AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1354870


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1354870 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1354870 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1354870 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1354870 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1354870 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1354870 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1354870 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
Msa1354870 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1354870 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 tig0014543:+571399 Msa1354870:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 tig0014543:-571661 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 tig0014543:-571365 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 tig0014543:+571316 Msa1354870:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 tig0014543:+571264 Msa1354870:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 tig0014543:+571357 Msa1354870:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 tig0014543:-571364 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 tig0014543:+571719 Msa1354870:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 tig0014543:-571432 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 tig0014543:-571667 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 tig0014543:-571322 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 tig0014543:+571273 Msa1354870:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 tig0014543:-571650 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 tig0014543:+571720 Msa1354870:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 tig0014543:+571248 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 tig0014543:+571378 Msa1354870:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 tig0014543:-571427 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 tig0014543:-571426 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 tig0014543:+571377 Msa1354870:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 tig0014543:+571361 Msa1354870:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 tig0014543:-571428 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 tig0014543:-571728 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 tig0014543:+571255 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 tig0014543:+571356 Msa1354870:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 tig0014543:-571360 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 tig0014543:-571361 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 tig0014543:+571721 Msa1354870:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + tig0014543:571509-571528 Msa1354870:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - tig0014543:571699-571718 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - tig0014543:571700-571719 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - tig0014543:571458-571477 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + tig0014543:571512-571531 Msa1354870:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - tig0014543:571613-571632 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + tig0014543:571316-571335 Msa1354870:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - tig0014543:571325-571344 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - tig0014543:571435-571454 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + tig0014543:571459-571478 Msa1354870:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - tig0014543:571485-571504 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - tig0014543:571564-571583 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + tig0014543:571399-571418 Msa1354870:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - tig0014543:571430-571449 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - tig0014543:571431-571450 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + tig0014543:571441-571460 Msa1354870:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - tig0014543:571471-571490 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - tig0014543:571559-571578 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + tig0014543:571559-571578 Msa1354870:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - tig0014543:571565-571584 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + tig0014543:571563-571582 Msa1354870:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - tig0014543:571653-571672 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - tig0014543:571664-571683 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - tig0014543:571670-571689 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + tig0014543:571356-571375 Msa1354870:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - tig0014543:571367-571386 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - tig0014543:571368-571387 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - tig0014543:571429-571448 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + tig0014543:571476-571495 Msa1354870:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - tig0014543:571540-571559 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - tig0014543:571547-571566 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + tig0014543:571603-571622 Msa1354870:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - tig0014543:571609-571628 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - tig0014543:571610-571629 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - tig0014543:571731-571750 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + tig0014543:571357-571376 Msa1354870:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + tig0014543:571377-571396 Msa1354870:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + tig0014543:571378-571397 Msa1354870:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + tig0014543:571532-571551 Msa1354870:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + tig0014543:571602-571621 Msa1354870:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + tig0014543:571719-571738 Msa1354870:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + tig0014543:571720-571739 Msa1354870:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + tig0014543:571721-571740 Msa1354870:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - tig0014543:571363-571382 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + tig0014543:571573-571592 Msa1354870:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + tig0014543:571264-571283 Msa1354870:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - tig0014543:571364-571383 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + tig0014543:571361-571380 Msa1354870:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + tig0014543:571581-571600 Msa1354870:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + tig0014543:571273-571292 Msa1354870:exon 60.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 571262 571795 571262 ID=Msa1354870;Name=Msa1354870
tig0014543 mRNA 571262 571795 571262 ID=Msa1354870-mRNA-1;Parent=Msa1354870;Name=Msa1354870-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
tig0014543 exon 571262 571439 571262 ID=Msa1354870-mRNA-1:exon:9262;Parent=Msa1354870-mRNA-1
tig0014543 exon 571645 571795 571645 ID=Msa1354870-mRNA-1:exon:9263;Parent=Msa1354870-mRNA-1
tig0014543 five_prime_UTR 571262 571278 571262 ID=Msa1354870-mRNA-1:five_prime_utr;Parent=Msa1354870-mRNA-1
tig0014543 CDS 571279 571439 571279 ID=Msa1354870-mRNA-1:cds;Parent=Msa1354870-mRNA-1
tig0014543 CDS 571645 571795 571645 ID=Msa1354870-mRNA-1:cds;Parent=Msa1354870-mRNA-1
Gene Sequence

>Msa1354870

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1354870

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN