AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1383230


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1383230 MtrunA17_Chr6g0455061 90.875 263 23 1 1 263 1 262 3.47e-175 483
Msa1383230 MtrunA17_Chr3g0144851 92.015 263 21 0 1 263 1 263 8.84e-175 482
Msa1383230 MtrunA17_Chr4g0035301 42.205 263 94 15 3 253 5 221 6.01e-32 117
Msa1383230 MtrunA17_Chr4g0035291 38.889 252 95 11 10 253 9 209 3.45e-26 102
Msa1383230 MtrunA17_Chr4g0035281 36.321 212 79 8 49 252 2 165 6.35e-25 97.4
Msa1383230 MtrunA17_Chr8g0372841 29.787 235 141 8 22 254 12 224 3.37e-21 89.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1383230 AT5G66440.1 27.574 272 147 7 1 255 1 239 1.99e-21 90.5
Msa1383230 AT4G34560.1 32.178 202 90 8 64 262 63 220 1.68e-16 76.6
Msa1383230 AT2G21560.1 26.471 272 173 10 1 253 1 264 2.72e-12 65.9

Find 29 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAGATTAGCTAGGAATAAA+TGG 0.252040 tig0020577:+50534 None:intergenic
AATGAAGTTGGAAGAGAAAC+AGG 0.271425 tig0020577:-50836 Msa1383230:CDS
TCGTTGCTCATTCCATCTTC+AGG 0.330037 tig0020577:+50625 None:intergenic
GAAAGATTGCTAATTTGTTT+CGG 0.382950 tig0020577:-51245 Msa1383230:CDS
GTGATAACGATAAGAGTAAG+AGG 0.395005 tig0020577:-50690 Msa1383230:CDS
ATCACACTCATTGCTCAATC+TGG 0.403087 tig0020577:-51078 Msa1383230:CDS
TCAAAGCCAATGGTAGTTGT+TGG 0.417819 tig0020577:+51175 None:intergenic
TGGAAGTGAAGGGATATAGA+AGG 0.441385 tig0020577:-50792 Msa1383230:CDS
AAAGTTGAGAACAACGTAAA+GGG 0.443322 tig0020577:-50931 Msa1383230:CDS
AGATGATAATAGAATGAAGT+TGG 0.450200 tig0020577:-50848 Msa1383230:CDS
TTCATTCCAACAACTACCAT+TGG 0.464826 tig0020577:-51181 Msa1383230:CDS
AGAGATGGGTTTGGAAGTGA+AGG 0.496963 tig0020577:-50803 Msa1383230:CDS
TCGAGTTTATATCCTGAAGA+TGG 0.500432 tig0020577:-50637 Msa1383230:CDS
GGGATATAGAAGGTGTCAAT+CGG 0.514951 tig0020577:-50782 Msa1383230:CDS
CTTGAGTTCTTCAAAGCCAA+TGG 0.531388 tig0020577:+51165 None:intergenic
AAAAGTTGAGAACAACGTAA+AGG 0.543362 tig0020577:-50932 Msa1383230:CDS
TAGAATAAACGATGGATGCA+TGG 0.556637 tig0020577:-50905 Msa1383230:CDS
ATCGGAAATTGAGTTGGTGA+GGG 0.576160 tig0020577:-50764 Msa1383230:CDS
AACATGTATCAGAAAATCCA+AGG 0.585434 tig0020577:-50979 Msa1383230:CDS
AATCGGAAATTGAGTTGGTG+AGG 0.606720 tig0020577:-50765 Msa1383230:CDS
GTGTCAATCGGAAATTGAGT+TGG 0.619603 tig0020577:-50770 Msa1383230:CDS
TCTTGCAATAAATGCCTCCA+CGG 0.627372 tig0020577:+50588 None:intergenic
TGTGAATAGTGATGATGTGA+AGG 0.638060 tig0020577:-50740 Msa1383230:CDS
AGGATCAAAGAGTGTTGCAA+AGG 0.643836 tig0020577:-50720 Msa1383230:CDS
GAGATGGGTTTGGAAGTGAA+GGG 0.651077 tig0020577:-50802 Msa1383230:CDS
TCGGAAATTGAGTTGGTGAG+GGG 0.662410 tig0020577:-50763 Msa1383230:CDS
CGAATTTCGTCGCACCGTGG+AGG 0.663215 tig0020577:-50602 Msa1383230:CDS
AAGGGTCGTAGAATAAACGA+TGG 0.676337 tig0020577:-50913 Msa1383230:CDS
CGACGAATTTCGTCGCACCG+TGG 0.721139 tig0020577:-50605 Msa1383230:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAAAGATTGCTAATTTGTTT+CGG - tig0020577:50613-50632 Msa1383230:CDS 25.0%
!!! TTGTGTTGATTTTGATTTCA+AGG - tig0020577:50652-50671 Msa1383230:CDS 25.0%
! AGATGATAATAGAATGAAGT+TGG - tig0020577:51010-51029 Msa1383230:CDS 25.0%
!!! GAAAGATTGCTAATTTGTTT+CGG - tig0020577:50613-50632 Msa1383230:CDS 25.0%
!!! TTGTGTTGATTTTGATTTCA+AGG - tig0020577:50652-50671 Msa1383230:CDS 25.0%
! AGATGATAATAGAATGAAGT+TGG - tig0020577:51010-51029 Msa1383230:CDS 25.0%
!! ACGATGTTTTTGAACTTTGT+TGG + tig0020577:50586-50605 None:intergenic 30.0%
! AACTCAAGTGAATATTTTCG+AGG - tig0020577:50708-50727 Msa1383230:CDS 30.0%
AACATGTATCAGAAAATCCA+AGG - tig0020577:50879-50898 Msa1383230:CDS 30.0%
!! AGAAAATCCAAGGTTTTGAT+CGG - tig0020577:50889-50908 Msa1383230:CDS 30.0%
AAAAGTTGAGAACAACGTAA+AGG - tig0020577:50926-50945 Msa1383230:CDS 30.0%
AAAGTTGAGAACAACGTAAA+GGG - tig0020577:50927-50946 Msa1383230:CDS 30.0%
!! ACGATGTTTTTGAACTTTGT+TGG + tig0020577:50586-50605 None:intergenic 30.0%
! AACTCAAGTGAATATTTTCG+AGG - tig0020577:50708-50727 Msa1383230:CDS 30.0%
AACATGTATCAGAAAATCCA+AGG - tig0020577:50879-50898 Msa1383230:CDS 30.0%
!! AGAAAATCCAAGGTTTTGAT+CGG - tig0020577:50889-50908 Msa1383230:CDS 30.0%
AAAAGTTGAGAACAACGTAA+AGG - tig0020577:50926-50945 Msa1383230:CDS 30.0%
AAAGTTGAGAACAACGTAAA+GGG - tig0020577:50927-50946 Msa1383230:CDS 30.0%
TTCATTCCAACAACTACCAT+TGG - tig0020577:50677-50696 Msa1383230:CDS 35.0%
AAAAACAAAACCAGGACCAA+CGG + tig0020577:50739-50758 None:intergenic 35.0%
CCAACAAGAAAAACAAAACC+AGG + tig0020577:50747-50766 None:intergenic 35.0%
!!! CCTGGTTTTGTTTTTCTTGT+TGG - tig0020577:50744-50763 Msa1383230:CDS 35.0%
! TCTGAACTTCTTCTTTTTGC+AGG + tig0020577:50825-50844 None:intergenic 35.0%
!!! GTTTTTTCCGATCAAAACCT+TGG + tig0020577:50899-50918 None:intergenic 35.0%
TAGAATAAACGATGGATGCA+TGG - tig0020577:50953-50972 Msa1383230:CDS 35.0%
AATGAAGTTGGAAGAGAAAC+AGG - tig0020577:51022-51041 Msa1383230:CDS 35.0%
ACAGGAGATAAAAACAGAGA+TGG - tig0020577:51040-51059 Msa1383230:CDS 35.0%
CAGGAGATAAAAACAGAGAT+GGG - tig0020577:51041-51060 Msa1383230:CDS 35.0%
! GATAAAAACAGAGATGGGTT+TGG - tig0020577:51046-51065 Msa1383230:CDS 35.0%
! TGTGAATAGTGATGATGTGA+AGG - tig0020577:51118-51137 Msa1383230:CDS 35.0%
! GTGATAACGATAAGAGTAAG+AGG - tig0020577:51168-51187 Msa1383230:CDS 35.0%
TCGAGTTTATATCCTGAAGA+TGG - tig0020577:51221-51240 Msa1383230:CDS 35.0%
TTCATTCCAACAACTACCAT+TGG - tig0020577:50677-50696 Msa1383230:CDS 35.0%
AAAAACAAAACCAGGACCAA+CGG + tig0020577:50739-50758 None:intergenic 35.0%
CCAACAAGAAAAACAAAACC+AGG + tig0020577:50747-50766 None:intergenic 35.0%
!!! CCTGGTTTTGTTTTTCTTGT+TGG - tig0020577:50744-50763 Msa1383230:CDS 35.0%
! TCTGAACTTCTTCTTTTTGC+AGG + tig0020577:50825-50844 None:intergenic 35.0%
!!! GTTTTTTCCGATCAAAACCT+TGG + tig0020577:50899-50918 None:intergenic 35.0%
TAGAATAAACGATGGATGCA+TGG - tig0020577:50953-50972 Msa1383230:CDS 35.0%
AATGAAGTTGGAAGAGAAAC+AGG - tig0020577:51022-51041 Msa1383230:CDS 35.0%
ACAGGAGATAAAAACAGAGA+TGG - tig0020577:51040-51059 Msa1383230:CDS 35.0%
CAGGAGATAAAAACAGAGAT+GGG - tig0020577:51041-51060 Msa1383230:CDS 35.0%
! GATAAAAACAGAGATGGGTT+TGG - tig0020577:51046-51065 Msa1383230:CDS 35.0%
! TGTGAATAGTGATGATGTGA+AGG - tig0020577:51118-51137 Msa1383230:CDS 35.0%
! GTGATAACGATAAGAGTAAG+AGG - tig0020577:51168-51187 Msa1383230:CDS 35.0%
TCGAGTTTATATCCTGAAGA+TGG - tig0020577:51221-51240 Msa1383230:CDS 35.0%
TCAAAGCCAATGGTAGTTGT+TGG + tig0020577:50686-50705 None:intergenic 40.0%
