AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268440


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268440 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268440 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268440 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268440 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0268440 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0268440 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0268440 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
Msa0268440 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0268440 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 2_2:-70230410 Msa0268440:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 2_2:+70230148 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 2_2:+70230444 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 2_2:-70230493 Msa0268440:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 2_2:-70230545 Msa0268440:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 2_2:-70230452 Msa0268440:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 2_2:+70230445 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 2_2:-70230090 Msa0268440:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 2_2:+70230377 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 2_2:+70230142 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 2_2:+70230487 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 2_2:-70230536 Msa0268440:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 2_2:+70230159 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 2_2:-70230089 Msa0268440:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 2_2:-70230561 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 2_2:-70230431 Msa0268440:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 2_2:+70230382 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 2_2:+70230383 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 2_2:-70230432 Msa0268440:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 2_2:-70230448 Msa0268440:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 2_2:+70230381 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 2_2:+70230081 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 2_2:-70230554 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 2_2:-70230453 Msa0268440:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 2_2:+70230449 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 2_2:+70230448 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 2_2:-70230088 Msa0268440:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - chr2_2:70230283-70230302 Msa0268440:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + chr2_2:70230473-70230492 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + chr2_2:70230474-70230493 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + chr2_2:70230232-70230251 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - chr2_2:70230286-70230305 Msa0268440:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + chr2_2:70230387-70230406 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - chr2_2:70230090-70230109 Msa0268440:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + chr2_2:70230099-70230118 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + chr2_2:70230209-70230228 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - chr2_2:70230233-70230252 Msa0268440:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + chr2_2:70230259-70230278 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + chr2_2:70230338-70230357 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - chr2_2:70230173-70230192 Msa0268440:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + chr2_2:70230204-70230223 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + chr2_2:70230205-70230224 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - chr2_2:70230215-70230234 Msa0268440:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + chr2_2:70230245-70230264 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + chr2_2:70230333-70230352 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - chr2_2:70230333-70230352 Msa0268440:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + chr2_2:70230339-70230358 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - chr2_2:70230337-70230356 Msa0268440:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + chr2_2:70230427-70230446 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + chr2_2:70230438-70230457 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + chr2_2:70230444-70230463 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - chr2_2:70230130-70230149 Msa0268440:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + chr2_2:70230141-70230160 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + chr2_2:70230142-70230161 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + chr2_2:70230203-70230222 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - chr2_2:70230250-70230269 Msa0268440:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + chr2_2:70230314-70230333 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + chr2_2:70230321-70230340 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - chr2_2:70230377-70230396 Msa0268440:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + chr2_2:70230383-70230402 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + chr2_2:70230384-70230403 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + chr2_2:70230505-70230524 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - chr2_2:70230131-70230150 Msa0268440:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - chr2_2:70230151-70230170 Msa0268440:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - chr2_2:70230152-70230171 Msa0268440:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - chr2_2:70230306-70230325 Msa0268440:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - chr2_2:70230376-70230395 Msa0268440:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - chr2_2:70230493-70230512 Msa0268440:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - chr2_2:70230494-70230513 Msa0268440:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - chr2_2:70230495-70230514 Msa0268440:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + chr2_2:70230137-70230156 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - chr2_2:70230347-70230366 Msa0268440:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - chr2_2:70230038-70230057 Msa0268440:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + chr2_2:70230138-70230157 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - chr2_2:70230135-70230154 Msa0268440:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - chr2_2:70230355-70230374 Msa0268440:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - chr2_2:70230047-70230066 Msa0268440:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70230036 70230569 70230036 ID=Msa0268440;Name=Msa0268440
chr2_2 mRNA 70230036 70230569 70230036 ID=Msa0268440-mRNA-1;Parent=Msa0268440;Name=Msa0268440-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr2_2 exon 70230392 70230569 70230392 ID=Msa0268440-mRNA-1:exon:22547;Parent=Msa0268440-mRNA-1
chr2_2 exon 70230036 70230186 70230036 ID=Msa0268440-mRNA-1:exon:22546;Parent=Msa0268440-mRNA-1
chr2_2 five_prime_UTR 70230553 70230569 70230553 ID=Msa0268440-mRNA-1:five_prime_utr;Parent=Msa0268440-mRNA-1
chr2_2 CDS 70230392 70230552 70230392 ID=Msa0268440-mRNA-1:cds;Parent=Msa0268440-mRNA-1
chr2_2 CDS 70230036 70230186 70230036 ID=Msa0268440-mRNA-1:cds;Parent=Msa0268440-mRNA-1
Gene Sequence

>Msa0268440

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0268440

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN