AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004060.t1 MTR_4g063510 92.308 182 12 1 1 180 1 182 1.53e-120 338
MS.gene004060.t1 MTR_1g076050 58.065 93 30 4 90 180 1 86 7.07e-24 90.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACATTGGTCTAGGAAAATT+TGG 0.153978 4.2:-41721606 None:intergenic
CATCATTCATTTGGAGGATT+GGG 0.266107 4.2:-41721824 None:intergenic
CCTCCATTTCATCATTCATT+TGG 0.297234 4.2:-41721833 None:intergenic
GTACTCTTTGAGAGCTGATA+TGG 0.314903 4.2:-41721575 None:intergenic
GAGATAATGAATCTGGAGTT+AGG 0.322546 4.2:+41721948 MS.gene004060:CDS
GGAACTGATGGAAACTTTGC+TGG 0.363889 4.2:+41721636 MS.gene004060:CDS
TCATCATTCATTTGGAGGAT+TGG 0.378564 4.2:-41721825 None:intergenic
GCACACACATTGTTATCAAT+TGG 0.381957 4.2:-41721903 None:intergenic
CAATGATGAGATAATGAATC+TGG 0.397042 4.2:+41721941 MS.gene004060:CDS
CCTCCAAATGAATGATGAAA+TGG 0.410720 4.2:+41721830 MS.gene004060:CDS
CCATTTCATCATTCATTTGG+AGG 0.421395 4.2:-41721830 None:intergenic
TCCTAGACCAATGTTGATGC+AGG 0.426807 4.2:+41721614 MS.gene004060:CDS
AATCTCCTATGCCATCTTTG+AGG 0.463913 4.2:+41721760 MS.gene004060:CDS
TTGACATTATTCCTCAAAGA+TGG 0.471350 4.2:-41721771 None:intergenic
GTTGGAAGTTGGTGAAAACT+TGG 0.482130 4.2:-41721491 None:intergenic
TTTGAAAATTGATTGACTCT+TGG 0.495953 4.2:-41721711 None:intergenic
CCCTGCATCAACATTGGTCT+AGG 0.502644 4.2:-41721615 None:intergenic
AACAAAGCTTGTTGTTGTTG+TGG 0.508962 4.2:-41721678 None:intergenic
AGATAATGAATCTGGAGTTA+GGG 0.518844 4.2:+41721949 MS.gene004060:CDS
ATCATTCATTTGGAGGATTG+GGG 0.520501 4.2:-41721823 None:intergenic
AAGGGAATATATCAATCAGT+TGG 0.520628 4.2:+41721875 MS.gene004060:CDS
TTGGTCTAGGAAAATTTGGT+TGG 0.530130 4.2:-41721602 None:intergenic
GGTTATGCCTTCTCATGGCA+AGG 0.540608 4.2:-41721554 None:intergenic
GAAGCAACAACCTGAAAGCT+AGG 0.549216 4.2:-41721735 None:intergenic
TTGATTGAAGATGGAAACAA+TGG 0.550348 4.2:-41721442 None:intergenic
TGTCTTCAATCGATGGAACA+AGG 0.554290 4.2:+41721856 MS.gene004060:CDS
AAGAAAACCTTGCCATGAGA+AGG 0.557385 4.2:+41721547 MS.gene004060:CDS
ATGTTGATGCAGGGAACTGA+TGG 0.564366 4.2:+41721624 MS.gene004060:CDS
CCTAGACCAATGTTGATGCA+GGG 0.568234 4.2:+41721615 MS.gene004060:CDS
ATGGAGGTGTCTTCAATCGA+TGG 0.576157 4.2:+41721849 MS.gene004060:CDS
TCAGTTCCCTGCATCAACAT+TGG 0.581528 4.2:-41721621 None:intergenic
TTATTCCTCAAAGATGGCAT+AGG 0.612129 4.2:-41721765 None:intergenic
TCATTCATTTGGAGGATTGG+GGG 0.612363 4.2:-41721822 None:intergenic
GTCTTCAATCGATGGAACAA+GGG 0.630717 4.2:+41721857 MS.gene004060:CDS
GATATGGTTATGCCTTCTCA+TGG 0.633947 4.2:-41721559 None:intergenic
CCAAATGAATGATGAAATGG+AGG 0.638819 4.2:+41721833 MS.gene004060:CDS
GATGGAAACAATGGTAGCCA+TGG 0.646684 4.2:-41721433 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAGAGTTGATTGAAGA+TGG - chr4.2:41721454-41721473 None:intergenic 25.0%
!! TTTGAAAATTGATTGACTCT+TGG - chr4.2:41721714-41721733 None:intergenic 25.0%
AAGGGAATATATCAATCAGT+TGG + chr4.2:41721875-41721894 MS.gene004060:CDS 30.0%
CAATGATGAGATAATGAATC+TGG + chr4.2:41721941-41721960 MS.gene004060:CDS 30.0%
TTGACATTATTCCTCAAAGA+TGG - chr4.2:41721774-41721793 None:intergenic 30.0%
TTGATTGAAGATGGAAACAA+TGG - chr4.2:41721445-41721464 None:intergenic 30.0%
! AACATTGGTCTAGGAAAATT+TGG - chr4.2:41721609-41721628 None:intergenic 30.0%
! AGATAATGAATCTGGAGTTA+GGG + chr4.2:41721949-41721968 MS.gene004060:CDS 30.0%
!! ATTTTCAAATCCTAGCTTTC+AGG + chr4.2:41721725-41721744 MS.gene004060:CDS 30.0%
!! CATGATGTGTTTTGAATAGT+TGG - chr4.2:41721512-41721531 None:intergenic 30.0%
!! TGTTTTGAATAGTTGGAAGT+TGG - chr4.2:41721505-41721524 None:intergenic 30.0%
ATCATTCATTTGGAGGATTG+GGG - chr4.2:41721826-41721845 None:intergenic 35.0%
CATCATTCATTTGGAGGATT+GGG - chr4.2:41721827-41721846 None:intergenic 35.0%
CCAAATGAATGATGAAATGG+AGG + chr4.2:41721833-41721852 MS.gene004060:CDS 35.0%
CCATTTCATCATTCATTTGG+AGG - chr4.2:41721833-41721852 None:intergenic 35.0%
CCTCCAAATGAATGATGAAA+TGG + chr4.2:41721830-41721849 MS.gene004060:CDS 35.0%
CCTCCATTTCATCATTCATT+TGG - chr4.2:41721836-41721855 None:intergenic 35.0%
GCACACACATTGTTATCAAT+TGG - chr4.2:41721906-41721925 None:intergenic 35.0%
TCATCATTCATTTGGAGGAT+TGG - chr4.2:41721828-41721847 None:intergenic 35.0%
TTATTCCTCAAAGATGGCAT+AGG - chr4.2:41721768-41721787 None:intergenic 35.0%
TTGGTCTAGGAAAATTTGGT+TGG - chr4.2:41721605-41721624 None:intergenic 35.0%
! GAGATAATGAATCTGGAGTT+AGG + chr4.2:41721948-41721967 MS.gene004060:CDS 35.0%
!! AACAAAGCTTGTTGTTGTTG+TGG - chr4.2:41721681-41721700 None:intergenic 35.0%
AAGAAAACCTTGCCATGAGA+AGG + chr4.2:41721547-41721566 MS.gene004060:CDS 40.0%
AATCTCCTATGCCATCTTTG+AGG + chr4.2:41721760-41721779 MS.gene004060:CDS 40.0%
GATATGGTTATGCCTTCTCA+TGG - chr4.2:41721562-41721581 None:intergenic 40.0%
GTCTTCAATCGATGGAACAA+GGG + chr4.2:41721857-41721876 MS.gene004060:CDS 40.0%
TCATTCATTTGGAGGATTGG+GGG - chr4.2:41721825-41721844 None:intergenic 40.0%
TGTCTTCAATCGATGGAACA+AGG + chr4.2:41721856-41721875 MS.gene004060:CDS 40.0%
! GTACTCTTTGAGAGCTGATA+TGG - chr4.2:41721578-41721597 None:intergenic 40.0%
! TGCTGGAAATAGAGCTTTTC+AGG + chr4.2:41721653-41721672 MS.gene004060:CDS 40.0%
!! GTTGGAAGTTGGTGAAAACT+TGG - chr4.2:41721494-41721513 None:intergenic 40.0%
ATGTTGATGCAGGGAACTGA+TGG + chr4.2:41721624-41721643 MS.gene004060:CDS 45.0%
CCTAGACCAATGTTGATGCA+GGG + chr4.2:41721615-41721634 MS.gene004060:CDS 45.0%
GAAGCAACAACCTGAAAGCT+AGG - chr4.2:41721738-41721757 None:intergenic 45.0%
GGAACTGATGGAAACTTTGC+TGG + chr4.2:41721636-41721655 MS.gene004060:CDS 45.0%
TCAGTTCCCTGCATCAACAT+TGG - chr4.2:41721624-41721643 None:intergenic 45.0%
TCCTAGACCAATGTTGATGC+AGG + chr4.2:41721614-41721633 MS.gene004060:CDS 45.0%
!! ATGGAGGTGTCTTCAATCGA+TGG + chr4.2:41721849-41721868 MS.gene004060:CDS 45.0%
GGTTATGCCTTCTCATGGCA+AGG - chr4.2:41721557-41721576 None:intergenic 50.0%
! CCCTGCATCAACATTGGTCT+AGG - chr4.2:41721618-41721637 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 41721435 41721977 41721435 ID=MS.gene004060
chr4.2 mRNA 41721435 41721977 41721435 ID=MS.gene004060.t1;Parent=MS.gene004060
chr4.2 exon 41721435 41721977 41721435 ID=MS.gene004060.t1.exon1;Parent=MS.gene004060.t1
chr4.2 CDS 41721435 41721977 41721435 ID=cds.MS.gene004060.t1;Parent=MS.gene004060.t1
Gene Sequence

>MS.gene004060

ATGGCTACCATTGTTTCCATCTTCAATCAACTCTTTTTTGCTTGCAAATTTTGCAACCAAGTTTTCACCAACTTCCAACTATTCAAAACACATCATGATTCTCATTTCGTTCAAGAAAACCTTGCCATGAGAAGGCATAACCATATCAGCTCTCAAAGAGTACTTCACCAACCAAATTTTCCTAGACCAATGTTGATGCAGGGAACTGATGGAAACTTTGCTGGAAATAGAGCTTTTCAGGAACCACAACAACAACAAGCTTTGTTGATCTCTCAACCAAGAGTCAATCAATTTTCAAATCCTAGCTTTCAGGTTGTTGCTTCACAATCTCCTATGCCATCTTTGAGGAATAATGTCAATGTTACTAACATGACATCATCTGTAGCTCCCCCAATCCTCCAAATGAATGATGAAATGGAGGTGTCTTCAATCGATGGAACAAGGGAATATATCAATCAGTTGGATAAACCAATTGATAACAATGTGTGTGCTGATTCTGCTAATATCAATGATGAGATAATGAATCTGGAGTTAGGGCTCTAG
Protein sequence

>MS.gene004060.t1

MATIVSIFNQLFFACKFCNQVFTNFQLFKTHHDSHFVQENLAMRRHNHISSQRVLHQPNFPRPMLMQGTDGNFAGNRAFQEPQQQQALLISQPRVNQFSNPSFQVVASQSPMPSLRNNVNVTNMTSSVAPPILQMNDEMEVSSIDGTREYINQLDKPIDNNVCADSANINDEIMNLELGL