTGGTGGATC+TGG - chr6.2:78355185-78355204 MS.gene05264:intron 45.0%
! TGGAGACACTATGTACTGGT+GGG - chr6.2:78355389-78355408 MS.gene05264:intron 45.0%
!! AAGAGGTGTCAGTGCTATAC+AGG - chr6.2:78354949-78354968 MS.gene05264:intron 45.0%
!! AGACTGGCTTTGCAAGAAGT+TGG - chr6.2:78355359-78355378 MS.gene05264:intron 45.0%
!! TCTCTCAGTGTTGACTATGC+TGG + chr6.2:78355022-78355041 None:intergenic 45.0%
AAGATCTCCCCTCCACATTC+TGG - chr6.2:78354917-78354936 MS.gene05264:CDS 50.0%
AAGGCGTATCCAGAATGTGG+AGG + chr6.2:78354929-78354948 None:intergenic 50.0%
ACTCGCCTTCTTTGGTCACA+TGG + chr6.2:78355731-78355750 None:intergenic 50.0%
AGGCGTATCCAGAATGTGGA+GGG + chr6.2:78354928-78354947 None:intergenic 50.0%
CTCAGCCATGTGACCAAAGA+AGG - chr6.2:78355723-78355742 MS.gene05264:CDS 50.0%
CTGGAGACACTATGTACTGG+TGG - chr6.2:78355388-78355407 MS.gene05264:intron 50.0%
GCTTCTCCTATTGAGAGGAC+AGG + chr6.2:78355303-78355322 None:intergenic 50.0%
GGAGGGGAGATCTTATGTAC+TGG + chr6.2:78354911-78354930 None:intergenic 50.0%
GGGGAGATCTTATGTACTGG+TGG + chr6.2:78354908-78354927 None:intergenic 50.0%
GGCGTATCCAGAATGTGGAG+GGG + chr6.2:78354927-78354946 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 78354890 78355755 78354890 ID=MS.gene05264
chr6.2 mRNA 78354890 78355755 78354890 ID=MS.gene05264.t1;Parent=MS.gene05264
chr6.2 exon 78355675 78355755 78355675 ID=MS.gene05264.t1.exon1;Parent=MS.gene05264.t1
chr6.2 CDS 78355675 78355755 78355675 ID=cds.MS.gene05264.t1;Parent=MS.gene05264.t1
chr6.2 exon 78355414 78355489 78355414 ID=MS.gene05264.t1.exon2;Parent=MS.gene05264.t1
chr6.2 CDS 78355414 78355489 78355414 ID=cds.MS.gene05264.t1;Parent=MS.gene05264.t1
chr6.2 exon 78355239 78355329 78355239 ID=MS.gene05264.t1.exon3;Parent=MS.gene05264.t1
chr6.2 CDS 78355239 78355329 78355239 ID=cds.MS.gene05264.t1;Parent=MS.gene05264.t1
chr6.2 exon 78354890 78354965 78354890 ID=MS.gene05264.t1.exon4;Parent=MS.gene05264.t1
chr6.2 CDS 78354890 78354965 78354890 ID=cds.MS.gene05264.t1;Parent=MS.gene05264.t1
Gene Sequence

>MS.gene05264

ATGTTGTTATCCAATCCACCAGTACATAAGATCTCCCCTCCACATTCTGGATACGCCTTAAGAGGTGTCAGTGCTATACAGGTTTGAAAATTGTCTCTTGTATGGATAGTTTGTCGACACACACACACACCAGCATAGTCAACACTGAGAGATTGTTGTTCGGTTCTTATGTTAAGCCTCAGAAAATGACTGCCCAAAAGTCTGGTGTTTTAAGCCTCAAAAAAGATTGCTCAACTTTACAGTCACAGAACGCAATGATGATTTAGTTGAAAATGGATATTCTGAGGACTGCAAATCCTTCATCATTGGTGGATCTGGTTAATGTGATTGACTCTATATTTGGTATGTTCTAATTCTATTTTATTATAATTCACTCGATTTCTTAGTAATAAACATTCTGGCTAACTAATCCTGTCCTCTCAATAGGAGAAGCTGAAGAACAGATTGAGATTTTGGAAAAGATTGTGCCAGACTGGCTTTGCAAGAAGTTGGTTATTTCTGGAGACACTATGTACTGGTGGGTCTTTTTCTTCACTGATAAACCTTTGTTCTTTTAGAGTATCAGTCTTTTAGGGACGTGAAAAATTCGAGTCAGAATTCTGAATTTATGCTTGTTATTTATTATGGAATAGCAGAACCTAGCAGTTTGGTAGAATATCAGAACTTTTGATGGCCTTATTTAGTGATTTGTGACCCAAAATCCTCTGGCATTTACTTAAAAGTAGTTATTTATTAATTTTTTTGATGAAGTTCTTATTCTTCTAGTTTCTATAACATGTTATATTTGCAGCATCAAGAATGTGTCAGATTTGGACTCAGTTCGATCAATACTTCTCAGCCATGTGACCAAAGAAGGCGAGTGTTAA
Protein sequence

>MS.gene05264.t1

MLLSNPPVHKISPPHSGYALRGVSAIQLKMDILRTANPSSLVDLVNVIDSIFGEAEEQIEILEKIVPDWLCKKLVISGDTMYCIKNVSDLDSVRSILLSHVTKEGEC