CTTGAGTTCTTCAAAGCCAA+TGG + tig0020577:50696-50715 None:intergenic 40.0%
!! TATTTTCGAGGTTTTGCCGT+TGG - tig0020577:50720-50739 Msa1383230:CDS 40.0%
ATCACACTCATTGCTCAATC+TGG - tig0020577:50780-50799 Msa1383230:CDS 40.0%
AAGGGTCGTAGAATAAACGA+TGG - tig0020577:50945-50964 Msa1383230:CDS 40.0%
TGGAAGTGAAGGGATATAGA+AGG - tig0020577:51066-51085 Msa1383230:CDS 40.0%
!! GGGATATAGAAGGTGTCAAT+CGG - tig0020577:51076-51095 Msa1383230:CDS 40.0%
GTGTCAATCGGAAATTGAGT+TGG - tig0020577:51088-51107 Msa1383230:CDS 40.0%
!! AATCGGAAATTGAGTTGGTG+AGG - tig0020577:51093-51112 Msa1383230:CDS 40.0%
!! ATCGGAAATTGAGTTGGTGA+GGG - tig0020577:51094-51113 Msa1383230:CDS 40.0%
!! AGGATCAAAGAGTGTTGCAA+AGG - tig0020577:51138-51157 Msa1383230:CDS 40.0%
TCTTGCAATAAATGCCTCCA+CGG + tig0020577:51273-51292 None:intergenic 40.0%
TCAAAGCCAATGGTAGTTGT+TGG + tig0020577:50686-50705 None:intergenic 40.0%
CTTGAGTTCTTCAAAGCCAA+TGG + tig0020577:50696-50715 None:intergenic 40.0%
!! TATTTTCGAGGTTTTGCCGT+TGG - tig0020577:50720-50739 Msa1383230:CDS 40.0%
ATCACACTCATTGCTCAATC+TGG - tig0020577:50780-50799 Msa1383230:CDS 40.0%
AAGGGTCGTAGAATAAACGA+TGG - tig0020577:50945-50964 Msa1383230:CDS 40.0%
TGGAAGTGAAGGGATATAGA+AGG - tig0020577:51066-51085 Msa1383230:CDS 40.0%
!! GGGATATAGAAGGTGTCAAT+CGG - tig0020577:51076-51095 Msa1383230:CDS 40.0%
GTGTCAATCGGAAATTGAGT+TGG - tig0020577:51088-51107 Msa1383230:CDS 40.0%
!! AATCGGAAATTGAGTTGGTG+AGG - tig0020577:51093-51112 Msa1383230:CDS 40.0%
!! ATCGGAAATTGAGTTGGTGA+GGG - tig0020577:51094-51113 Msa1383230:CDS 40.0%
!! AGGATCAAAGAGTGTTGCAA+AGG - tig0020577:51138-51157 Msa1383230:CDS 40.0%
TCTTGCAATAAATGCCTCCA+CGG + tig0020577:51273-51292 None:intergenic 40.0%
! AGAGATGGGTTTGGAAGTGA+AGG - tig0020577:51055-51074 Msa1383230:CDS 45.0%
! GAGATGGGTTTGGAAGTGAA+GGG - tig0020577:51056-51075 Msa1383230:CDS 45.0%
!! TCGGAAATTGAGTTGGTGAG+GGG - tig0020577:51095-51114 Msa1383230:CDS 45.0%
TCGTTGCTCATTCCATCTTC+AGG + tig0020577:51236-51255 None:intergenic 45.0%
! AGAGATGGGTTTGGAAGTGA+AGG - tig0020577:51055-51074 Msa1383230:CDS 45.0%
! GAGATGGGTTTGGAAGTGAA+GGG - tig0020577:51056-51075 Msa1383230:CDS 45.0%
!! TCGGAAATTGAGTTGGTGAG+GGG - tig0020577:51095-51114 Msa1383230:CDS 45.0%
TCGTTGCTCATTCCATCTTC+AGG + tig0020577:51236-51255 None:intergenic 45.0%
! CGAGGTTTTGCCGTTGGTCC+TGG - tig0020577:50726-50745 Msa1383230:CDS 60.0%
CGACGAATTTCGTCGCACCG+TGG - tig0020577:51253-51272 Msa1383230:CDS 60.0%
CGAATTTCGTCGCACCGTGG+AGG - tig0020577:51256-51275 Msa1383230:CDS 60.0%
! CGAGGTTTTGCCGTTGGTCC+TGG - tig0020577:50726-50745 Msa1383230:CDS 60.0%
CGACGAATTTCGTCGCACCG+TGG - tig0020577:51253-51272 Msa1383230:CDS 60.0%
CGAATTTCGTCGCACCGTGG+AGG - tig0020577:51256-51275 Msa1383230:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0020577 gene 50543 51337 50543 ID=Msa1383230;Name=Msa1383230
tig0020577 mRNA 50543 51337 50543 ID=Msa1383230-mRNA-1;Parent=Msa1383230;Name=Msa1383230-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|264
tig0020577 exon 50543 51337 50543 ID=Msa1383230-mRNA-1:exon:8487;Parent=Msa1383230-mRNA-1
tig0020577 CDS 50543 51337 50543 ID=Msa1383230-mRNA-1:cds;Parent=Msa1383230-mRNA-1
Gene Sequence

