AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060011


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060011.t1 MTR_8g038580 89.796 98 10 0 14 111 297 394 3.26e-56 182
MS.gene060011.t1 MTR_6g045483 87.755 98 6 1 14 111 297 388 3.53e-53 171
MS.gene060011.t1 MTR_6g045483 87.755 98 6 1 14 111 297 388 1.38e-52 171
MS.gene060011.t1 MTR_6g045483 87.755 98 6 1 14 111 297 388 2.35e-52 171
MS.gene060011.t1 MTR_6g045483 87.755 98 6 1 14 111 297 388 1.05e-51 170
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060011.t1 AT1G02260 83.019 53 9 0 59 111 302 354 2.91e-24 95.9
MS.gene060011.t1 AT1G02260 83.019 53 9 0 59 111 302 354 2.91e-24 95.9

Find 20 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGTTTATATGATTACATT+AGG 0.308469 6.3:-40412833 MS.gene060011:CDS
TCATTATTAGTCCCTTCCTT+TGG 0.384907 6.3:+40412998 None:intergenic
TATGTCGTGGACTGCAATTT+CGG 0.400089 6.3:-40412780 MS.gene060011:CDS
ATTGTATGACATTAGGAATA+AGG 0.417042 6.3:-40412462 None:intergenic
ATGTTGATTGCAATGCTTCT+TGG 0.424623 6.3:-40412809 MS.gene060011:CDS
TTTAGTACCTTCTCTAAACT+TGG 0.448984 6.3:+40412716 None:intergenic
AATTTCGGCTGCATTAGCTT+TGG 0.452114 6.3:-40412765 MS.gene060011:CDS
TGACTTGGCATCTCAAACAA+AGG 0.524594 6.3:-40412978 MS.gene060011:CDS
TTTGATCTCTTCGGAAGGAA+AGG 0.533553 6.3:-40412897 MS.gene060011:CDS
GATGTAGATAGAACAATAGA+AGG 0.539083 6.3:-40412926 MS.gene060011:CDS
CTAGAAATTCAACCAAAGGA+AGG 0.551351 6.3:-40413010 MS.gene060011:CDS
TTCTTGATTTCAAAGATGCT+AGG 0.551545 6.3:-40412739 MS.gene060011:CDS
TTCTTGGTTTAAATATGTCG+TGG 0.568745 6.3:-40412793 MS.gene060011:CDS
GGAAGGGACTAATAATGACT+TGG 0.586286 6.3:-40412993 MS.gene060011:CDS
TGCTAGGCCAAGTTTAGAGA+AGG 0.593210 6.3:-40412723 MS.gene060011:intron
TCTGCTAGAAATTCAACCAA+AGG 0.599482 6.3:-40413014 MS.gene060011:CDS
TAGAAATTCAACCAAAGGAA+GGG 0.616514 6.3:-40413009 MS.gene060011:CDS
CTTGGCATCTCAAACAAAGG+AGG 0.666280 6.3:-40412975 MS.gene060011:CDS
CTGAGTGGAAGCGTAGACTG+TGG 0.666710 6.3:-40412862 MS.gene060011:CDS
AGGACTGTTTAAGCGCTGAG+TGG 0.679075 6.3:-40412877 MS.gene060011:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATTATATGAAAGAACAC+TGG - chr6.3:40412913-40412932 MS.gene060011:CDS 20.0%
!! TGTGTTTATATGATTACATT+AGG - chr6.3:40412665-40412684 MS.gene060011:intron 20.0%
!! TTATAGCACATCTAATAATA+TGG - chr6.3:40412980-40412999 MS.gene060011:CDS 20.0%
! ACTAAAAAACTATGAACACT+TGG - chr6.3:40412799-40412818 MS.gene060011:CDS 25.0%
AGATGTGCTATAATTGTCAT+GGG + chr6.3:40412973-40412992 None:intergenic 30.0%
GATGTAGATAGAACAATAGA+AGG - chr6.3:40412572-40412591 MS.gene060011:intron 30.0%
TAGAAATTCAACCAAAGGAA+GGG - chr6.3:40412489-40412508 MS.gene060011:intron 30.0%
TAGATGTGCTATAATTGTCA+TGG + chr6.3:40412974-40412993 None:intergenic 30.0%
TGTGATCATTGTATGACATT+AGG - chr6.3:40413029-40413048 MS.gene060011:CDS 30.0%
TTCTTGATTTCAAAGATGCT+AGG - chr6.3:40412759-40412778 MS.gene060011:CDS 30.0%
TTCTTGGTTTAAATATGTCG+TGG - chr6.3:40412705-40412724 MS.gene060011:intron 30.0%
TTTAGTACCTTCTCTAAACT+TGG + chr6.3:40412785-40412804 None:intergenic 30.0%
CTAGAAATTCAACCAAAGGA+AGG - chr6.3:40412488-40412507 MS.gene060011:intron 35.0%
GGAATTATCAATCATGGACA+TGG + chr6.3:40412952-40412971 None:intergenic 35.0%
GTCATGGGAATTATCAATCA+TGG + chr6.3:40412958-40412977 None:intergenic 35.0%
TCATTATTAGTCCCTTCCTT+TGG + chr6.3:40412503-40412522 None:intergenic 35.0%
TCTGCTAGAAATTCAACCAA+AGG - chr6.3:40412484-40412503 MS.gene060011:intron 35.0%
! ATGTTGATTGCAATGCTTCT+TGG - chr6.3:40412689-40412708 MS.gene060011:intron 35.0%
!!! AGGACATGTTTTGATCTCTT+CGG - chr6.3:40412592-40412611 MS.gene060011:intron 35.0%
GGAAGGGACTAATAATGACT+TGG - chr6.3:40412505-40412524 MS.gene060011:intron 40.0%
TTTGATCTCTTCGGAAGGAA+AGG - chr6.3:40412601-40412620 MS.gene060011:intron 40.0%
! AATTTCGGCTGCATTAGCTT+TGG - chr6.3:40412733-40412752 MS.gene060011:CDS 40.0%
! ACATCGACAACAGTTTTCGA+CGG + chr6.3:40412557-40412576 None:intergenic 40.0%
! TATGTCGTGGACTGCAATTT+CGG - chr6.3:40412718-40412737 MS.gene060011:intron 40.0%
! TGACTTGGCATCTCAAACAA+AGG - chr6.3:40412520-40412539 MS.gene060011:intron 40.0%
!!! CATGTTTTGATCTCTTCGGA+AGG - chr6.3:40412596-40412615 MS.gene060011:intron 40.0%
CTTGGCATCTCAAACAAAGG+AGG - chr6.3:40412523-40412542 MS.gene060011:intron 45.0%
TGCTAGGCCAAGTTTAGAGA+AGG - chr6.3:40412775-40412794 MS.gene060011:CDS 45.0%
!! AGGACTGTTTAAGCGCTGAG+TGG - chr6.3:40412621-40412640 MS.gene060011:intron 50.0%
! CTGAGTGGAAGCGTAGACTG+TGG - chr6.3:40412636-40412655 MS.gene060011:intron 55.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 40412464 40413056 40412464 ID=MS.gene060011
chr6.3 mRNA 40412464 40413056 40412464 ID=MS.gene060011.t1;Parent=MS.gene060011
chr6.3 exon 40412724 40413056 40412724 ID=MS.gene060011.t1.exon1;Parent=MS.gene060011.t1
chr6.3 CDS 40412724 40413056 40412724 ID=cds.MS.gene060011.t1;Parent=MS.gene060011.t1
chr6.3 exon 40412464 40412469 40412464 ID=MS.gene060011.t1.exon2;Parent=MS.gene060011.t1
chr6.3 CDS 40412464 40412469 40412464 ID=cds.MS.gene060011.t1;Parent=MS.gene060011.t1
Gene Sequence

>MS.gene060011

ATGCTGGTAGCACAATTGATTCTGCTAGAAATTCAACCAAAGGAAGGGACTAATAATGACTTGGCATCTCAAACAAAGGAGGAAACTAGTCCGTCGAAAACTGTTGTCGATGTAGATAGAACAATAGAAGGACATGTTTTGATCTCTTCGGAAGGAAAGGACTGTTTAAGCGCTGAGTGGAAGCGTAGACTGTGGAAATCTTGTGTTTATATGATTACATTAGGAATGTTGATTGCAATGCTTCTTGGTTTAAATATGTCGTGGACTGCAATTTCGGCTGCATTAGCTTTGGTTGTTCTTGATTTCAAAGATGCTAGGCCAAGTTTAGAGAAGGTACTAAAAAACTATGAACACTTGGCTACTATCATTCTTGTGCTAGTTGAAGATTGAACAAATGTCTTGAAAATATACATATATGTAAATGAGTACTGAGTTTTCTGTGTTTTGAAAATATTATATGAAAGAACACTGGTAGCGTTTGCTTACCATGTCCATGATTGATAATTCCCATGACAATTATAGCACATCTAATAATATGGTGAAAGATTTTTCAATAAAATATATTTGTGATCATTGTATGACATTAGGAATAA

Protein sequence

>MS.gene060011.t1

MLVAQLILLEIQPKEGTNNDLASQTKEETSPSKTVVDVDRTIEGHVLISSEGKDCLSAEWKRRLWKSCVYMITLGMLIAMLLGLNMSWTAISAALALVVLDFKDARPSLEKE