AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0582550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582550 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0582550 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0582550 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0582550 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0582550 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0582550 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0582550 MtrunA17_Chr6g0451331 90.323 31 3 0 24 54 41 71 5.28e-14 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582550 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0582550 ATCG00560.1 97.297 37 1 0 68 104 2 38 3.75e-19 73.9

Find 27 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTAGCTTACGATGTATT+TGG 0.244623 4_2:-1071298 Msa0582550:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 4_2:+1071036 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 4_2:+1071332 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 4_2:-1071381 Msa0582550:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 4_2:-1071433 Msa0582550:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 4_2:-1071340 Msa0582550:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 4_2:+1071333 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 4_2:-1070978 Msa0582550:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 4_2:+1071265 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 4_2:+1071030 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 4_2:+1071375 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 4_2:-1071424 Msa0582550:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 4_2:+1071047 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 4_2:-1070977 Msa0582550:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 4_2:-1071449 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 4_2:-1071319 Msa0582550:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 4_2:+1071270 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 4_2:+1071271 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 4_2:-1071320 Msa0582550:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 4_2:-1071336 Msa0582550:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 4_2:+1071269 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 4_2:+1070969 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 4_2:-1071442 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 4_2:-1071341 Msa0582550:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 4_2:+1071337 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 4_2:+1071336 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 4_2:-1070976 Msa0582550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - chr4_2:1071171-1071190 Msa0582550:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + chr4_2:1071361-1071380 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + chr4_2:1071362-1071381 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + chr4_2:1071120-1071139 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - chr4_2:1071174-1071193 Msa0582550:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + chr4_2:1071275-1071294 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - chr4_2:1070978-1070997 Msa0582550:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + chr4_2:1070987-1071006 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + chr4_2:1071097-1071116 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - chr4_2:1071121-1071140 Msa0582550:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + chr4_2:1071147-1071166 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + chr4_2:1071226-1071245 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - chr4_2:1071061-1071080 Msa0582550:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + chr4_2:1071092-1071111 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + chr4_2:1071093-1071112 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - chr4_2:1071103-1071122 Msa0582550:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + chr4_2:1071133-1071152 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + chr4_2:1071221-1071240 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - chr4_2:1071221-1071240 Msa0582550:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + chr4_2:1071227-1071246 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - chr4_2:1071225-1071244 Msa0582550:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + chr4_2:1071315-1071334 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + chr4_2:1071326-1071345 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + chr4_2:1071332-1071351 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - chr4_2:1071018-1071037 Msa0582550:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + chr4_2:1071029-1071048 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + chr4_2:1071030-1071049 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + chr4_2:1071091-1071110 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - chr4_2:1071138-1071157 Msa0582550:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + chr4_2:1071202-1071221 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + chr4_2:1071209-1071228 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - chr4_2:1071265-1071284 Msa0582550:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + chr4_2:1071271-1071290 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + chr4_2:1071272-1071291 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + chr4_2:1071393-1071412 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - chr4_2:1071019-1071038 Msa0582550:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - chr4_2:1071039-1071058 Msa0582550:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - chr4_2:1071040-1071059 Msa0582550:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - chr4_2:1071194-1071213 Msa0582550:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - chr4_2:1071264-1071283 Msa0582550:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - chr4_2:1071381-1071400 Msa0582550:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - chr4_2:1071382-1071401 Msa0582550:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - chr4_2:1071383-1071402 Msa0582550:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + chr4_2:1071025-1071044 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - chr4_2:1071235-1071254 Msa0582550:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - chr4_2:1070926-1070945 Msa0582550:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + chr4_2:1071026-1071045 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - chr4_2:1071023-1071042 Msa0582550:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - chr4_2:1071243-1071262 Msa0582550:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - chr4_2:1070935-1070954 Msa0582550:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 1070924 1071457 1070924 ID=Msa0582550;Name=Msa0582550
chr4_2 mRNA 1070924 1071457 1070924 ID=Msa0582550-mRNA-1;Parent=Msa0582550;Name=Msa0582550-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr4_2 exon 1071280 1071457 1071280 ID=Msa0582550-mRNA-1:exon:217;Parent=Msa0582550-mRNA-1
chr4_2 exon 1070924 1071074 1070924 ID=Msa0582550-mRNA-1:exon:216;Parent=Msa0582550-mRNA-1
chr4_2 five_prime_UTR 1071441 1071457 1071441 ID=Msa0582550-mRNA-1:five_prime_utr;Parent=Msa0582550-mRNA-1
chr4_2 CDS 1071280 1071440 1071280 ID=Msa0582550-mRNA-1:cds;Parent=Msa0582550-mRNA-1
chr4_2 CDS 1070924 1071074 1070924 ID=Msa0582550-mRNA-1:cds;Parent=Msa0582550-mRNA-1
Gene Sequence

>Msa0582550

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0582550

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN