AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene86356

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene86356.t1 MTR_2g103290 88.950 181 17 1 1 178 1 181 2.06e-110 312
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTGAGTCTTAATCCTCATA+TGG 0.366307 2.3:+1700444 None:intergenic
TCTGCTGCTGCTACAACTAA+TGG 0.397952 2.3:-1699056 MS.gene86356:CDS
CATTGTGTTTCTGTCAGATA+AGG 0.400716 2.3:+1698908 None:intergenic
GCCATGTGCATAGTTGCATT+GGG 0.419796 2.3:+1700379 None:intergenic
TCATTCGTCTCTATGCTGAT+TGG 0.440080 2.3:-1698878 MS.gene86356:CDS
AACGACCTCAGAACAGCAAC+AGG 0.451715 2.3:-1700353 MS.gene86356:CDS
AAAATTCACAAACCCATATG+AGG 0.470113 2.3:-1700457 MS.gene86356:CDS
ACTACCTCTTTACATAAGAA+TGG 0.478765 2.3:-1698948 MS.gene86356:CDS
ATGAACATTCTACAGAATCT+TGG 0.480970 2.3:+1700329 None:intergenic
AGCCATGTGCATAGTTGCAT+TGG 0.488645 2.3:+1700378 None:intergenic
CTGAGTCTTAATCCTCATAT+GGG 0.496970 2.3:+1700445 None:intergenic
CATAAGAATGGACCGTATGC+TGG 0.500563 2.3:-1698936 MS.gene86356:CDS
CGGTCCATTCTTATGTAAAG+AGG 0.523765 2.3:+1698944 None:intergenic
TGATACAAAATGCAGAATGC+AGG 0.549025 2.3:-1699091 MS.gene86356:CDS
TTGGTCCTGTTGCTGTTCTG+AGG 0.555812 2.3:+1700348 None:intergenic
ATGGCTGAGGTATTTGTAGC+AGG 0.556435 2.3:+1698981 None:intergenic
CCCCAATGCAACTATGCACA+TGG 0.558064 2.3:-1700380 MS.gene86356:CDS
GTGTCCGTAGCTACAATGTC+TGG 0.558270 2.3:+1700301 None:intergenic
TTCTCATGCTGCTGTTGCTG+AGG 0.564103 2.3:+1700227 None:intergenic
CACACCAGACATTGTAGCTA+CGG 0.572650 2.3:-1700305 MS.gene86356:CDS
TTGCATTGGGGTGCAACAAG+AGG 0.590171 2.3:+1700392 None:intergenic
TGAACATAATGACTAGGTAG+AGG 0.590759 2.3:+1700251 None:intergenic
GATAAGGATTTACCAGCATA+CGG 0.594337 2.3:+1698924 None:intergenic
GTAGAGGAGGAGTTGCATGA+AGG 0.626678 2.3:+1700267 None:intergenic
TGAGGATGAACATAATGACT+AGG 0.643549 2.3:+1700245 None:intergenic
ACATAATGACTAGGTAGAGG+AGG 0.645792 2.3:+1700254 None:intergenic
CTGACAGAAACACAATGCAA+AGG 0.652310 2.3:-1698902 MS.gene86356:CDS
AGTTGCCACTGTGATGGCTG+AGG 0.653448 2.3:+1698968 None:intergenic
CCATGTGCATAGTTGCATTG+GGG 0.656451 2.3:+1700380 None:intergenic
AGAGGTAGTTGCCACTGTGA+TGG 0.670611 2.3:+1698962 None:intergenic
CTATGCAAAAGATTCATGCA+AGG 0.677580 2.3:-1700422 MS.gene86356:CDS
AGTTTGTGAATGCAGAACCA+GGG 0.698116 2.3:-1699115 MS.gene86356:intron
AAATACCTCAGCCATCACAG+TGG 0.797236 2.3:-1698973 MS.gene86356:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTAAACATTATTACT+TGG - chr2.3:1699451-1699470 MS.gene86356:intron 10.0%
!! AATAAGCTAAAAACAATTTA+TGG + chr2.3:1699956-1699975 None:intergenic 15.0%
!! TTAATTAATAAGTAATGTCT+CGG - chr2.3:1699606-1699625 MS.gene86356:intron 15.0%
!! ACATAAACACTTATATGATA+TGG - chr2.3:1700071-1700090 MS.gene86356:intron 20.0%
!! TCTTAGTATTAGAACAAAAA+GGG - chr2.3:1699222-1699241 MS.gene86356:intron 20.0%
!! TTCTTAGTATTAGAACAAAA+AGG - chr2.3:1699221-1699240 MS.gene86356:intron 20.0%
! AAACAACAAACACATAATGT+TGG - chr2.3:1699559-1699578 MS.gene86356:intron 25.0%
! AATAGAATATAGAACTGTGT+TGG - chr2.3:1700185-1700204 MS.gene86356:intron 25.0%
! AGTAGAAAATTGTCAAATAG+TGG + chr2.3:1699846-1699865 None:intergenic 25.0%
! ATAAATGGAAAAATGTGCAT+CGG - chr2.3:1699640-1699659 MS.gene86356:intron 25.0%
! TAATTAAGCAACCTCATAAT+CGG + chr2.3:1699593-1699612 None:intergenic 25.0%
!! CAATTTTCTACTAAATATCG+TGG - chr2.3:1699854-1699873 MS.gene86356:intron 25.0%
!!! ACACTTTTGATTAAATGTGT+CGG + chr2.3:1699265-1699284 None:intergenic 25.0%
AAAATTCACAAACCCATATG+AGG - chr2.3:1698888-1698907 MS.gene86356:CDS 30.0%
ACTACCTCTTTACATAAGAA+TGG - chr2.3:1700397-1700416 MS.gene86356:CDS 30.0%
AGAAGTTGAAGAAAAATACG+TGG + chr2.3:1699157-1699176 None:intergenic 30.0%
AGCTTTCATGGAAATCATAT+TGG + chr2.3:1700154-1700173 None:intergenic 30.0%
ATGAACATTCTACAGAATCT+TGG + chr2.3:1699019-1699038 None:intergenic 30.0%
TGAATCACAAAAAGCTTTCA+TGG + chr2.3:1700166-1700185 None:intergenic 30.0%
! GACTTCAGTTTATCTTTTGT+TGG - chr2.3:1700035-1700054 MS.gene86356:intron 30.0%
!! ACTACACTAACACTACTTTT+TGG - chr2.3:1699184-1699203 MS.gene86356:intron 30.0%
AAATAGACCCTAACTCATAG+GGG + chr2.3:1699676-1699695 None:intergenic 35.0%
ATCATATTGGACCTGGAATA+AGG + chr2.3:1700141-1700160 None:intergenic 35.0%
ATTAAGCTGTTTACCCAAAC+AGG - chr2.3:1700114-1700133 MS.gene86356:intron 35.0%
CAAATAGACCCTAACTCATA+GGG + chr2.3:1699677-1699696 None:intergenic 35.0%
CTATGCAAAAGATTCATGCA+AGG - chr2.3:1698923-1698942 MS.gene86356:CDS 35.0%
CTGAGTCTTAATCCTCATAT+GGG + chr2.3:1698903-1698922 None:intergenic 35.0%
GATAAGGATTTACCAGCATA+CGG + chr2.3:1700424-1700443 None:intergenic 35.0%
GCTGTTTGTATAAGCTATCA+TGG + chr2.3:1699991-1700010 None:intergenic 35.0%
TCAAATAGACCCTAACTCAT+AGG + chr2.3:1699678-1699697 None:intergenic 35.0%
TGAACATAATGACTAGGTAG+AGG + chr2.3:1699097-1699116 None:intergenic 35.0%
TGAAGAAAAATACGTGGTTG+TGG + chr2.3:1699151-1699170 None:intergenic 35.0%
TGAGGATGAACATAATGACT+AGG + chr2.3:1699103-1699122 None:intergenic 35.0%
TGATACAAAATGCAGAATGC+AGG - chr2.3:1700254-1700273 MS.gene86356:CDS 35.0%
! ATGCTCTCAATTTTGAATCG+CGG - chr2.3:1699774-1699793 MS.gene86356:intron 35.0%
! CAATTTTGAATCGCGGAAAT+TGG - chr2.3:1699781-1699800 MS.gene86356:intron 35.0%
! CATTGTGTTTCTGTCAGATA+AGG + chr2.3:1700440-1700459 None:intergenic 35.0%
! TCGGATTCGAGTCTTATAAA+TGG - chr2.3:1699625-1699644 MS.gene86356:intron 35.0%
! TGTTTGTGTTGGTGCTTTAT+AGG - chr2.3:1699352-1699371 MS.gene86356:intron 35.0%
!! CAAACACATAATGTTGGTTC+TGG - chr2.3:1699565-1699584 MS.gene86356:intron 35.0%
ACATAATGACTAGGTAGAGG+AGG + chr2.3:1699094-1699113 None:intergenic 40.0%
AGTTTGTGAATGCAGAACCA+GGG - chr2.3:1700230-1700249 MS.gene86356:CDS 40.0%
CACATTTGTCAGTGTTGTGT+TGG + chr2.3:1699305-1699324 None:intergenic 40.0%
CATGGAAATCATATTGGACC+TGG + chr2.3:1700148-1700167 None:intergenic 40.0%
CGGTCCATTCTTATGTAAAG+AGG + chr2.3:1700404-1700423 None:intergenic 40.0%
CTGACAGAAACACAATGCAA+AGG - chr2.3:1700443-1700462 MS.gene86356:CDS 40.0%
GCTGAGTCTTAATCCTCATA+TGG + chr2.3:1698904-1698923 None:intergenic 40.0%
GCTTAATCAGTTATGGCATG+TGG - chr2.3:1699494-1699513 MS.gene86356:intron 40.0%
TCATTCGTCTCTATGCTGAT+TGG - chr2.3:1700467-1700486 MS.gene86356:CDS 40.0%
TGTGGTGAATTTAGCTAGGA+TGG - chr2.3:1699512-1699531 MS.gene86356:intron 40.0%
! ATGATTTGCCCCTATGAGTT+AGG - chr2.3:1699665-1699684 MS.gene86356:intron 40.0%
! GCAGCTTGCTTAATCAGTTA+TGG - chr2.3:1699487-1699506 MS.gene86356:intron 40.0%
! TAAAGCACCAACACAAACAC+CGG + chr2.3:1699351-1699370 None:intergenic 40.0%
! TCTGCATTTTGTATCATCCC+TGG + chr2.3:1700250-1700269 None:intergenic 40.0%
! TGATTTGCCCCTATGAGTTA+GGG - chr2.3:1699666-1699685 MS.gene86356:intron 40.0%
! TTTTGAATCGCGGAAATTGG+CGG - chr2.3:1699784-1699803 MS.gene86356:intron 40.0%
!!! TGTTGTTTTGTGCAGAAGAG+TGG + chr2.3:1700315-1700334 None:intergenic 40.0%
AAATACCTCAGCCATCACAG+TGG - chr2.3:1700372-1700391 MS.gene86356:CDS 45.0%