>Msa1383230

ATGGGTTCAATCAATTTACACAAACACAAAGCAGAGAAATCCAACAAAGTTCAAAAACATCGTCATCTTAGAAAGATTGCTAATTTGTTTCGGTATTTAGAGATGTGTGTTGTGTTGATTTTGATTTCAAGGCTTTCATTCCAACAACTACCATTGGCTTTGAAGAACTCAAGTGAATATTTTCGAGGTTTTGCCGTTGGTCCTGGTTTTGTTTTTCTTGTTGGAAACATTATCATCATCACACTCATTGCTCAATCTGGTCACTTCTCACAACATGATCCTGCAAAAAGAAGAAGTTCAGAACATGATCTTTATCTCGAGTTTCTCAAGAATAGCAACATGTATCAGAAAATCCAAGGTTTTGATCGGAAAAAACTGAGCGTAAAAGTTGAGAACAACGTAAAGGGTCGTAGAATAAACGATGGATGCATGGTGAAATTCTCTGAGAAAGAGAGTAAAAAGAGTGAAGATGATAATAGAATGAAGTTGGAAGAGAAACAGGAGATAAAAACAGAGATGGGTTTGGAAGTGAAGGGATATAGAAGGTGTCAATCGGAAATTGAGTTGGTGAGGGGTGTGAATAGTGATGATGTGAAGGATCAAAGAGTGTTGCAAAGGTGTGAGAGTGATAACGATAAGAGTAAGAGGAAAAACATTGAAGTTGATAAAGTGAAAAAATCGAGTTTATATCCTGAAGATGGAATGAGCAACGACGAATTTCGTCGCACCGTGGAGGCATTTATTGCAAGACAACAGAAGCTACGAATAAACGAAGTACAAACCATTTATTCCTAG

Protein sequence

>Msa1383230

MGSINLHKHKAEKSNKVQKHRHLRKIANLFRYLEMCVVLILISRLSFQQLPLALKNSSEYFRGFAVGPGFVFLVGNIIIITLIAQSGHFSQHDPAKRRSSEHDLYLEFLKNSNMYQKIQGFDRKKLSVKVENNVKGRRINDGCMVKFSEKESKKSEDDNRMKLEEKQEIKTEMGLEVKGYRRCQSEIELVRGVNSDDVKDQRVLQRCESDNDKSKRKNIEVDKVKKSSLYPEDGMSNDEFRRTVEAFIARQQKLRINEVQTIYS*