AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene014345

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene014345.t1 MTR_5g005130 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene014345.t1 MTR_3g115330 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene014345.t1 MTR_1g106755 100.000 56 0 0 1 56 1 56 9.62e-38 119
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene014345.t1 AT4G33865 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene014345.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene014345.t1 AT3G43980 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene014345.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109

Find 21 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAGCAATGCCAAAGAAAT+TGG 0.219417 3.2:+91149499 MS.gene014345:CDS
CTTAATGAAGCCAATTTCTT+TGG 0.258338 3.2:-91149509 None:intergenic
CAAAGAAATTGGCTTCATTA+AGG 0.273794 3.2:+91149510 MS.gene014345:CDS
TCATGGGTCACTCCAACGTT+TGG 0.416385 3.2:+91148937 None:intergenic
GAACCAGGACCATAGGTCTT+GGG 0.430692 3.2:-91148969 None:intergenic
AGAACCAGGACCATAGGTCT+TGG 0.460388 3.2:-91148970 None:intergenic
GAAATTCTCATGGATTGATC+AGG 0.469054 3.2:+91149443 MS.gene014345:CDS
CCATACCATGTGCGAGAACC+AGG 0.488541 3.2:-91148984 None:intergenic
CACCCCAAGACCTATGGTCC+TGG 0.491604 3.2:+91148966 MS.gene014345:CDS
AACTCCCACCCCAAGACCTA+TGG 0.502032 3.2:+91148960 MS.gene014345:CDS
AGTACGGACTCATGTGCTGC+AGG 0.547263 3.2:+91149467 MS.gene014345:CDS
ATGGTCCTGGTTCTCGCACA+TGG 0.572066 3.2:+91148979 MS.gene014345:CDS
CATGGATTGATCAGGAAGTA+CGG 0.575110 3.2:+91149451 MS.gene014345:CDS
TGTGCGAGAACCAGGACCAT+AGG 0.585453 3.2:-91148976 None:intergenic
CAATTTCTTTGGCATTGCTG+TGG 0.593734 3.2:-91149498 None:intergenic
CGTGTGTGTGGAAATTCTCA+TGG 0.604249 3.2:+91149433 MS.gene014345:CDS
AACCAGGACCATAGGTCTTG+GGG 0.607026 3.2:-91148968 None:intergenic
CATGAGAATTTCCACACACA+CGG 0.624222 3.2:-91149432 None:intergenic
GGGGTGGGAGTTCCAAACGT+TGG 0.630320 3.2:-91148949 None:intergenic
AGGACCATAGGTCTTGGGGT+GGG 0.650323 3.2:-91148964 None:intergenic
CAGGACCATAGGTCTTGGGG+TGG 0.662828 3.2:-91148965 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CCTTAATTTGAAATTAAAAT+CGG + chr3.2:91149229-91149248 MS.gene014345:intron 15.0%
!!! TTTCATTTTTAAAATTTCTG+AGG + chr3.2:91149123-91149142 MS.gene014345:intron 15.0%
!!! CCGATTTTAATTTCAAATTA+AGG - chr3.2:91149232-91149251 None:intergenic 20.0%
! AAACACAGTAATCAGAAATA+GGG - chr3.2:91149070-91149089 None:intergenic 25.0%
! TAAACACAGTAATCAGAAAT+AGG - chr3.2:91149071-91149090 None:intergenic 25.0%
AGAAATCTAGACCAACAAAT+AGG - chr3.2:91149556-91149575 None:intergenic 30.0%
ATACTGCAACACAGAAAAAA+AGG - chr3.2:91149619-91149638 None:intergenic 30.0%
ATCGAAGATTCATTCTTCAA+GGG - chr3.2:91149047-91149066 None:intergenic 30.0%
CTTAATGAAGCCAATTTCTT+TGG - chr3.2:91149512-91149531 None:intergenic 30.0%
GATTACTGTGATTCATGATT+TGG + chr3.2:91149155-91149174 MS.gene014345:intron 30.0%
TCAAGGGATGAAAGAAAAAA+AGG - chr3.2:91149031-91149050 None:intergenic 30.0%
TCATGAATCACAGTAATCTA+TGG - chr3.2:91149153-91149172 None:intergenic 30.0%
TGATGTACTTTCCTATTTGT+TGG + chr3.2:91149542-91149561 MS.gene014345:intron 30.0%
! CAAAGAAATTGGCTTCATTA+AGG + chr3.2:91149510-91149529 MS.gene014345:CDS 30.0%
ATATGACCTAGCGTTTAGAT+GGG + chr3.2:91149094-91149113 MS.gene014345:intron 35.0%
GATCGAAGATTCATTCTTCA+AGG - chr3.2:91149048-91149067 None:intergenic 35.0%
! GAAATTCTCATGGATTGATC+AGG + chr3.2:91149443-91149462 MS.gene014345:CDS 35.0%
CAATTTCTTTGGCATTGCTG+TGG - chr3.2:91149501-91149520 None:intergenic 40.0%
CACAGCAATGCCAAAGAAAT+TGG + chr3.2:91149499-91149518 MS.gene014345:CDS 40.0%
CATATGACCTAGCGTTTAGA+TGG + chr3.2:91149093-91149112 MS.gene014345:intron 40.0%
CATGAGAATTTCCACACACA+CGG - chr3.2:91149435-91149454 None:intergenic 40.0%
TTAAAACCGTCTCCAATGCT+AGG + chr3.2:91149198-91149217 MS.gene014345:intron 40.0%
! CATGGATTGATCAGGAAGTA+CGG + chr3.2:91149451-91149470 MS.gene014345:CDS 40.0%
ACACACACGGCTACAAAACA+TGG - chr3.2:91149422-91149441 None:intergenic 45.0%
CGTGTGTGTGGAAATTCTCA+TGG + chr3.2:91149433-91149452 MS.gene014345:CDS 45.0%
TCGAATCCCATCTAAACGCT+AGG - chr3.2:91149103-91149122 None:intergenic 45.0%
! AAGGCATCTTGACCTAGCAT+TGG - chr3.2:91149213-91149232 None:intergenic 45.0%
! ATGTTTTGTAGCCGTGTGTG+TGG + chr3.2:91149421-91149440 MS.gene014345:intron 45.0%
! TCTTGACCTAGCATTGGAGA+CGG - chr3.2:91149207-91149226 None:intergenic 45.0%
AACCAGGACCATAGGTCTTG+GGG - chr3.2:91148971-91148990 None:intergenic 50.0%
AGAACCAGGACCATAGGTCT+TGG - chr3.2:91148973-91148992 None:intergenic 50.0%
GAACCAGGACCATAGGTCTT+GGG - chr3.2:91148972-91148991 None:intergenic 50.0%
AACTCCCACCCCAAGACCTA+TGG + chr3.2:91148960-91148979 MS.gene014345:CDS 55.0%
AGGACCATAGGTCTTGGGGT+GGG - chr3.2:91148967-91148986 None:intergenic 55.0%
AGTACGGACTCATGTGCTGC+AGG + chr3.2:91149467-91149486 MS.gene014345:CDS 55.0%
CCATACCATGTGCGAGAACC+AGG - chr3.2:91148987-91149006 None:intergenic 55.0%
TGTGCGAGAACCAGGACCAT+AGG - chr3.2:91148979-91148998 None:intergenic 55.0%
! ATGGTCCTGGTTCTCGCACA+TGG + chr3.2:91148979-91148998 MS.gene014345:CDS 55.0%
! CCTGGTTCTCGCACATGGTA+TGG + chr3.2:91148984-91149003 MS.gene014345:intron 55.0%
CACCCCAAGACCTATGGTCC+TGG + chr3.2:91148966-91148985 MS.gene014345:CDS 60.0%
CAGGACCATAGGTCTTGGGG+TGG - chr3.2:91148968-91148987 None:intergenic 60.0%
GGGGTGGGAGTTCCAAACGT+TGG - chr3.2:91148952-91148971 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 91148939 91149644 91148939 ID=MS.gene014345
chr3.2 mRNA 91148939 91149644 91148939 ID=MS.gene014345.t1;Parent=MS.gene014345
chr3.2 exon 91148939 91149000 91148939 ID=MS.gene014345.t1.exon1;Parent=MS.gene014345.t1
chr3.2 CDS 91148939 91149000 91148939 ID=cds.MS.gene014345.t1;Parent=MS.gene014345.t1
chr3.2 exon 91149432 91149531 91149432 ID=MS.gene014345.t1.exon2;Parent=MS.gene014345.t1
chr3.2 CDS 91149432 91149531 91149432 ID=cds.MS.gene014345.t1;Parent=MS.gene014345.t1
chr3.2 exon 91149636 91149644 91149636 ID=MS.gene014345.t1.exon3;Parent=MS.gene014345.t1
chr3.2 CDS 91149636 91149644 91149636 ID=cds.MS.gene014345.t1;Parent=MS.gene014345.t1
Gene Sequence

>MS.gene014345

ATGGGTCACTCCAACGTTTGGAACTCCCACCCCAAGACCTATGGTCCTGGTTCTCGCACATGGTATGGTATCTATCTCTTCATTTTCTGCCTTTTTTTCTTTCATCCCTTGAAGAATGAATCTTCGATCCCTATTTCTGATTACTGTGTTTATGCATATGACCTAGCGTTTAGATGGGATTCGATTTCATTTTTAAAATTTCTGAGGATTTCCATAGATTACTGTGATTCATGATTTGGTTCTGAAAGAAATTTATGAATTAAAACCGTCTCCAATGCTAGGTCAAGATGCCTTAATTTGAAATTAAAATCGGATTCTTAAAGCTTAAACAATGCAATTTTTGTTGTAAATTTCAGTGTTATCTTATAACTATTGTCTTAAGATGAGTATGATTTAGTTATTGTGACATTTCAACAGTTCTTTCTTAGTTACATGTACATACTTGACATTGCTTGATTGTAAATGTTGTCTACTGTTGTTCCATGTTTTGTAGCCGTGTGTGTGGAAATTCTCATGGATTGATCAGGAAGTACGGACTCATGTGCTGCAGGCAATGCTTCCACAGCAATGCCAAAGAAATTGGCTTCATTAAGGTGAATATTTTGATGTACTTTCCTATTTGTTGGTCTAGATTTCTAATTGTTTGCTTGTTTTAGCATGAACTCTCATCACTTTGTCCTTTTTTTCTGTGTTGCAGTATCGCTGA
Protein sequence

>MS.gene014345.t1

MGHSNVWNSHPKTYGPGSRTCRVCGNSHGLIRKYGLMCCRQCFHSNAKEIGFIKYR