AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0371870


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0371870 MtrunA17_Chr3g0119011 92.969 128 8 1 1 127 1 128 1.02e-82 238
Msa0371870 MtrunA17_Chr3g0118991 73.770 61 13 2 68 127 1 59 8.43e-23 84.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0371870 AT5G20935.1 79.012 81 17 0 45 125 37 117 4.46e-41 132
Msa0371870 AT5G20935.2 77.083 48 11 0 45 92 37 84 1.89e-19 77.4

Find 42 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAATGACACTGAAATATT+TGG 0.193807 3_1:+70088937 None:intergenic
CCTTGCCTCAGAGTTAATTC+TGG 0.251411 3_1:-70088790 Msa0371870:CDS
GATTTGTGGTTTCAATGTTT+TGG 0.261828 3_1:+70089067 None:intergenic
CGTACTGCCCACACATCTTT+TGG 0.272835 3_1:+70088333 None:intergenic
ACTATACTCAACCAGATCTA+AGG 0.289522 3_1:+70088266 None:intergenic
TGGAGCTTCGATGATAATAA+TGG 0.291436 3_1:+70088840 None:intergenic
AAACGTTCAAAGTTGGATAA+AGG 0.314200 3_1:-70088868 Msa0371870:CDS
ATTGGAACTTATCTTATTGA+TGG 0.358224 3_1:-70088303 Msa0371870:CDS
CCCAACCAGCAGGTGGCTCT+TGG 0.375234 3_1:-70088187 Msa0371870:three_prime_UTR
GTTGCAATGTTTCTGATTTG+TGG 0.375721 3_1:+70089053 None:intergenic
CCAAGAGCCACCTGCTGGTT+GGG 0.395859 3_1:+70088187 None:intergenic
TATGTGTGAGGAAGGATATT+AGG 0.413182 3_1:+70089143 None:intergenic
GGAGCTTCGATGATAATAAT+GGG 0.430762 3_1:+70088841 None:intergenic
AACGTTCAAAGTTGGATAAA+GGG 0.431347 3_1:-70088867 Msa0371870:CDS
ATATTTCAAGCCCTTAGATC+TGG 0.435238 3_1:-70088277 Msa0371870:CDS
ACACATACACTGCAAATGAT+TGG 0.445934 3_1:-70089127 Msa0371870:five_prime_UTR
ATATTTCAGTGTCATTAGTA+AGG 0.457947 3_1:-70088933 Msa0371870:CDS
CTGTTGTTGAACTTTAGAAA+TGG 0.461418 3_1:+70088982 None:intergenic
GCCAAGAGCCACCTGCTGGT+TGG 0.499573 3_1:+70088186 None:intergenic
ATGTCTTTGTCCCTTTCTTG+TGG 0.510900 3_1:-70089015 Msa0371870:CDS
CTTTGTGATACCACAAGAAA+GGG 0.530774 3_1:+70089005 None:intergenic
GCTTTGTGATACCACAAGAA+AGG 0.545899 3_1:+70089004 None:intergenic
CAAAAGATGTGTGGGCAGTA+CGG 0.550493 3_1:-70088332 Msa0371870:CDS
AATTCTGGCTTAGTCAAACC+TGG 0.553371 3_1:-70088775 Msa0371870:CDS
AGTCAAGCAAAATATTACAT+TGG 0.554810 3_1:-70088129 Msa0371870:three_prime_UTR
CAGAATTAACTCTGAGGCAA+GGG 0.557005 3_1:+70088791 None:intergenic
CTATACTCAACCAGATCTAA+GGG 0.566149 3_1:+70088267 None:intergenic
TGGGCAGTACGGCTCAACAT+TGG 0.579445 3_1:-70088321 Msa0371870:CDS
TCAAACCTGGTGATGTTGGA+AGG 0.583959 3_1:-70088762 Msa0371870:intron
AAGAAAGCCAAAAGATGTGT+GGG 0.587735 3_1:-70088340 Msa0371870:CDS
CCAGAATTAACTCTGAGGCA+AGG 0.590927 3_1:+70088790 None:intergenic
CAAGAAAGCCAAAAGATGTG+TGG 0.602135 3_1:-70088341 Msa0371870:CDS
TTAGTCAAACCTGGTGATGT+TGG 0.604419 3_1:-70088766 Msa0371870:CDS
AAATACCTTCCAACATCACC+AGG 0.606725 3_1:+70088757 None:intergenic
TTTGTTTCCCAACCAGCAGG+TGG 0.609564 3_1:-70088194 Msa0371870:three_prime_UTR
GTATGCCAAGAGCCACCTGC+TGG 0.623688 3_1:+70088182 None:intergenic
TTGCAGTGTATGTGTGAGGA+AGG 0.631311 3_1:+70089135 None:intergenic
TGAATCAAAAGAGTCATCAG+AGG 0.675313 3_1:-70088908 Msa0371870:CDS
CTAAGCCAGAATTAACTCTG+AGG 0.700737 3_1:+70088785 None:intergenic
ACAGCTTGAAGTATCAACAA+CGG 0.721755 3_1:-70088963 Msa0371870:CDS
TCATTTGCAGTGTATGTGTG+AGG 0.727329 3_1:+70089131 None:intergenic
GCTTGAAGTATCAACAACGG+AGG 0.739120 3_1:-70088960 Msa0371870:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGTATAAATGATTTAATT+TGG - chr3_1:70088721-70088740 Msa0371870:intron 10.0%
!! AATTAATATCATGTATAAAA+TGG - chr3_1:70088874-70088893 Msa0371870:CDS 10.0%
!! AATGTATAAATGATTTAATT+TGG - chr3_1:70088721-70088740 Msa0371870:intron 10.0%
!! AATTAATATCATGTATAAAA+TGG - chr3_1:70088874-70088893 Msa0371870:CDS 10.0%
!! GTAAATAATTATATATCACT+TGG - chr3_1:70088904-70088923 Msa0371870:CDS 15.0%
!! GTAAATAATTATATATCACT+TGG - chr3_1:70088904-70088923 Msa0371870:CDS 15.0%
!! AATGAAAAACTTAAAAGATG+AGG + chr3_1:70088552-70088571 None:intergenic 20.0%
!! GATTAGATACATAGTAAAAA+AGG + chr3_1:70088752-70088771 None:intergenic 20.0%
!! AATGAAAAACTTAAAAGATG+AGG + chr3_1:70088552-70088571 None:intergenic 20.0%
!! GATTAGATACATAGTAAAAA+AGG + chr3_1:70088752-70088771 None:intergenic 20.0%
!!! TTCAATGTTTTGGAATTTGT+TGG + chr3_1:70088207-70088226 None:intergenic 25.0%
! ACTAATGACACTGAAATATT+TGG + chr3_1:70088347-70088366 None:intergenic 25.0%
!! ATATTTCAGTGTCATTAGTA+AGG - chr3_1:70088348-70088367 Msa0371870:CDS 25.0%
!! TTACGTGTAGAAATTTTGTA+AGG - chr3_1:70088843-70088862 Msa0371870:CDS 25.0%
! TATCATGTATAAAATGGCAA+TGG - chr3_1:70088880-70088899 Msa0371870:CDS 25.0%
! ATTGGAACTTATCTTATTGA+TGG - chr3_1:70088978-70088997 Msa0371870:CDS 25.0%
! AGTCAAGCAAAATATTACAT+TGG - chr3_1:70089152-70089171 Msa0371870:five_prime_UTR 25.0%
!!! TTCAATGTTTTGGAATTTGT+TGG + chr3_1:70088207-70088226 None:intergenic 25.0%
! ACTAATGACACTGAAATATT+TGG + chr3_1:70088347-70088366 None:intergenic 25.0%
!! ATATTTCAGTGTCATTAGTA+AGG - chr3_1:70088348-70088367 Msa0371870:CDS 25.0%
!! TTACGTGTAGAAATTTTGTA+AGG - chr3_1:70088843-70088862 Msa0371870:CDS 25.0%
! TATCATGTATAAAATGGCAA+TGG - chr3_1:70088880-70088899 Msa0371870:CDS 25.0%
! ATTGGAACTTATCTTATTGA+TGG - chr3_1:70088978-70088997 Msa0371870:CDS 25.0%
! AGTCAAGCAAAATATTACAT+TGG - chr3_1:70089152-70089171 Msa0371870:five_prime_UTR 25.0%
!!! GTTTTGGAATTTGTTGGTTA+TGG + chr3_1:70088201-70088220 None:intergenic 30.0%
! GATTTGTGGTTTCAATGTTT+TGG + chr3_1:70088217-70088236 None:intergenic 30.0%
! CTGTTGTTGAACTTTAGAAA+TGG + chr3_1:70088302-70088321 None:intergenic 30.0%
AAACGTTCAAAGTTGGATAA+AGG - chr3_1:70088413-70088432 Msa0371870:intron 30.0%
AACGTTCAAAGTTGGATAAA+GGG - chr3_1:70088414-70088433 Msa0371870:intron 30.0%
CTTATCCCATTAAATTGGAT+CGG - chr3_1:70088663-70088682 Msa0371870:intron 30.0%
!!! GTTTTGGAATTTGTTGGTTA+TGG + chr3_1:70088201-70088220 None:intergenic 30.0%
! GATTTGTGGTTTCAATGTTT+TGG + chr3_1:70088217-70088236 None:intergenic 30.0%
! CTGTTGTTGAACTTTAGAAA+TGG + chr3_1:70088302-70088321 None:intergenic 30.0%
AAACGTTCAAAGTTGGATAA+AGG - chr3_1:70088413-70088432 Msa0371870:intron 30.0%
AACGTTCAAAGTTGGATAAA+GGG - chr3_1:70088414-70088433 Msa0371870:intron 30.0%
CTTATCCCATTAAATTGGAT+CGG - chr3_1:70088663-70088682 Msa0371870:intron 30.0%
TATGTGTGAGGAAGGATATT+AGG + chr3_1:70088141-70088160 None:intergenic 35.0%
ACACATACACTGCAAATGAT+TGG - chr3_1:70088154-70088173 Msa0371870:three_prime_UTR 35.0%
! GTTGCAATGTTTCTGATTTG+TGG + chr3_1:70088231-70088250 None:intergenic 35.0%
CTTTGTGATACCACAAGAAA+GGG + chr3_1:70088279-70088298 None:intergenic 35.0%
! ACAGCTTGAAGTATCAACAA+CGG - chr3_1:70088318-70088337 Msa0371870:CDS 35.0%
TGAATCAAAAGAGTCATCAG+AGG - chr3_1:70088373-70088392 Msa0371870:intron 35.0%
GCTTGAAAAACGTTCAAAGT+TGG - chr3_1:70088406-70088425 Msa0371870:intron 35.0%
GGAGCTTCGATGATAATAAT+GGG + chr3_1:70088443-70088462 None:intergenic 35.0%
TGGAGCTTCGATGATAATAA+TGG + chr3_1:70088444-70088463 None:intergenic 35.0%
CAATTTAATGGGATAAGGCT+TGG + chr3_1:70088660-70088679 None:intergenic 35.0%
! CAAGCCTTATCCCATTAAAT+TGG - chr3_1:70088658-70088677 Msa0371870:intron 35.0%
CGATCCAATTTAATGGGATA+AGG + chr3_1:70088665-70088684 None:intergenic 35.0%
TGTTGCCGATCCAATTTAAT+GGG + chr3_1:70088671-70088690 None:intergenic 35.0%
ATGTTGCCGATCCAATTTAA+TGG + chr3_1:70088672-70088691 None:intergenic 35.0%
AAGAAAGCCAAAAGATGTGT+GGG - chr3_1:70088941-70088960 Msa0371870:CDS 35.0%
ATATTTCAAGCCCTTAGATC+TGG - chr3_1:70089004-70089023 Msa0371870:CDS 35.0%
CTATACTCAACCAGATCTAA+GGG + chr3_1:70089017-70089036 None:intergenic 35.0%
ACTATACTCAACCAGATCTA+AGG + chr3_1:70089018-70089037 None:intergenic 35.0%
TATGTGTGAGGAAGGATATT+AGG + chr3_1:70088141-70088160 None:intergenic 35.0%
ACACATACACTGCAAATGAT+TGG - chr3_1:70088154-70088173 Msa0371870:three_prime_UTR 35.0%
! GTTGCAATGTTTCTGATTTG+TGG + chr3_1:70088231-70088250 None:intergenic 35.0%
CTTTGTGATACCACAAGAAA+GGG + chr3_1:70088279-70088298 None:intergenic 35.0%
! ACAGCTTGAAGTATCAACAA+CGG - chr3_1:70088318-70088337 Msa0371870:CDS 35.0%
TGAATCAAAAGAGTCATCAG+AGG - chr3_1:70088373-70088392 Msa0371870:intron 35.0%
GCTTGAAAAACGTTCAAAGT+TGG - chr3_1:70088406-70088425 Msa0371870:intron 35.0%
GGAGCTTCGATGATAATAAT+GGG + chr3_1:70088443-70088462 None:intergenic 35.0%
TGGAGCTTCGATGATAATAA+TGG + chr3_1:70088444-70088463 None:intergenic 35.0%
CAATTTAATGGGATAAGGCT+TGG + chr3_1:70088660-70088679 None:intergenic 35.0%
! CAAGCCTTATCCCATTAAAT+TGG - chr3_1:70088658-70088677 Msa0371870:intron 35.0%
CGATCCAATTTAATGGGATA+AGG + chr3_1:70088665-70088684 None:intergenic 35.0%
TGTTGCCGATCCAATTTAAT+GGG + chr3_1:70088671-70088690 None:intergenic 35.0%
ATGTTGCCGATCCAATTTAA+TGG + chr3_1:70088672-70088691 None:intergenic 35.0%
AAGAAAGCCAAAAGATGTGT+GGG - chr3_1:70088941-70088960 Msa0371870:CDS 35.0%
ATATTTCAAGCCCTTAGATC+TGG - chr3_1:70089004-70089023 Msa0371870:CDS 35.0%
CTATACTCAACCAGATCTAA+GGG + chr3_1:70089017-70089036 None:intergenic 35.0%
ACTATACTCAACCAGATCTA+AGG + chr3_1:70089018-70089037 None:intergenic 35.0%
TCATTTGCAGTGTATGTGTG+AGG + chr3_1:70088153-70088172 None:intergenic 40.0%
ATGTCTTTGTCCCTTTCTTG+TGG - chr3_1:70088266-70088285 Msa0371870:CDS 40.0%
GCTTTGTGATACCACAAGAA+AGG + chr3_1:70088280-70088299 None:intergenic 40.0%
!! GCTGCAGTTTTGATCATCTT+TGG + chr3_1:70088464-70088483 None:intergenic 40.0%
!! CAGAATTAACTCTGAGGCAA+GGG + chr3_1:70088493-70088512 None:intergenic 40.0%
CTAAGCCAGAATTAACTCTG+AGG + chr3_1:70088499-70088518 None:intergenic 40.0%
!! AATTCTGGCTTAGTCAAACC+TGG - chr3_1:70088506-70088525 Msa0371870:intron 40.0%
! TTAGTCAAACCTGGTGATGT+TGG - chr3_1:70088515-70088534 Msa0371870:intron 40.0%
AAATACCTTCCAACATCACC+AGG + chr3_1:70088527-70088546 None:intergenic 40.0%
CAAGAAAGCCAAAAGATGTG+TGG - chr3_1:70088940-70088959 Msa0371870:CDS 40.0%
!! ATTTTTGTTTCCCAACCAGC+AGG - chr3_1:70089084-70089103 Msa0371870:five_prime_UTR 40.0%
TCATTTGCAGTGTATGTGTG+AGG + chr3_1:70088153-70088172 None:intergenic 40.0%
ATGTCTTTGTCCCTTTCTTG+TGG - chr3_1:70088266-70088285 Msa0371870:CDS 40.0%
GCTTTGTGATACCACAAGAA+AGG + chr3_1:70088280-70088299 None:intergenic 40.0%
!! GCTGCAGTTTTGATCATCTT+TGG + chr3_1:70088464-70088483 None:intergenic 40.0%
!! CAGAATTAACTCTGAGGCAA+GGG + chr3_1:70088493-70088512 None:intergenic 40.0%
CTAAGCCAGAATTAACTCTG+AGG + chr3_1:70088499-70088518 None:intergenic 40.0%
!! AATTCTGGCTTAGTCAAACC+TGG - chr3_1:70088506-70088525 Msa0371870:intron 40.0%
! TTAGTCAAACCTGGTGATGT+TGG - chr3_1:70088515-70088534 Msa0371870:intron 40.0%
AAATACCTTCCAACATCACC+AGG + chr3_1:70088527-70088546 None:intergenic 40.0%
CAAGAAAGCCAAAAGATGTG+TGG - chr3_1:70088940-70088959 Msa0371870:CDS 40.0%
!! ATTTTTGTTTCCCAACCAGC+AGG - chr3_1:70089084-70089103 Msa0371870:five_prime_UTR 40.0%
TTGCAGTGTATGTGTGAGGA+AGG + chr3_1:70088149-70088168 None:intergenic 45.0%
! GCTTGAAGTATCAACAACGG+AGG - chr3_1:70088321-70088340 Msa0371870:CDS 45.0%
!! CCAGAATTAACTCTGAGGCA+AGG + chr3_1:70088494-70088513 None:intergenic 45.0%
CCTTGCCTCAGAGTTAATTC+TGG - chr3_1:70088491-70088510 Msa0371870:intron 45.0%
! TCAAACCTGGTGATGTTGGA+AGG - chr3_1:70088519-70088538 Msa0371870:intron 45.0%
CAAAAGATGTGTGGGCAGTA+CGG - chr3_1:70088949-70088968 Msa0371870:CDS 45.0%
TTGCAGTGTATGTGTGAGGA+AGG + chr3_1:70088149-70088168 None:intergenic 45.0%
! GCTTGAAGTATCAACAACGG+AGG - chr3_1:70088321-70088340 Msa0371870:CDS 45.0%
!! CCAGAATTAACTCTGAGGCA+AGG + chr3_1:70088494-70088513 None:intergenic 45.0%
CCTTGCCTCAGAGTTAATTC+TGG - chr3_1:70088491-70088510 Msa0371870:intron 45.0%
! TCAAACCTGGTGATGTTGGA+AGG - chr3_1:70088519-70088538 Msa0371870:intron 45.0%
CAAAAGATGTGTGGGCAGTA+CGG - chr3_1:70088949-70088968 Msa0371870:CDS 45.0%
! CGTACTGCCCACACATCTTT+TGG + chr3_1:70088951-70088970 None:intergenic 50.0%
TTTGTTTCCCAACCAGCAGG+TGG - chr3_1:70089087-70089106 Msa0371870:five_prime_UTR 50.0%
! CGTACTGCCCACACATCTTT+TGG + chr3_1:70088951-70088970 None:intergenic 50.0%
TTTGTTTCCCAACCAGCAGG+TGG - chr3_1:70089087-70089106 Msa0371870:five_prime_UTR 50.0%
TGGGCAGTACGGCTCAACAT+TGG - chr3_1:70088960-70088979 Msa0371870:CDS 55.0%
TGGGCAGTACGGCTCAACAT+TGG - chr3_1:70088960-70088979 Msa0371870:CDS 55.0%
! CCAAGAGCCACCTGCTGGTT+GGG + chr3_1:70089097-70089116 None:intergenic 60.0%
GTATGCCAAGAGCCACCTGC+TGG + chr3_1:70089102-70089121 None:intergenic 60.0%
! CCAAGAGCCACCTGCTGGTT+GGG + chr3_1:70089097-70089116 None:intergenic 60.0%
GTATGCCAAGAGCCACCTGC+TGG + chr3_1:70089102-70089121 None:intergenic 60.0%
CCCAACCAGCAGGTGGCTCT+TGG - chr3_1:70089094-70089113 Msa0371870:five_prime_UTR 65.0%
GCCAAGAGCCACCTGCTGGT+TGG + chr3_1:70089098-70089117 None:intergenic 65.0%
CCCAACCAGCAGGTGGCTCT+TGG - chr3_1:70089094-70089113 Msa0371870:five_prime_UTR 65.0%
GCCAAGAGCCACCTGCTGGT+TGG + chr3_1:70089098-70089117 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 70088076 70089227 70088076 ID=Msa0371870;Name=Msa0371870
chr3_1 mRNA 70088076 70089227 70088076 ID=Msa0371870-mRNA-1;Parent=Msa0371870;Name=Msa0371870-mRNA-1;_AED=0.00;_eAED=0.00;_QI=190|1|1|1|1|1|2|187|127
chr3_1 exon 70088076 70088371 70088076 ID=Msa0371870-mRNA-1:exon:15075;Parent=Msa0371870-mRNA-1
chr3_1 exon 70088763 70089227 70088763 ID=Msa0371870-mRNA-1:exon:15074;Parent=Msa0371870-mRNA-1
chr3_1 five_prime_UTR 70089038 70089227 70089038 ID=Msa0371870-mRNA-1:five_prime_utr;Parent=Msa0371870-mRNA-1
chr3_1 CDS 70088763 70089037 70088763 ID=Msa0371870-mRNA-1:cds;Parent=Msa0371870-mRNA-1
chr3_1 CDS 70088263 70088371 70088263 ID=Msa0371870-mRNA-1:cds;Parent=Msa0371870-mRNA-1
chr3_1 three_prime_UTR 70088076 70088262 70088076 ID=Msa0371870-mRNA-1:three_prime_utr;Parent=Msa0371870-mRNA-1
Gene Sequence

>Msa0371870

ATGTCTTTGTCCCTTTCTTGTGGTATCACAAAGCCATTTCTAAAGTTCAACAACAGCTTGAAGTATCAACAACGGAGGCCAAATATTTCAGTGTCATTAGTAAGGTGTGAATCAAAAGAGTCATCAGAGGAGAATGAGTTGCTTGAAAAACGTTCAAAGTTGGATAAAGGGTCTCCCATTATTATCATCGAAGCTCCAAAGATGATCAAAACTGCAGCTTCTGTCCCTTGCCTCAGAGTTAATTCTGGCTTAGTCAAACCTGGTGATGTTGGAAGAATTGTTTCAAGAAAGCCAAAAGATGTGTGGGCAGTACGGCTCAACATTGGAACTTATCTTATTGATGGCAAATATTTCAAGCCCTTAGATCTGGTTGAGTATAGTTAG

Protein sequence

>Msa0371870

MSLSLSCGITKPFLKFNNSLKYQQRRPNISVSLVRCESKESSEENELLEKRSKLDKGSPIIIIEAPKMIKTAASVPCLRVNSGLVKPGDVGRIVSRKPKDVWAVRLNIGTYLIDGKYFKPLDLVEYS*