AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1041570


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1041570 MtrunA17_Chr7g0268601 86.813 182 19 2 1 177 1 182 2.18e-100 286
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1041570 AT4G03150.1 60.000 130 50 1 44 171 52 181 6.00e-52 164

Find 60 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGGGTTACTTTACATAAA+TGG 0.225005 7_1:+79143109 Msa1041570:CDS
TTCTCATTAAACTCTTTAAC+TGG 0.232983 7_1:-79143534 None:intergenic
ATTGGAAACCATTTCTTATA+AGG 0.243835 7_1:+79143260 Msa1041570:CDS
TGGAGCTATGAAATTCAATT+TGG 0.253108 7_1:-79143360 None:intergenic
GTTCAATCCGCTGCGCGATT+AGG 0.295554 7_1:-79143326 None:intergenic
ACTTGGTCGTCATCGGGTTC+TGG 0.304693 7_1:-79142685 None:intergenic
CAAAGAATTGTAGTAGGATT+TGG 0.316745 7_1:-79143187 None:intergenic
ATTAGGAATCAGAGTGGCTT+AGG 0.341814 7_1:+79143091 Msa1041570:intron
AAAACTTTCCTTATAAGAAA+TGG 0.350129 7_1:-79143268 None:intergenic
ACGAATGGCTCATATTATAT+TGG 0.370827 7_1:+79142401 Msa1041570:five_prime_UTR
ATCTCCACATTTGTTTCCTC+AGG 0.391134 7_1:-79143150 None:intergenic
TTTCATAGCTCCACATGGTT+TGG 0.395953 7_1:+79143370 Msa1041570:three_prime_UTR
GTTGAATATGGCACGTGAAT+TGG 0.399859 7_1:+79143242 Msa1041570:CDS
GTCTTCAACTTGGTCGTCAT+CGG 0.400136 7_1:-79142692 None:intergenic
TCGTCATCGGGTTCTGGAAA+TGG 0.412464 7_1:-79142679 None:intergenic
GAGGAGGAAGATGGTGTGAA+TGG 0.458635 7_1:-79142559 None:intergenic
AAAGTGAGTTAGGAAATTCT+AGG 0.459966 7_1:-79143441 None:intergenic
TCTTCAACTTGGTCGTCATC+GGG 0.460270 7_1:-79142691 None:intergenic
CCGTATCAAAGAATTGTAGT+AGG 0.472999 7_1:-79143193 None:intergenic
CTACCTGGGAGGCATTGGTT+GGG 0.478796 7_1:-79142741 None:intergenic
AGTACCTACCTGGGAGGCAT+TGG 0.485202 7_1:-79142746 None:intergenic
AAGATGAAGAAGAAGCGTAT+TGG 0.486292 7_1:-79142606 None:intergenic
GGAGCTATGAAATTCAATTT+GGG 0.488254 7_1:-79143359 None:intergenic
GGTTACTTTACATAAATGGT+TGG 0.503773 7_1:+79143113 Msa1041570:CDS
GAAATGGATGAGAATGTGAA+TGG 0.509383 7_1:-79142663 None:intergenic
AGAAGCAATTGCACAGGGAC+AGG 0.510296 7_1:-79142429 None:intergenic
AGGAGGAAGATGGTGTGAAT+GGG 0.510323 7_1:-79142558 None:intergenic
CCTACTACAATTCTTTGATA+CGG 0.511408 7_1:+79143193 Msa1041570:CDS
TTAGGAATCAGAGTGGCTTA+GGG 0.523126 7_1:+79143092 Msa1041570:intron
ATGAAGAAGAAGCGTATTGG+TGG 0.538072 7_1:-79142603 None:intergenic
ACTCCCAACCAATGCCTCCC+AGG 0.538117 7_1:+79142738 Msa1041570:CDS
AAATAAAGAAGCAATTGCAC+AGG 0.543286 7_1:-79142435 None:intergenic
CCTACCTGGGAGGCATTGGT+TGG 0.555347 7_1:-79142742 None:intergenic
TAATAAAGTTTCTGAACGAA+TGG 0.564551 7_1:+79142386 None:intergenic
TGTGAATGGGATGATGCTGC+GGG 0.566309 7_1:-79142545 None:intergenic
GAACACGAAGGTCTTCAACT+TGG 0.573094 7_1:-79142702 None:intergenic
GAATGTTACTGTCACGGAGG+AGG 0.577024 7_1:-79142575 None:intergenic
GTGTGAATGGGATGATGCTG+CGG 0.578527 7_1:-79142546 None:intergenic
ACTGTCACGGAGGAGGAAGA+TGG 0.589440 7_1:-79142568 None:intergenic
TCTCATTAAACTCTTTAACT+GGG 0.593475 7_1:-79143533 None:intergenic
TGGTTGGGAGTAACCAATGA+GGG 0.597474 7_1:-79142726 None:intergenic
AGCCGCATTTGCAGATGTGT+AGG 0.600800 7_1:-79143298 None:intergenic
CTGTCCTGAGGAAACAAATG+TGG 0.608003 7_1:+79143146 Msa1041570:CDS
GCTATGAAATTCAATTTGGG+TGG 0.608458 7_1:-79143356 None:intergenic
TTGAATTTCATAGCTCCACA+TGG 0.618128 7_1:+79143365 Msa1041570:exon
GGCCTACACATCTGCAAATG+CGG 0.641836 7_1:+79143296 Msa1041570:CDS
GTGAATGGGTACGAGTAGTG+TGG 0.653357 7_1:-79142648 None:intergenic
AAATGGATGAGAATGTGAAT+GGG 0.656050 7_1:-79142662 None:intergenic
TTGGTTGGGAGTAACCAATG+AGG 0.663293 7_1:-79142727 None:intergenic
AATAAAGAAGCAATTGCACA+GGG 0.666063 7_1:-79142434 None:intergenic
ACAATTATTAGGAATCAGAG+TGG 0.674841 7_1:+79143085 Msa1041570:intron
CTGTAAACCTAATCGCGCAG+CGG 0.684704 7_1:+79143319 Msa1041570:CDS
GTGAGTGAATGTTACTGTCA+CGG 0.689434 7_1:-79142581 None:intergenic
GCTGCGGGGAGATAGAATGA+TGG 0.699964 7_1:-79142530 None:intergenic
GTTGGGAGTAACCAATGAGG+GGG 0.704622 7_1:-79142724 None:intergenic
GGTTGGGAGTAACCAATGAG+GGG 0.709296 7_1:-79142725 None:intergenic
GGATGATGAATACTGTCCTG+AGG 0.725475 7_1:+79143134 Msa1041570:CDS
GTGAATGGGATGATGCTGCG+GGG 0.726743 7_1:-79142544 None:intergenic
GAAAAGAGTACCTACCTGGG+AGG 0.727204 7_1:-79142752 None:intergenic
AGTGAATGTTACTGTCACGG+AGG 0.780859 7_1:-79142578 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTCCATTCACAATTATT+AGG + chr7_1:79143074-79143093 Msa1041570:intron 20.0%
!! AAAACTTTCCTTATAAGAAA+TGG - chr7_1:79143271-79143290 None:intergenic 20.0%
! GAATTGGTTACATATTGTTA+AGG + chr7_1:79142836-79142855 Msa1041570:intron 25.0%
! TGATTCCTAATAATTGTGAA+TGG - chr7_1:79143082-79143101 None:intergenic 25.0%
!! TTAGGGTTACTTTACATAAA+TGG + chr7_1:79143109-79143128 Msa1041570:CDS 25.0%
! ATTGGAAACCATTTCTTATA+AGG + chr7_1:79143260-79143279 Msa1041570:CDS 25.0%
!! TCTTATAAGGAAAGTTTTCA+TGG + chr7_1:79143273-79143292 Msa1041570:CDS 25.0%
!! CTTATAAGGAAAGTTTTCAT+GGG + chr7_1:79143274-79143293 Msa1041570:CDS 25.0%
!! TTATAAGGAAAGTTTTCATG+GGG + chr7_1:79143275-79143294 Msa1041570:CDS 25.0%
! TCTCATTAAACTCTTTAACT+GGG - chr7_1:79143536-79143555 None:intergenic 25.0%
! TTCTCATTAAACTCTTTAAC+TGG - chr7_1:79143537-79143556 None:intergenic 25.0%
ACGAATGGCTCATATTATAT+TGG + chr7_1:79142401-79142420 Msa1041570:five_prime_UTR 30.0%
AATAAAGAAGCAATTGCACA+GGG - chr7_1:79142437-79142456 None:intergenic 30.0%
AAATAAAGAAGCAATTGCAC+AGG - chr7_1:79142438-79142457 None:intergenic 30.0%
AAATGGATGAGAATGTGAAT+GGG - chr7_1:79142665-79142684 None:intergenic 30.0%
!! ACGTGTTTCTAAAATTTGAG+AGG - chr7_1:79142785-79142804 None:intergenic 30.0%
TGAGATGTTCATGTTAGAAT+TGG + chr7_1:79142820-79142839 Msa1041570:intron 30.0%
ACAATTATTAGGAATCAGAG+TGG + chr7_1:79143085-79143104 Msa1041570:intron 30.0%
! GGTTACTTTACATAAATGGT+TGG + chr7_1:79143113-79143132 Msa1041570:CDS 30.0%
CAAAGAATTGTAGTAGGATT+TGG - chr7_1:79143190-79143209 None:intergenic 30.0%
CCTACTACAATTCTTTGATA+CGG + chr7_1:79143193-79143212 Msa1041570:CDS 30.0%
! AGCTGACATTTTGTTGAATA+TGG + chr7_1:79143230-79143249 Msa1041570:CDS 30.0%
GGAGCTATGAAATTCAATTT+GGG - chr7_1:79143362-79143381 None:intergenic 30.0%
TGGAGCTATGAAATTCAATT+TGG - chr7_1:79143363-79143382 None:intergenic 30.0%
AAAGTGAGTTAGGAAATTCT+AGG - chr7_1:79143444-79143463 None:intergenic 30.0%
!! GAATTTCCTAACTCACTTTT+TGG + chr7_1:79143445-79143464 Msa1041570:three_prime_UTR 30.0%
!! TATTTTTCTAGTCGAGCAAG+CGG + chr7_1:79142453-79142472 Msa1041570:five_prime_UTR 35.0%
! AAGATGAAGAAGAAGCGTAT+TGG - chr7_1:79142609-79142628 None:intergenic 35.0%
GAAATGGATGAGAATGTGAA+TGG - chr7_1:79142666-79142685 None:intergenic 35.0%
!! AATGAAAAGAGTACCTACCT+GGG - chr7_1:79142758-79142777 None:intergenic 35.0%
ATGAAGATATAAATGAGCGC+AGG - chr7_1:79143044-79143063 None:intergenic 35.0%
CCGTATCAAAGAATTGTAGT+AGG - chr7_1:79143196-79143215 None:intergenic 35.0%
GCTATGAAATTCAATTTGGG+TGG - chr7_1:79143359-79143378 None:intergenic 35.0%
TTGAATTTCATAGCTCCACA+TGG + chr7_1:79143365-79143384 Msa1041570:exon 35.0%
AGTGAAAAAACCAAACCATG+TGG - chr7_1:79143383-79143402 None:intergenic 35.0%
GTGAGTGAATGTTACTGTCA+CGG - chr7_1:79142584-79142603 None:intergenic 40.0%
! ATGAAGAAGAAGCGTATTGG+TGG - chr7_1:79142606-79142625 None:intergenic 40.0%
!!! GTGGACAATTTTTGGTGAAG+AGG - chr7_1:79142632-79142651 None:intergenic 40.0%
! CGAGTAGTGTGGACAATTTT+TGG - chr7_1:79142640-79142659 None:intergenic 40.0%
!! GAATGAAAAGAGTACCTACC+TGG - chr7_1:79142759-79142778 None:intergenic 40.0%
AAAGTAATCACATGTGTCCG+TGG + chr7_1:79142965-79142984 Msa1041570:intron 40.0%
CTAGTGATTTCAACACCGAA+AGG - chr7_1:79142991-79143010 None:intergenic 40.0%
!! CTTTCGGTGTTGAAATCACT+AGG + chr7_1:79142989-79143008 Msa1041570:intron 40.0%
GTTGAAATCACTAGGTGGTT+AGG + chr7_1:79142997-79143016 Msa1041570:intron 40.0%
ATTAGGAATCAGAGTGGCTT+AGG + chr7_1:79143091-79143110 Msa1041570:intron 40.0%
TTAGGAATCAGAGTGGCTTA+GGG + chr7_1:79143092-79143111 Msa1041570:intron 40.0%
ATCTCCACATTTGTTTCCTC+AGG - chr7_1:79143153-79143172 None:intergenic 40.0%
GTTGAATATGGCACGTGAAT+TGG + chr7_1:79143242-79143261 Msa1041570:CDS 40.0%
TTTCATAGCTCCACATGGTT+TGG + chr7_1:79143370-79143389 Msa1041570:three_prime_UTR 40.0%
GAGTCACCAAAAAGTGAGTT+AGG - chr7_1:79143454-79143473 None:intergenic 40.0%
AGGAGGAAGATGGTGTGAAT+GGG - chr7_1:79142561-79142580 None:intergenic 45.0%
AGTGAATGTTACTGTCACGG+AGG - chr7_1:79142581-79142600 None:intergenic 45.0%
TCTTCAACTTGGTCGTCATC+GGG - chr7_1:79142694-79142713 None:intergenic 45.0%
GTCTTCAACTTGGTCGTCAT+CGG - chr7_1:79142695-79142714 None:intergenic 45.0%
GAACACGAAGGTCTTCAACT+TGG - chr7_1:79142705-79142724 None:intergenic 45.0%
TGGTTGGGAGTAACCAATGA+GGG - chr7_1:79142729-79142748 None:intergenic 45.0%
TTGGTTGGGAGTAACCAATG+AGG - chr7_1:79142730-79142749 None:intergenic 45.0%
! TAGTTAGCTTAGACCGACGA+AGG + chr7_1:79142901-79142920 Msa1041570:intron 45.0%
ATTTCAACACCGAAAGGCCA+CGG - chr7_1:79142985-79143004 None:intergenic 45.0%
!! TCGGTGTTGAAATCACTAGG+TGG + chr7_1:79142992-79143011 Msa1041570:intron 45.0%
GGATGATGAATACTGTCCTG+AGG + chr7_1:79143134-79143153 Msa1041570:CDS 45.0%
CTGTCCTGAGGAAACAAATG+TGG + chr7_1:79143146-79143165 Msa1041570:CDS 45.0%
AGAAGCAATTGCACAGGGAC+AGG - chr7_1:79142432-79142451 None:intergenic 50.0%
TGTGAATGGGATGATGCTGC+GGG - chr7_1:79142548-79142567 None:intergenic 50.0%
GTGTGAATGGGATGATGCTG+CGG - chr7_1:79142549-79142568 None:intergenic 50.0%
GAGGAGGAAGATGGTGTGAA+TGG - chr7_1:79142562-79142581 None:intergenic 50.0%
GAATGTTACTGTCACGGAGG+AGG - chr7_1:79142578-79142597 None:intergenic 50.0%
GTGAATGGGTACGAGTAGTG+TGG - chr7_1:79142651-79142670 None:intergenic 50.0%
!! TCGTCATCGGGTTCTGGAAA+TGG - chr7_1:79142682-79142701 None:intergenic 50.0%
GTTGGGAGTAACCAATGAGG+GGG - chr7_1:79142727-79142746 None:intergenic 50.0%
GGTTGGGAGTAACCAATGAG+GGG - chr7_1:79142728-79142747 None:intergenic 50.0%
!! GAAAAGAGTACCTACCTGGG+AGG - chr7_1:79142755-79142774 None:intergenic 50.0%
GGCCTACACATCTGCAAATG+CGG + chr7_1:79143296-79143315 Msa1041570:CDS 50.0%
AGCCGCATTTGCAGATGTGT+AGG - chr7_1:79143301-79143320 None:intergenic 50.0%
CTGTAAACCTAATCGCGCAG+CGG + chr7_1:79143319-79143338 Msa1041570:CDS 50.0%
GCTGCGGGGAGATAGAATGA+TGG - chr7_1:79142533-79142552 None:intergenic 55.0%
GTGAATGGGATGATGCTGCG+GGG - chr7_1:79142547-79142566 None:intergenic 55.0%
ACTGTCACGGAGGAGGAAGA+TGG - chr7_1:79142571-79142590 None:intergenic 55.0%
ACTTGGTCGTCATCGGGTTC+TGG - chr7_1:79142688-79142707 None:intergenic 55.0%
ACCTTCGTGTTCCCCCTCAT+TGG + chr7_1:79142713-79142732 Msa1041570:CDS 55.0%
ACCAATGAGGGGGAACACGA+AGG - chr7_1:79142717-79142736 None:intergenic 55.0%
!! CTACCTGGGAGGCATTGGTT+GGG - chr7_1:79142744-79142763 None:intergenic 55.0%
! AGTACCTACCTGGGAGGCAT+TGG - chr7_1:79142749-79142768 None:intergenic 55.0%
! CGTGTTGACGTGTCCTTCGT+CGG - chr7_1:79142917-79142936 None:intergenic 55.0%
CGACGAAGGACACGTCAACA+CGG + chr7_1:79142915-79142934 Msa1041570:intron 55.0%
CACATGTGTCCGTGGCCTTT+CGG + chr7_1:79142973-79142992 Msa1041570:intron 55.0%
GTTCAATCCGCTGCGCGATT+AGG - chr7_1:79143329-79143348 None:intergenic 55.0%
ACTCCCAACCAATGCCTCCC+AGG + chr7_1:79142738-79142757 Msa1041570:CDS 60.0%
!! CCTACCTGGGAGGCATTGGT+TGG - chr7_1:79142745-79142764 None:intergenic 60.0%
CCAACCAATGCCTCCCAGGT+AGG + chr7_1:79142742-79142761 Msa1041570:intron 60.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 79142393 79143616 79142393 ID=Msa1041570;Name=Msa1041570
chr7_1 mRNA 79142393 79143616 79142393 ID=Msa1041570-mRNA-1;Parent=Msa1041570;Name=Msa1041570-mRNA-1;_AED=0.00;_eAED=0.00;_QI=106|1|1|1|1|1|2|248|177
chr7_1 exon 79142393 79142759 79142393 ID=Msa1041570-mRNA-1:exon:21264;Parent=Msa1041570-mRNA-1
chr7_1 exon 79143096 79143616 79143096 ID=Msa1041570-mRNA-1:exon:21265;Parent=Msa1041570-mRNA-1
chr7_1 five_prime_UTR 79142393 79142498 79142393 ID=Msa1041570-mRNA-1:five_prime_utr;Parent=Msa1041570-mRNA-1
chr7_1 CDS 79142499 79142759 79142499 ID=Msa1041570-mRNA-1:cds;Parent=Msa1041570-mRNA-1
chr7_1 CDS 79143096 79143368 79143096 ID=Msa1041570-mRNA-1:cds;Parent=Msa1041570-mRNA-1
chr7_1 three_prime_UTR 79143369 79143616 79143369 ID=Msa1041570-mRNA-1:three_prime_utr;Parent=Msa1041570-mRNA-1
Gene Sequence

>Msa1041570

ATGTCAAGCTTGAAATTGAATCTAGTTCATACCATCATTCTATCTCCCCGCAGCATCATCCCATTCACACCATCTTCCTCCTCCGTGACAGTAACATTCACTCACCACCAATACGCTTCTTCTTCATCTTCCTCTTCACCAAAAATTGTCCACACTACTCGTACCCATTCACATTCTCATCCATTTCCAGAACCCGATGACGACCAAGTTGAAGACCTTCGTGTTCCCCCTCATTGGTTACTCCCAACCAATGCCTCCCAGGAATCAGAGTGGCTTAGGGTTACTTTACATAAATGGTTGGATGATGAATACTGTCCTGAGGAAACAAATGTGGAGATAAGCAGAGTTGCTGCCAAATCCTACTACAATTCTTTGATACGGAAACAAGCTGATTTAGCTGACATTTTGTTGAATATGGCACGTGAATTGGAAACCATTTCTTATAAGGAAAGTTTTCATGGGGCCTACACATCTGCAAATGCGGCTGTAAACCTAATCGCGCAGCGGATTGAACAATTCTGCCACCCAAATTGA

Protein sequence

>Msa1041570

MSSLKLNLVHTIILSPRSIIPFTPSSSSVTVTFTHHQYASSSSSSSPKIVHTTRTHSHSHPFPEPDDDQVEDLRVPPHWLLPTNASQESEWLRVTLHKWLDDEYCPEETNVEISRVAAKSYYNSLIRKQADLADILLNMARELETISYKESFHGAYTSANAAVNLIAQRIEQFCHPN*