AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1405180


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1405180 MtrunA17_Chr4g0063301 96.262 107 4 0 1 107 1 107 7.81e-74 214
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1405180 AT1G75125.1 60.638 94 37 0 13 106 11 104 1.20e-39 128

Find 30 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTGGAAATCGCCTTGGAAT+TGG 0.320897 tig0023115:+6056 None:intergenic
AATCATCACAGTCTAAATTA+AGG 0.339781 tig0023115:+5517 None:intergenic
GTCCTACTTGCGATGGAAAC+AGG 0.354255 tig0023115:-5714 Msa1405180:intron
ACTTTGTGTCCGAGAATAAA+CGG 0.396004 tig0023115:-5953 Msa1405180:CDS
AATCTTTACCCGTTTATTCT+CGG 0.396090 tig0023115:+5944 None:intergenic
CGATTTCCAACATGGATTAC+CGG 0.398072 tig0023115:-6044 Msa1405180:CDS
ACAACGTTGTCTGAATTGTC+TGG 0.418889 tig0023115:-5573 Msa1405180:CDS
ACACATGGGTTAATTGCAAC+AGG 0.458488 tig0023115:+5739 None:intergenic
CTTTGTGTCCGAGAATAAAC+GGG 0.475435 tig0023115:-5952 Msa1405180:intron
TGTCTGAATTGTCTGGGAAA+AGG 0.496121 tig0023115:-5566 Msa1405180:CDS
TTCCAAGGCGATTTCCAACA+TGG 0.513408 tig0023115:-6052 Msa1405180:CDS
ATCCATGTTGGAAATCGCCT+TGG 0.531843 tig0023115:+6050 None:intergenic
ATATATGCAAGTTATGCAGC+GGG 0.546291 tig0023115:-5795 Msa1405180:CDS
TGTAAAAGTTGTAGAGGGAA+AGG 0.556567 tig0023115:-5823 Msa1405180:CDS
GTAAAAGTTGTAGAGGGAAA+GGG 0.562827 tig0023115:-5822 Msa1405180:CDS
CAACGTTGTCTGAATTGTCT+GGG 0.565752 tig0023115:-5572 Msa1405180:CDS
GCGGGAATTCAACCATAGCT+TGG 0.577529 tig0023115:-5777 Msa1405180:CDS
CCCCAGTATTACAAAAGCAC+CGG 0.584681 tig0023115:+6025 None:intergenic
AAAGCACCGGTAATCCATGT+TGG 0.590454 tig0023115:+6038 None:intergenic
TGTGTTTGTCCTACTTGCGA+TGG 0.598415 tig0023115:-5721 Msa1405180:CDS
TTGCCGTGTAAAAGTTGTAG+AGG 0.598560 tig0023115:-5829 Msa1405180:CDS
ATTGCAACAGGATCATACAT+TGG 0.599710 tig0023115:+5751 None:intergenic
AAGAAATGAATCCAATTCCA+AGG 0.602574 tig0023115:-6067 Msa1405180:exon
ATACATTGGAGACCAAGCTA+TGG 0.629079 tig0023115:+5765 None:intergenic
TCGCAAGTAGGACAAACACA+TGG 0.629902 tig0023115:+5724 None:intergenic
GGGAATTGCAACTCTGAACG+TGG 0.644672 tig0023115:-6003 Msa1405180:CDS
TATATATGCAAGTTATGCAG+CGG 0.648101 tig0023115:-5796 Msa1405180:CDS
TGCCGTGTAAAAGTTGTAGA+GGG 0.654823 tig0023115:-5828 Msa1405180:CDS
CGCAAGTAGGACAAACACAT+GGG 0.656170 tig0023115:+5725 None:intergenic
AACCTGTTTCCATCGCAAGT+AGG 0.668457 tig0023115:+5712 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGCTTTCATTTGAATAT+TGG - tig0023115:5915-5934 Msa1405180:intron 20.0%
!! TTTGCTTTCATTTGAATATT+GGG - tig0023115:5916-5935 Msa1405180:intron 20.0%
!! GAAATTATAGTAACTGATAA+TGG - tig0023115:5968-5987 Msa1405180:CDS 20.0%
!! TTTTCTATGTCACGTATTTT+GGG - tig0023115:5429-5448 Msa1405180:three_prime_UTR 25.0%
!! TAAATTGTCTCTGAGAAAAA+AGG - tig0023115:5478-5497 Msa1405180:three_prime_UTR 25.0%
! TTGCTTTCATTTGAATATTG+GGG - tig0023115:5917-5936 Msa1405180:intron 25.0%
! AATCATCACAGTCTAAATTA+AGG + tig0023115:6064-6083 None:intergenic 25.0%
!!! TGATTATTTTAGTGCTTATG+AGG - tig0023115:6079-6098 Msa1405180:exon 25.0%
! GTTTTCTATGTCACGTATTT+TGG - tig0023115:5428-5447 Msa1405180:three_prime_UTR 30.0%
AAGAAATGAATCCAATTCCA+AGG - tig0023115:5511-5530 Msa1405180:three_prime_UTR 30.0%
AATCTTTACCCGTTTATTCT+CGG + tig0023115:5637-5656 None:intergenic 30.0%
GATAATATTGATGTGCTTTC+TGG - tig0023115:5693-5712 Msa1405180:intron 30.0%
TATATATGCAAGTTATGCAG+CGG - tig0023115:5782-5801 Msa1405180:CDS 30.0%
TGTCTTGAAATTGAATTGCA+AGG - tig0023115:5946-5965 Msa1405180:intron 30.0%
!! TTCGTTGTCAACTTTTTCTT+TGG - tig0023115:6110-6129 Msa1405180:five_prime_UTR 30.0%
ACTTTGTGTCCGAGAATAAA+CGG - tig0023115:5625-5644 Msa1405180:intron 35.0%
! TTGATGTGCTTTCTGGAAAT+TGG - tig0023115:5700-5719 Msa1405180:intron 35.0%
! TTCCCTCTACAACTTTTACA+CGG + tig0023115:5755-5774 None:intergenic 35.0%
TGTAAAAGTTGTAGAGGGAA+AGG - tig0023115:5755-5774 Msa1405180:CDS 35.0%
GTAAAAGTTGTAGAGGGAAA+GGG - tig0023115:5756-5775 Msa1405180:CDS 35.0%
ATATATGCAAGTTATGCAGC+GGG - tig0023115:5783-5802 Msa1405180:CDS 35.0%
ATTGCAACAGGATCATACAT+TGG + tig0023115:5830-5849 None:intergenic 35.0%
!!! ACTGATAATGGTTTTGTTGC+AGG - tig0023115:5980-5999 Msa1405180:CDS 35.0%
!!! CTGATAATGGTTTTGTTGCA+GGG - tig0023115:5981-6000 Msa1405180:CDS 35.0%
! CGATTTCCAACATGGATTAC+CGG - tig0023115:5534-5553 Msa1405180:three_prime_UTR 40.0%
! TACCGGTGCTTTTGTAATAC+TGG - tig0023115:5551-5570 Msa1405180:exon 40.0%
! ACCGGTGCTTTTGTAATACT+GGG - tig0023115:5552-5571 Msa1405180:exon 40.0%
CTTTGTGTCCGAGAATAAAC+GGG - tig0023115:5626-5645 Msa1405180:intron 40.0%
TTGCCGTGTAAAAGTTGTAG+AGG - tig0023115:5749-5768 Msa1405180:CDS 40.0%
TGCCGTGTAAAAGTTGTAGA+GGG - tig0023115:5750-5769 Msa1405180:CDS 40.0%
ATACATTGGAGACCAAGCTA+TGG + tig0023115:5816-5835 None:intergenic 40.0%
! ACACATGGGTTAATTGCAAC+AGG + tig0023115:5842-5861 None:intergenic 40.0%
ACAACGTTGTCTGAATTGTC+TGG - tig0023115:6005-6024 Msa1405180:CDS 40.0%
CAACGTTGTCTGAATTGTCT+GGG - tig0023115:6006-6025 Msa1405180:CDS 40.0%
TGTCTGAATTGTCTGGGAAA+AGG - tig0023115:6012-6031 Msa1405180:CDS 40.0%
GTTGGAAATCGCCTTGGAAT+TGG + tig0023115:5525-5544 None:intergenic 45.0%
TTCCAAGGCGATTTCCAACA+TGG - tig0023115:5526-5545 Msa1405180:three_prime_UTR 45.0%
ATCCATGTTGGAAATCGCCT+TGG + tig0023115:5531-5550 None:intergenic 45.0%
!! AAAGCACCGGTAATCCATGT+TGG + tig0023115:5543-5562 None:intergenic 45.0%
! CCCCAGTATTACAAAAGCAC+CGG + tig0023115:5556-5575 None:intergenic 45.0%
! CCGGTGCTTTTGTAATACTG+GGG - tig0023115:5553-5572 Msa1405180:exon 45.0%
! CGGTGCTTTTGTAATACTGG+GGG - tig0023115:5554-5573 Msa1405180:exon 45.0%
! GGTGCTTTTGTAATACTGGG+GGG - tig0023115:5555-5574 Msa1405180:exon 45.0%
CGCAAGTAGGACAAACACAT+GGG + tig0023115:5856-5875 None:intergenic 45.0%
TCGCAAGTAGGACAAACACA+TGG + tig0023115:5857-5876 None:intergenic 45.0%
TGTGTTTGTCCTACTTGCGA+TGG - tig0023115:5857-5876 Msa1405180:intron 45.0%
AACCTGTTTCCATCGCAAGT+AGG + tig0023115:5869-5888 None:intergenic 45.0%
GGGAATTGCAACTCTGAACG+TGG - tig0023115:5575-5594 Msa1405180:CDS 50.0%
GCGGGAATTCAACCATAGCT+TGG - tig0023115:5801-5820 Msa1405180:CDS 50.0%
GTCCTACTTGCGATGGAAAC+AGG - tig0023115:5864-5883 Msa1405180:intron 50.0%
Chromosome Type Strat End Strand Name
tig0023115 gene 5428 6172 5428 ID=Msa1405180;Name=Msa1405180
tig0023115 mRNA 5428 6172 5428 ID=Msa1405180-mRNA-1;Parent=Msa1405180;Name=Msa1405180-mRNA-1;_AED=0.09;_eAED=0.09;_QI=88|1|1|1|1|1|3|128|107
tig0023115 exon 5428 5598 5428 ID=Msa1405180-mRNA-1:exon:23989;Parent=Msa1405180-mRNA-1
tig0023115 exon 5715 5863 5715 ID=Msa1405180-mRNA-1:exon:23988;Parent=Msa1405180-mRNA-1
tig0023115 exon 5953 6172 5953 ID=Msa1405180-mRNA-1:exon:23987;Parent=Msa1405180-mRNA-1
tig0023115 five_prime_UTR 6085 6172 6085 ID=Msa1405180-mRNA-1:five_prime_utr;Parent=Msa1405180-mRNA-1
tig0023115 CDS 5953 6084 5953 ID=Msa1405180-mRNA-1:cds;Parent=Msa1405180-mRNA-1
tig0023115 CDS 5715 5863 5715 ID=Msa1405180-mRNA-1:cds;Parent=Msa1405180-mRNA-1
tig0023115 CDS 5556 5598 5556 ID=Msa1405180-mRNA-1:cds;Parent=Msa1405180-mRNA-1
tig0023115 three_prime_UTR 5428 5555 5428 ID=Msa1405180-mRNA-1:three_prime_utr;Parent=Msa1405180-mRNA-1
Gene Sequence

>Msa1405180

ATGAATCCAATTCCAAGGCGATTTCCAACATGGATTACCGGTGCTTTTGTAATACTGGGGGGAATTGCAACTCTGAACGTGGCTTCTACACTTACACTCAAAACACTTCACTTTGTGTCCGAGAATAAACGGAAAAAAACAGCGTTGCCGTGTAAAAGTTGTAGAGGGAAAGGGTTTTATATATGCAAGTTATGCAGCGGGAATTCAACCATAGCTTGGTCTCCAATGTATGATCCTGTTGCAATTAACCCATGTGTTTGTCCTACTTGCGATGGAAACAGGGTACAACGTTGTCTGAATTGTCTGGGAAAAGGCTATGACTAA

Protein sequence

>Msa1405180

MNPIPRRFPTWITGAFVILGGIATLNVASTLTLKTLHFVSENKRKKTALPCKSCRGKGFYICKLCSGNSTIAWSPMYDPVAINPCVCPTCDGNRVQRCLNCLGKGYD*