ACCTGGAATAAGGTCCTGTT+TGG + chr2.3:1700131-1700150 None:intergenic 45.0%
AGCCATGTGCATAGTTGCAT+TGG + chr2.3:1698970-1698989 None:intergenic 45.0%
ATAGTGTCACCATAGCGTAG+TGG + chr2.3:1699900-1699919 None:intergenic 45.0%
CACACCAGACATTGTAGCTA+CGG - chr2.3:1699040-1699059 MS.gene86356:CDS 45.0%
CATAAGAATGGACCGTATGC+TGG - chr2.3:1700409-1700428 MS.gene86356:CDS 45.0%
CATTCGATCAGTGTTGTGTC+CGG - chr2.3:1699329-1699348 MS.gene86356:intron 45.0%
CCATGTGCATAGTTGCATTG+GGG + chr2.3:1698968-1698987 None:intergenic 45.0%
CCTGGAATAAGGTCCTGTTT+GGG + chr2.3:1700130-1700149 None:intergenic 45.0%
GAGTTTGTGAATGCAGAACC+AGG - chr2.3:1700229-1700248 MS.gene86356:CDS 45.0%
GCCATGTGCATAGTTGCATT+GGG + chr2.3:1698969-1698988 None:intergenic 45.0%
GGCATGTGGTGAATTTAGCT+AGG - chr2.3:1699508-1699527 MS.gene86356:intron 45.0%
GTTCGAATTCCACTACGCTA+TGG - chr2.3:1699888-1699907 MS.gene86356:intron 45.0%
TAGTGGCGCTGTAGCATTAT+AGG + chr2.3:1699829-1699848 None:intergenic 45.0%
TCTGCTGCTGCTACAACTAA+TGG - chr2.3:1700289-1700308 MS.gene86356:CDS 45.0%
! ATGGCTGAGGTATTTGTAGC+AGG + chr2.3:1700367-1700386 None:intergenic 45.0%
!!! TTTTGTTATTAAAATAAAAT+GGG - chr2.3:1699418-1699437 MS.gene86356:intron 5.0%
!!! TTTTTGTTATTAAAATAAAA+TGG - chr2.3:1699417-1699436 MS.gene86356:intron 5.0%
AACGACCTCAGAACAGCAAC+AGG - chr2.3:1698992-1699011 MS.gene86356:CDS 50.0%
AGAGGTAGTTGCCACTGTGA+TGG + chr2.3:1700386-1700405 None:intergenic 50.0%
CCCAAACAGGACCTTATTCC+AGG - chr2.3:1700127-1700146 MS.gene86356:intron 50.0%
CCCCAATGCAACTATGCACA+TGG - chr2.3:1698965-1698984 MS.gene86356:CDS 50.0%
GTAGAGGAGGAGTTGCATGA+AGG + chr2.3:1699081-1699100 None:intergenic 50.0%
GTGTCCGTAGCTACAATGTC+TGG + chr2.3:1699047-1699066 None:intergenic 50.0%
GTTGTGTCCGGTGTTTGTGT+TGG - chr2.3:1699341-1699360 MS.gene86356:intron 50.0%
TTCTCATGCTGCTGTTGCTG+AGG + chr2.3:1699121-1699140 None:intergenic 50.0%
TTGCATTGGGGTGCAACAAG+AGG + chr2.3:1698956-1698975 None:intergenic 50.0%
! TTGGTCCTGTTGCTGTTCTG+AGG + chr2.3:1699000-1699019 None:intergenic 50.0%
!! TGGTTCTGGTGCCGATTATG+AGG - chr2.3:1699579-1699598 MS.gene86356:intron 50.0%
AGTTGCCACTGTGATGGCTG+AGG + chr2.3:1700380-1700399 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 1698872 1700495 1698872 ID=MS.gene86356
chr2.3 mRNA 1698872 1700495 1698872 ID=MS.gene86356.t1;Parent=MS.gene86356
chr2.3 exon 1700210 1700495 1700210 ID=MS.gene86356.t1.exon1;Parent=MS.gene86356.t1
chr2.3 CDS 1700210 1700495 1700210 ID=cds.MS.gene86356.t1;Parent=MS.gene86356.t1
chr2.3 exon 1698872 1699122 1698872 ID=MS.gene86356.t1.exon2;Parent=MS.gene86356.t1
chr2.3 CDS 1698872 1699122 1698872 ID=cds.MS.gene86356.t1;Parent=MS.gene86356.t1
Gene Sequence

>MS.gene86356

ATGGATTCAGAAGCTGAAAATTCACAAACCCATATGAGGATTAAGACTCAGCTATGCAAAAGATTCATGCAAGGAACGTGTCCTCTTGTTGCACCCCAATGCAACTATGCACATGGCTACAACGACCTCAGAACAGCAACAGGACCAAGATTCTGTAGAATGTTCATGCACACCAGACATTGTAGCTACGGACACAACTGTCGTTTCCTTCATGCAACTCCTCCTCTACCTAGTCATTATGTTCATCCTCAGCAACAGCAGCATGAGAACTTTTCTCCACAACCACGTATTTTTCTTCAACTTCTTTCATTTACTACACTAACACTACTTTTTGGTCTTGTTTGTTCATTTCTTAGTATTAGAACAAAAAGGGTTTTCTTTTCTGTAGCACCGACACATTTAATCAAAAGTGTGTTTGTCAGTTCTTAAACCAACACAACACTGACAAATGTGAATACATTCGATCAGTGTTGTGTCCGGTGTTTGTGTTGGTGCTTTATAGGTTTTATGTAATCTAGTGAATTTTGTGCTTGTTTAATAACTTTTTTTTGTTATTAAAATAAAATGGGTTTTTTTATTTTTTTTTAAACATTATTACTTGGACTGTGAAATTGTGCAGCTTGCTTAATCAGTTATGGCATGTGGTGAATTTAGCTAGGATGGCATACTGTTAAAATATTTCAATAAAAACAACAAACACATAATGTTGGTTCTGGTGCCGATTATGAGGTTGCTTAATTAATAAGTAATGTCTCGGATTCGAGTCTTATAAATGGAAAAATGTGCATCGGAAATGATTTGCCCCTATGAGTTAGGGTCTATTTGAATTGACTTATTTGAGTTTATTTACTGACATAAAATATTGTGAGATTGTTTGTAAGAGTTTATGAAAACAAATTACAATGCTCTCAATTTTGAATCGCGGAAATTGGCGGTCTGTTCAATTTCTGCTATCCTATAATGCTACAGCGCCACTATTTGACAATTTTCTACTAAATATCGTGGAACAATAGTTTGTTCGAATTCCACTACGCTATGGTGACACTATAACTGCTATTTGACAACACTGTTTATGACATATCCATAAATTGTTTTTAGCTTATTTTTATAAGCTCTCCATGATAGCTTATACAAACAGCTTATAGTATATATGAAAACAATTTGACTTCAGTTTATCTTTTGTTGGAAAAATAGCTTATACATAAACACTTATATGATATGGACTTATGCTATGAGTGTTTAATTAAGCTGTTTACCCAAACAGGACCTTATTCCAGGTCCAATATGATTTCCATGAAAGCTTTTTGTGATTCAATAGAATATAGAACTGTGTTGGTGTAAGTAAATTTTGACTCGAGAGTTTGTGAATGCAGAACCAGGGATGATACAAAATGCAGAATGCAGGATCATGCAAACTTCTGCTGCTGCTACAACTAATGGCCACTCTTCTGCACAAAACAACACAACGCAATTGCAAACTTATAGCTCTACTCCTGCTACAAATACCTCAGCCATCACAGTGGCAACTACCTCTTTACATAAGAATGGACCGTATGCTGGTAAATCCTTATCTGACAGAAACACAATGCAAAGGATCATTCGTCTCTATGCTGATTGGATTTAA
Protein sequence

>MS.gene86356.t1

MDSEAENSQTHMRIKTQLCKRFMQGTCPLVAPQCNYAHGYNDLRTATGPRFCRMFMHTRHCSYGHNCRFLHATPPLPSHYVHPQQQQHENFSPQPQPGMIQNAECRIMQTSAAATTNGHSSAQNNTTQLQTYSSTPATNTSAITVATTSLHKNGPYAGKSLSDRNTMQRIIRLYADWI