AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0619330


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0619330 MtrunA17_Chr8g0383001 98.837 86 1 0 1 86 251 336 6.52e-56 175
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0619330 AT2G21960.1 80.000 80 16 0 7 86 253 332 2.87e-43 143

Find 15 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCGATCCATGAAGCCTTAA+TGG 0.219380 4_2:-70418772 Msa0619330:CDS
ATCTTTGCTGAGTTGTGGTT+TGG 0.340177 4_2:+70418984 None:intergenic
CTTTGCCATCGATGCCATTA+AGG 0.360946 4_2:+70418758 None:intergenic
AGCAACAAAATCTCACTAGA+TGG 0.367508 4_2:-70418960 Msa0619330:CDS
CAGATTGGCTGTTGTATCAA+TGG 0.423423 4_2:-70419194 Msa0619330:exon
TCGATGCCATTAAGGCTTCA+TGG 0.429892 4_2:+70418766 None:intergenic
TGTTGTATCAATGGCTGGAC+TGG 0.438705 4_2:-70419185 Msa0619330:exon
TTAACATATGACAAGGTTGT+TGG 0.456845 4_2:-70419151 Msa0619330:CDS
TGCTGATCTTTGCTGAGTTG+TGG 0.475443 4_2:+70418979 None:intergenic
AATGGCATCGATGGCAAAGA+AGG 0.499709 4_2:-70418754 Msa0619330:CDS
TTGGCTGTTGTATCAATGGC+TGG 0.512860 4_2:-70419190 Msa0619330:exon
TGAAGCCTTAATGGCATCGA+TGG 0.543498 4_2:-70418763 Msa0619330:CDS
GCAACAAAATCTCACTAGAT+GGG 0.575785 4_2:-70418959 Msa0619330:CDS
ATGGCTGGACTGGCAGCAGA+AGG 0.600695 4_2:-70419175 Msa0619330:CDS
AGAAGGTTTAACATATGACA+AGG 0.674545 4_2:-70419158 Msa0619330:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAACAAATGACTACAAATT+GGG + chr4_2:70418792-70418811 None:intergenic 20.0%
!!! TTCACATATTTTGAAAATAG+AGG + chr4_2:70418969-70418988 None:intergenic 20.0%
!! TTAACAAATGACTACAAATT+GGG + chr4_2:70418792-70418811 None:intergenic 20.0%
!!! TTCACATATTTTGAAAATAG+AGG + chr4_2:70418969-70418988 None:intergenic 20.0%
! GATAGATAGGTATATTTACT+AGG - chr4_2:70418591-70418610 Msa0619330:three_prime_UTR 25.0%
! TAGTGCATATTCTTAAATCA+CGG - chr4_2:70418620-70418639 Msa0619330:three_prime_UTR 25.0%
!! ATATAGGAGTTTTCTAAACT+AGG + chr4_2:70418690-70418709 None:intergenic 25.0%
! TATATGATATGACATGAACA+CGG - chr4_2:70418705-70418724 Msa0619330:exon 25.0%
! CTTAACAAATGACTACAAAT+TGG + chr4_2:70418793-70418812 None:intergenic 25.0%
!!! TATTGCTTGTTTTTTCAGAT+TGG - chr4_2:70418849-70418868 Msa0619330:intron 25.0%
!! AAGTATATATTTTGCTACAG+AGG - chr4_2:70419038-70419057 Msa0619330:intron 25.0%
! ATTTCAAAAGCTCATATTTG+TGG - chr4_2:70419174-70419193 Msa0619330:CDS 25.0%
!! CTGCAAATATAAGCTTTTTA+AGG + chr4_2:70419231-70419250 None:intergenic 25.0%
! CTTAAAAAGCTTATATTTGC+AGG - chr4_2:70419229-70419248 Msa0619330:intron 25.0%
! GATAGATAGGTATATTTACT+AGG - chr4_2:70418591-70418610 Msa0619330:three_prime_UTR 25.0%
! TAGTGCATATTCTTAAATCA+CGG - chr4_2:70418620-70418639 Msa0619330:three_prime_UTR 25.0%
!! ATATAGGAGTTTTCTAAACT+AGG + chr4_2:70418690-70418709 None:intergenic 25.0%
! TATATGATATGACATGAACA+CGG - chr4_2:70418705-70418724 Msa0619330:exon 25.0%
! CTTAACAAATGACTACAAAT+TGG + chr4_2:70418793-70418812 None:intergenic 25.0%
!!! TATTGCTTGTTTTTTCAGAT+TGG - chr4_2:70418849-70418868 Msa0619330:intron 25.0%
!! AAGTATATATTTTGCTACAG+AGG - chr4_2:70419038-70419057 Msa0619330:intron 25.0%
! ATTTCAAAAGCTCATATTTG+TGG - chr4_2:70419174-70419193 Msa0619330:CDS 25.0%
!! CTGCAAATATAAGCTTTTTA+AGG + chr4_2:70419231-70419250 None:intergenic 25.0%
! CTTAAAAAGCTTATATTTGC+AGG - chr4_2:70419229-70419248 Msa0619330:intron 25.0%
TGTCGAATTTCACAAAATCA+TGG + chr4_2:70418651-70418670 None:intergenic 30.0%
GTGTTCATGTCATATCATAT+AGG + chr4_2:70418706-70418725 None:intergenic 30.0%
AAGTACCAATGTGAAGAAAT+AGG - chr4_2:70418817-70418836 Msa0619330:intron 30.0%
! CTTTACCTATTTCTTCACAT+TGG + chr4_2:70418825-70418844 None:intergenic 30.0%
AGAAGGTTTAACATATGACA+AGG - chr4_2:70418900-70418919 Msa0619330:intron 30.0%
TTAACATATGACAAGGTTGT+TGG - chr4_2:70418907-70418926 Msa0619330:intron 30.0%
GACAAAAATGCATAAACTTG+AGG + chr4_2:70419209-70419228 None:intergenic 30.0%
TGTCGAATTTCACAAAATCA+TGG + chr4_2:70418651-70418670 None:intergenic 30.0%
GTGTTCATGTCATATCATAT+AGG + chr4_2:70418706-70418725 None:intergenic 30.0%
AAGTACCAATGTGAAGAAAT+AGG - chr4_2:70418817-70418836 Msa0619330:intron 30.0%
! CTTTACCTATTTCTTCACAT+TGG + chr4_2:70418825-70418844 None:intergenic 30.0%
AGAAGGTTTAACATATGACA+AGG - chr4_2:70418900-70418919 Msa0619330:intron 30.0%
TTAACATATGACAAGGTTGT+TGG - chr4_2:70418907-70418926 Msa0619330:intron 30.0%
GACAAAAATGCATAAACTTG+AGG + chr4_2:70419209-70419228 None:intergenic 30.0%
TTGATGCTAAGGAGATAGAT+AGG - chr4_2:70418578-70418597 Msa0619330:three_prime_UTR 35.0%
TTCTAAACTAGGTGTCTGTT+TGG + chr4_2:70418679-70418698 None:intergenic 35.0%
AGCAACAAAATCTCACTAGA+TGG - chr4_2:70419098-70419117 Msa0619330:intron 35.0%
GCAACAAAATCTCACTAGAT+GGG - chr4_2:70419099-70419118 Msa0619330:intron 35.0%
TCAAAAGCTCATATTTGTGG+AGG - chr4_2:70419177-70419196 Msa0619330:CDS 35.0%
ATCTATCTCCTTAGCATCAA+GGG + chr4_2:70418578-70418597 None:intergenic 35.0%
TATCTATCTCCTTAGCATCA+AGG + chr4_2:70418579-70418598 None:intergenic 35.0%
TTGATGCTAAGGAGATAGAT+AGG - chr4_2:70418578-70418597 Msa0619330:three_prime_UTR 35.0%
TTCTAAACTAGGTGTCTGTT+TGG + chr4_2:70418679-70418698 None:intergenic 35.0%
AGCAACAAAATCTCACTAGA+TGG - chr4_2:70419098-70419117 Msa0619330:intron 35.0%
GCAACAAAATCTCACTAGAT+GGG - chr4_2:70419099-70419118 Msa0619330:intron 35.0%
TCAAAAGCTCATATTTGTGG+AGG - chr4_2:70419177-70419196 Msa0619330:CDS 35.0%
AACTAGGTGTCTGTTTGGAT+TGG + chr4_2:70418674-70418693 None:intergenic 40.0%
TATGACATGAACACGGAATG+TGG - chr4_2:70418712-70418731 Msa0619330:CDS 40.0%
! CAGATTGGCTGTTGTATCAA+TGG - chr4_2:70418864-70418883 Msa0619330:intron 40.0%
GAAAATAGAGGTCTCAAACC+TGG + chr4_2:70418957-70418976 None:intergenic 40.0%
ATCTTTGCTGAGTTGTGGTT+TGG + chr4_2:70419077-70419096 None:intergenic 40.0%
AACTAGGTGTCTGTTTGGAT+TGG + chr4_2:70418674-70418693 None:intergenic 40.0%
TATGACATGAACACGGAATG+TGG - chr4_2:70418712-70418731 Msa0619330:CDS 40.0%
! CAGATTGGCTGTTGTATCAA+TGG - chr4_2:70418864-70418883 Msa0619330:intron 40.0%
GAAAATAGAGGTCTCAAACC+TGG + chr4_2:70418957-70418976 None:intergenic 40.0%
ATCTTTGCTGAGTTGTGGTT+TGG + chr4_2:70419077-70419096 None:intergenic 40.0%
TTGGCTGTTGTATCAATGGC+TGG - chr4_2:70418868-70418887 Msa0619330:intron 45.0%
TGTTGTATCAATGGCTGGAC+TGG - chr4_2:70418873-70418892 Msa0619330:intron 45.0%
! TGCTGATCTTTTCACTCTCC+AGG - chr4_2:70418936-70418955 Msa0619330:intron 45.0%
TGCTGATCTTTGCTGAGTTG+TGG + chr4_2:70419082-70419101 None:intergenic 45.0%
GTCGATCCATGAAGCCTTAA+TGG - chr4_2:70419286-70419305 Msa0619330:intron 45.0%
TCGATGCCATTAAGGCTTCA+TGG + chr4_2:70419295-70419314 None:intergenic 45.0%
! TGAAGCCTTAATGGCATCGA+TGG - chr4_2:70419295-70419314 Msa0619330:intron 45.0%
CTTTGCCATCGATGCCATTA+AGG + chr4_2:70419303-70419322 None:intergenic 45.0%
!! AATGGCATCGATGGCAAAGA+AGG - chr4_2:70419304-70419323 Msa0619330:intron 45.0%
TTGGCTGTTGTATCAATGGC+TGG - chr4_2:70418868-70418887 Msa0619330:intron 45.0%
TGTTGTATCAATGGCTGGAC+TGG - chr4_2:70418873-70418892 Msa0619330:intron 45.0%
! TGCTGATCTTTTCACTCTCC+AGG - chr4_2:70418936-70418955 Msa0619330:intron 45.0%
TGCTGATCTTTGCTGAGTTG+TGG + chr4_2:70419082-70419101 None:intergenic 45.0%
GTCGATCCATGAAGCCTTAA+TGG - chr4_2:70419286-70419305 Msa0619330:intron 45.0%
TCGATGCCATTAAGGCTTCA+TGG + chr4_2:70419295-70419314 None:intergenic 45.0%
! TGAAGCCTTAATGGCATCGA+TGG - chr4_2:70419295-70419314 Msa0619330:intron 45.0%
CTTTGCCATCGATGCCATTA+AGG + chr4_2:70419303-70419322 None:intergenic 45.0%
!! AATGGCATCGATGGCAAAGA+AGG - chr4_2:70419304-70419323 Msa0619330:intron 45.0%
!! ATGGCTGGACTGGCAGCAGA+AGG - chr4_2:70418883-70418902 Msa0619330:intron 60.0%
!! ATGGCTGGACTGGCAGCAGA+AGG - chr4_2:70418883-70418902 Msa0619330:intron 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 70418577 70419503 70418577 ID=Msa0619330;Name=Msa0619330
chr4_2 mRNA 70418577 70419503 70418577 ID=Msa0619330-mRNA-1;Parent=Msa0619330;Name=Msa0619330-mRNA-1;_AED=0.00;_eAED=0.00;_QI=39|1|1|1|0.66|0.75|4|133|86
chr4_2 exon 70418577 70418829 70418577 ID=Msa0619330-mRNA-1:exon:20561;Parent=Msa0619330-mRNA-1
chr4_2 exon 70418957 70419022 70418957 ID=Msa0619330-mRNA-1:exon:20560;Parent=Msa0619330-mRNA-1
chr4_2 exon 70419123 70419213 70419123 ID=Msa0619330-mRNA-1:exon:20559;Parent=Msa0619330-mRNA-1
chr4_2 exon 70419481 70419503 70419481 ID=Msa0619330-mRNA-1:exon:20558;Parent=Msa0619330-mRNA-1
chr4_2 five_prime_UTR 70419481 70419503 70419481 ID=Msa0619330-mRNA-1:five_prime_utr;Parent=Msa0619330-mRNA-1
chr4_2 five_prime_UTR 70419198 70419213 70419198 ID=Msa0619330-mRNA-1:five_prime_utr;Parent=Msa0619330-mRNA-1
chr4_2 CDS 70419123 70419197 70419123 ID=Msa0619330-mRNA-1:cds;Parent=Msa0619330-mRNA-1
chr4_2 CDS 70418957 70419022 70418957 ID=Msa0619330-mRNA-1:cds;Parent=Msa0619330-mRNA-1
chr4_2 CDS 70418710 70418829 70418710 ID=Msa0619330-mRNA-1:cds;Parent=Msa0619330-mRNA-1
chr4_2 three_prime_UTR 70418577 70418709 70418577 ID=Msa0619330-mRNA-1:three_prime_utr;Parent=Msa0619330-mRNA-1
Gene Sequence

>Msa0619330

ATGGCTGGACTGGCAGCAGAAGGTTTAACATATGACAAGGTTGTTGGTCAATCTGCTGATCTTTTCACTCTCCAGAGGTTTATAAACAGAACCAAACCACAACTCAGCAAAGATCAGCAACAAAATCTCACTAGATGGGCAGTTTTGTTCGCTGCTTCTCTATTGAAAAACAACAAGTCGATCCATGAAGCCTTAATGGCATCGATGGCAAAGAAGGCAAGTGTACTCGAGTGCATTCAAACAATCGAAAGTGCATCATAG

Protein sequence

>Msa0619330

MAGLAAEGLTYDKVVGQSADLFTLQRFINRTKPQLSKDQQQNLTRWAVLFAASLLKNNKSIHEALMASMAKKASVLECIQTIESAS*