AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene88748

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88748.t1 MTR_3g034200 35.252 139 73 4 4 131 2 134 8.53e-13 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88748.t1 AT5G13780 36.296 135 69 4 4 127 2 130 3.10e-12 61.6

Find 30 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCGTAATCCAAGGCCTTT+TGG 0.266555 5.4:+54638520 None:intergenic
AAACCTGTTCCAAATCCTTA+TGG 0.275073 5.4:+54638829 None:intergenic
CTTATCTTGCCTTTGAGTAC+TGG 0.344775 5.4:-54639035 MS.gene88748:CDS
GACTGCCGCCCATAAGGATT+TGG 0.362443 5.4:-54638838 MS.gene88748:CDS
CGCCCATAAGGATTTGGAAC+AGG 0.390119 5.4:-54638832 MS.gene88748:intron
GAAGGAGGAGGAGGTTAAGA+AGG 0.410903 5.4:-54638940 MS.gene88748:CDS
TTTATAAGCTGATGTCTTCT+CGG 0.421224 5.4:-54638461 MS.gene88748:CDS
AACCTGTTCCAAATCCTTAT+GGG 0.424723 5.4:+54638830 None:intergenic
TTATAAGCTGATGTCTTCTC+GGG 0.444062 5.4:-54638460 MS.gene88748:CDS
GCTTGTGACTGCCGCCCATA+AGG 0.446228 5.4:-54638844 MS.gene88748:CDS
CTCTATTAAGAAGGAGGAGG+AGG 0.487768 5.4:-54638949 MS.gene88748:CDS
AGCGATTCCAAGTCTCTGAT+AGG 0.494064 5.4:+54638872 None:intergenic
CTCGCAACCTATCAGAGACT+TGG 0.513871 5.4:-54638879 MS.gene88748:CDS
GGAGGAGGAGGTTAAGAAGG+AGG 0.522170 5.4:-54638937 MS.gene88748:CDS
AAGCTGGAATGTTGTACCTC+GGG 0.522913 5.4:+54638553 None:intergenic
CGCTGAAATCAGTCACGTCA+TGG 0.528842 5.4:-54638904 MS.gene88748:CDS
TTATGTCTGCTCTATTAAGA+AGG 0.559468 5.4:-54638958 MS.gene88748:CDS
TTCATAAATATCGTAATCCA+AGG 0.569142 5.4:+54638512 None:intergenic
GCAAGATAAGATCATATTCG+CGG 0.579984 5.4:+54639048 None:intergenic
TTTCACGTCGCGGTCAGGAA+CGG 0.583681 5.4:-54639002 MS.gene88748:CDS
CTGCTCTATTAAGAAGGAGG+AGG 0.589794 5.4:-54638952 MS.gene88748:CDS
CACGTCGCGGTCAGGAACGG+CGG 0.594718 5.4:-54638999 MS.gene88748:CDS
TGTTCATCTCCAGTACTCAA+AGG 0.610835 5.4:+54639026 None:intergenic
AAAGCTGGAATGTTGTACCT+CGG 0.618480 5.4:+54638552 None:intergenic
ACATCTCAGCGCTCGTCCCG+AGG 0.619758 5.4:-54638569 MS.gene88748:CDS
GGCGGCCGTCGCAATATCGT+CGG 0.625495 5.4:-54638981 MS.gene88748:CDS
ACGAGCGCTGAGATGTACTC+AGG 0.636447 5.4:+54638576 None:intergenic
TGTCTGCTCTATTAAGAAGG+AGG 0.648646 5.4:-54638955 MS.gene88748:CDS
CTGTTCCAAATCCTTATGGG+CGG 0.673914 5.4:+54638833 None:intergenic
CATAACCGACGATATTGCGA+CGG 0.695901 5.4:+54638976 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGACATATTAATTATACAAA+AGG + chr5.4:54638893-54638912 None:intergenic 15.0%
!! ACATATAGAATTATAGAACT+AGG + chr5.4:54638810-54638829 None:intergenic 20.0%
!! CATATAGAATTATAGAACTA+GGG + chr5.4:54638809-54638828 None:intergenic 20.0%
!! GTTCTATAATTCTATATGTT+AGG - chr5.4:54638811-54638830 MS.gene88748:intron 20.0%
! TTCATAAATATCGTAATCCA+AGG + chr5.4:54639041-54639060 None:intergenic 25.0%
TTATGTCTGCTCTATTAAGA+AGG - chr5.4:54638592-54638611 MS.gene88748:intron 30.0%
TTTATAAGCTGATGTCTTCT+CGG - chr5.4:54639089-54639108 MS.gene88748:CDS 30.0%
! AGCTTTCATTTTGTTCCAAA+AGG - chr5.4:54639015-54639034 MS.gene88748:CDS 30.0%
!!! TTTTGGAACAAAATGAAAGC+TGG + chr5.4:54639016-54639035 None:intergenic 30.0%
AAACCTGTTCCAAATCCTTA+TGG + chr5.4:54638724-54638743 None:intergenic 35.0%
AACCTGTTCCAAATCCTTAT+GGG + chr5.4:54638723-54638742 None:intergenic 35.0%
GCAAGATAAGATCATATTCG+CGG + chr5.4:54638505-54638524 None:intergenic 35.0%
TTATAAGCTGATGTCTTCTC+GGG - chr5.4:54639090-54639109 MS.gene88748:CDS 35.0%
AAAGCTGGAATGTTGTACCT+CGG + chr5.4:54639001-54639020 None:intergenic 40.0%
CTTATCTTGCCTTTGAGTAC+TGG - chr5.4:54638515-54638534 MS.gene88748:CDS 40.0%
TGTCTGCTCTATTAAGAAGG+AGG - chr5.4:54638595-54638614 MS.gene88748:intron 40.0%
TGTTCATCTCCAGTACTCAA+AGG + chr5.4:54638527-54638546 None:intergenic 40.0%
! AGATGAACATTTTCACGTCG+CGG - chr5.4:54638538-54638557 MS.gene88748:CDS 40.0%
! CATTTTGTTCCAAAAGGCCT+TGG - chr5.4:54639021-54639040 MS.gene88748:CDS 40.0%
! TATCGTAATCCAAGGCCTTT+TGG + chr5.4:54639033-54639052 None:intergenic 40.0%
AAGCTGGAATGTTGTACCTC+GGG + chr5.4:54639000-54639019 None:intergenic 45.0%
AGCGATTCCAAGTCTCTGAT+AGG + chr5.4:54638681-54638700 None:intergenic 45.0%
CATAACCGACGATATTGCGA+CGG + chr5.4:54638577-54638596 None:intergenic 45.0%
CTCTATTAAGAAGGAGGAGG+AGG - chr5.4:54638601-54638620 MS.gene88748:intron 45.0%
CTGCTCTATTAAGAAGGAGG+AGG - chr5.4:54638598-54638617 MS.gene88748:intron 45.0%
CTGTTCCAAATCCTTATGGG+CGG + chr5.4:54638720-54638739 None:intergenic 45.0%
CGCTGAAATCAGTCACGTCA+TGG - chr5.4:54638646-54638665 MS.gene88748:intron 50.0%
CTCGCAACCTATCAGAGACT+TGG - chr5.4:54638671-54638690 MS.gene88748:intron 50.0%
GAAGGAGGAGGAGGTTAAGA+AGG - chr5.4:54638610-54638629 MS.gene88748:intron 50.0%
! AACATTTTCACGTCGCGGTC+AGG - chr5.4:54638543-54638562 MS.gene88748:CDS 50.0%
! CGCCCATAAGGATTTGGAAC+AGG - chr5.4:54638718-54638737 MS.gene88748:intron 50.0%
GACTGCCGCCCATAAGGATT+TGG - chr5.4:54638712-54638731 MS.gene88748:intron 55.0%
GGAGGAGGAGGTTAAGAAGG+AGG - chr5.4:54638613-54638632 MS.gene88748:intron 55.0%
TTTCACGTCGCGGTCAGGAA+CGG - chr5.4:54638548-54638567 MS.gene88748:CDS 55.0%
!! ACGAGCGCTGAGATGTACTC+AGG + chr5.4:54638977-54638996 None:intergenic 55.0%
GCTTGTGACTGCCGCCCATA+AGG - chr5.4:54638706-54638725 MS.gene88748:intron 60.0%
ACATCTCAGCGCTCGTCCCG+AGG - chr5.4:54638981-54639000 MS.gene88748:CDS 65.0%
GGCGGCCGTCGCAATATCGT+CGG - chr5.4:54638569-54638588 MS.gene88748:CDS 65.0%
CACGTCGCGGTCAGGAACGG+CGG - chr5.4:54638551-54638570 MS.gene88748:CDS 70.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 54638449 54639123 54638449 ID=MS.gene88748
chr5.4 mRNA 54638449 54639123 54638449 ID=MS.gene88748.t1;Parent=MS.gene88748
chr5.4 exon 54638833 54639123 54638833 ID=MS.gene88748.t1.exon1;Parent=MS.gene88748.t1
chr5.4 CDS 54638833 54639123 54638833 ID=cds.MS.gene88748.t1;Parent=MS.gene88748.t1
chr5.4 exon 54638449 54638607 54638449 ID=MS.gene88748.t1.exon2;Parent=MS.gene88748.t1
chr5.4 CDS 54638449 54638607 54638449 ID=cds.MS.gene88748.t1;Parent=MS.gene88748.t1
Gene Sequence

>MS.gene88748

ATGTCGAACGTGAGCATAAGAGCTGCAACATGCAACGACATGTCTGAGCTTTGCCGCGAATATGATCTTATCTTGCCTTTGAGTACTGGAGATGAACATTTTCACGTCGCGGTCAGGAACGGCGGCCGTCGCAATATCGTCGGTTATGTCTGCTCTATTAAGAAGGAGGAGGAGGTTAAGAAGGAGGTTAAGATTTACGCTGAAATCAGTCACGTCATGGTTCTCGCAACCTATCAGAGACTTGGAATCGCTACAAAGCTTGTGACTGCCGCCCATAAGGATTTGGAACAGGTTTCTTTGTTTGTTTGTTATTATAAGATTTTGTTTCAATTACTTTGTTTGTTATATCACAGTGATCCCTAGTTCTATAATTCTATATGTTAGGAGTTAGATTTTGTTCAAAAATATAAAAACATGTTAGAAGTTAGATTTATTCATCAACCTTTTGTATAATTAATATGTCTTCAATGTGTGTAAACTTTAATATCGTTGCTGTTACTACTGTGTTTGTCACAGAATTATCATCCTGAGTACATCTCAGCGCTCGTCCCGAGGTACAACATTCCAGCTTTCATTTTGTTCCAAAAGGCCTTGGATTACGATATTTATGAAGCTGATTGTACGAAAAACAGTTATCACTTTTATAAGCTGATGTCTTCTCGGGAGACCAAATGA
Protein sequence

>MS.gene88748.t1

MSNVSIRAATCNDMSELCREYDLILPLSTGDEHFHVAVRNGGRRNIVGYVCSIKKEEEVKKEVKIYAEISHVMVLATYQRLGIATKLVTAAHKDLEQNYHPEYISALVPRYNIPAFILFQKALDYDIYEADCTKNSYHFYKLMSSRETK