AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1394070


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394070 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1394070 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1394070 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1394070 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1394070 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1394070 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1394070 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
Msa1394070 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1394070 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 tig0021785:-17562 Msa1394070:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 tig0021785:+17300 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 tig0021785:+17596 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 tig0021785:-17645 Msa1394070:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 tig0021785:-17697 Msa1394070:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 tig0021785:-17604 Msa1394070:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 tig0021785:+17597 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 tig0021785:-17242 Msa1394070:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 tig0021785:+17529 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 tig0021785:+17294 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 tig0021785:+17639 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 tig0021785:-17688 Msa1394070:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 tig0021785:+17311 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 tig0021785:-17241 Msa1394070:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 tig0021785:-17713 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 tig0021785:-17583 Msa1394070:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 tig0021785:+17534 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 tig0021785:+17535 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 tig0021785:-17584 Msa1394070:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 tig0021785:-17600 Msa1394070:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 tig0021785:+17533 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 tig0021785:+17233 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 tig0021785:-17706 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 tig0021785:-17605 Msa1394070:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 tig0021785:+17601 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 tig0021785:+17600 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 tig0021785:-17240 Msa1394070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - tig0021785:17435-17454 Msa1394070:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + tig0021785:17625-17644 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + tig0021785:17626-17645 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + tig0021785:17384-17403 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - tig0021785:17438-17457 Msa1394070:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + tig0021785:17539-17558 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - tig0021785:17242-17261 Msa1394070:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + tig0021785:17251-17270 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + tig0021785:17361-17380 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - tig0021785:17385-17404 Msa1394070:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + tig0021785:17411-17430 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + tig0021785:17490-17509 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - tig0021785:17325-17344 Msa1394070:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + tig0021785:17356-17375 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + tig0021785:17357-17376 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - tig0021785:17367-17386 Msa1394070:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + tig0021785:17397-17416 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + tig0021785:17485-17504 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - tig0021785:17485-17504 Msa1394070:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + tig0021785:17491-17510 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - tig0021785:17489-17508 Msa1394070:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + tig0021785:17579-17598 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + tig0021785:17590-17609 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + tig0021785:17596-17615 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - tig0021785:17282-17301 Msa1394070:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + tig0021785:17293-17312 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + tig0021785:17294-17313 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + tig0021785:17355-17374 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - tig0021785:17402-17421 Msa1394070:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + tig0021785:17466-17485 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + tig0021785:17473-17492 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - tig0021785:17529-17548 Msa1394070:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + tig0021785:17535-17554 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + tig0021785:17536-17555 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + tig0021785:17657-17676 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - tig0021785:17283-17302 Msa1394070:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - tig0021785:17303-17322 Msa1394070:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - tig0021785:17304-17323 Msa1394070:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - tig0021785:17458-17477 Msa1394070:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - tig0021785:17528-17547 Msa1394070:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - tig0021785:17645-17664 Msa1394070:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - tig0021785:17646-17665 Msa1394070:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - tig0021785:17647-17666 Msa1394070:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + tig0021785:17289-17308 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - tig0021785:17499-17518 Msa1394070:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - tig0021785:17190-17209 Msa1394070:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + tig0021785:17290-17309 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - tig0021785:17287-17306 Msa1394070:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - tig0021785:17507-17526 Msa1394070:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - tig0021785:17199-17218 Msa1394070:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0021785 gene 17188 17721 17188 ID=Msa1394070;Name=Msa1394070
tig0021785 mRNA 17188 17721 17188 ID=Msa1394070-mRNA-1;Parent=Msa1394070;Name=Msa1394070-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
tig0021785 exon 17544 17721 17544 ID=Msa1394070-mRNA-1:exon:14245;Parent=Msa1394070-mRNA-1
tig0021785 exon 17188 17338 17188 ID=Msa1394070-mRNA-1:exon:14244;Parent=Msa1394070-mRNA-1
tig0021785 five_prime_UTR 17705 17721 17705 ID=Msa1394070-mRNA-1:five_prime_utr;Parent=Msa1394070-mRNA-1
tig0021785 CDS 17544 17704 17544 ID=Msa1394070-mRNA-1:cds;Parent=Msa1394070-mRNA-1
tig0021785 CDS 17188 17338 17188 ID=Msa1394070-mRNA-1:cds;Parent=Msa1394070-mRNA-1
Gene Sequence

>Msa1394070

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1394070

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN