AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene021094

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene021094.t1 MTR_4g063510 92.308 182 12 1 1 180 1 182 2.17e-120 338
MS.gene021094.t1 MTR_1g076050 59.140 93 29 4 90 180 1 86 1.32e-24 92.4
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 4.3:-40170568 None:intergenic
CATCATTCATTTGGAGGATT+GGG 0.266107 4.3:-40170786 None:intergenic
CCTCCATTTCATCATTCATT+TGG 0.297234 4.3:-40170795 None:intergenic
GTACTCTTTGAGAGCTGATA+TGG 0.314903 4.3:-40170537 None:intergenic
GAGATAATGAATCTGGAGTT+AGG 0.322546 4.3:+40170910 MS.gene021094:CDS
GGAACTGATGGAAACTTTGC+TGG 0.363889 4.3:+40170598 MS.gene021094:CDS
TCATCATTCATTTGGAGGAT+TGG 0.378564 4.3:-40170787 None:intergenic
GCACACACATTGTTATCAAT+TGG 0.381957 4.3:-40170865 None:intergenic
CAATGATGAGATAATGAATC+TGG 0.397042 4.3:+40170903 MS.gene021094:CDS
CCTCCAAATGAATGATGAAA+TGG 0.410720 4.3:+40170792 MS.gene021094:CDS
CCATTTCATCATTCATTTGG+AGG 0.421395 4.3:-40170792 None:intergenic
TCCTAGACCAATGTTGATGC+AGG 0.426807 4.3:+40170576 MS.gene021094:CDS
AATCTCCTATGCCATCTTTG+AGG 0.463913 4.3:+40170722 MS.gene021094:CDS
TTGACATTATTCCTCAAAGA+TGG 0.471350 4.3:-40170733 None:intergenic
GTTGGAAGTTGGTGAAAACT+TGG 0.482130 4.3:-40170453 None:intergenic
TTTGAAAATTGATTGACTCT+TGG 0.495953 4.3:-40170673 None:intergenic
CCCTGCATCAACATTGGTCT+AGG 0.502644 4.3:-40170577 None:intergenic
AACAAAGCTTGTTGTTGTTG+TGG 0.508962 4.3:-40170640 None:intergenic
AGATAATGAATCTGGAGTTA+GGG 0.518844 4.3:+40170911 MS.gene021094:CDS
ATCATTCATTTGGAGGATTG+GGG 0.520501 4.3:-40170785 None:intergenic
AAGGGAATATATCAATCAGT+TGG 0.520628 4.3:+40170837 MS.gene021094:CDS
TTGGTCTAGGAAAATTTGGT+TGG 0.530130 4.3:-40170564 None:intergenic
GGTTATGCCTTCTCATGGCA+AGG 0.540608 4.3:-40170516 None:intergenic
GAAGCAACAACCTGAAAGCT+AGG 0.549216 4.3:-40170697 None:intergenic
TTGATTGAAGATGGAAACAA+TGG 0.550348 4.3:-40170404 None:intergenic
TGTCTTCAATCGATGGAACA+AGG 0.554290 4.3:+40170818 MS.gene021094:CDS
AAGAAAACCTTGCCATGAGA+AGG 0.557385 4.3:+40170509 MS.gene021094:CDS
ATGTTGATGCAGGGAACTGA+TGG 0.564366 4.3:+40170586 MS.gene021094:CDS
CCTAGACCAATGTTGATGCA+GGG 0.568234 4.3:+40170577 MS.gene021094:CDS
ATGGAGGTGTCTTCAATCGA+TGG 0.576157 4.3:+40170811 MS.gene021094:CDS
TCAGTTCCCTGCATCAACAT+TGG 0.581528 4.3:-40170583 None:intergenic
TTATTCCTCAAAGATGGCAT+AGG 0.612129 4.3:-40170727 None:intergenic
TCATTCATTTGGAGGATTGG+GGG 0.612363 4.3:-40170784 None:intergenic
GTCTTCAATCGATGGAACAA+GGG 0.630717 4.3:+40170819 MS.gene021094:CDS
GATATGGTTATGCCTTCTCA+TGG 0.633947 4.3:-40170521 None:intergenic
CCAAATGAATGATGAAATGG+AGG 0.638819 4.3:+40170795 MS.gene021094:CDS
GATGGAAACAATGGTAGCCA+TGG 0.646684 4.3:-40170395 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAGAGTTGATTGAAGA+TGG - chr4.3:40170416-40170435 None:intergenic 25.0%
!! TTTGAAAATTGATTGACTCT+TGG - chr4.3:40170676-40170695 None:intergenic 25.0%
AAGGGAATATATCAATCAGT+TGG + chr4.3:40170837-40170856 MS.gene021094:CDS 30.0%
CAATGATGAGATAATGAATC+TGG + chr4.3:40170903-40170922 MS.gene021094:CDS 30.0%
TTGACATTATTCCTCAAAGA+TGG - chr4.3:40170736-40170755 None:intergenic 30.0%
TTGATTGAAGATGGAAACAA+TGG - chr4.3:40170407-40170426 None:intergenic 30.0%
! AACATTGGTCTAGGAAAATT+TGG - chr4.3:40170571-40170590 None:intergenic 30.0%
! AGATAATGAATCTGGAGTTA+GGG + chr4.3:40170911-40170930 MS.gene021094:CDS 30.0%
!! ATTTTCAAATCCTAGCTTTC+AGG + chr4.3:40170687-40170706 MS.gene021094:CDS 30.0%
!! CATGATGTGTTTTGAATAGT+TGG - chr4.3:40170474-40170493 None:intergenic 30.0%
!! TGTTTTGAATAGTTGGAAGT+TGG - chr4.3:40170467-40170486 None:intergenic 30.0%
ATCATTCATTTGGAGGATTG+GGG - chr4.3:40170788-40170807 None:intergenic 35.0%
CATCATTCATTTGGAGGATT+GGG - chr4.3:40170789-40170808 None:intergenic 35.0%
CCAAATGAATGATGAAATGG+AGG + chr4.3:40170795-40170814 MS.gene021094:CDS 35.0%
CCATTTCATCATTCATTTGG+AGG - chr4.3:40170795-40170814 None:intergenic 35.0%
CCTCCAAATGAATGATGAAA+TGG + chr4.3:40170792-40170811 MS.gene021094:CDS 35.0%
CCTCCATTTCATCATTCATT+TGG - chr4.3:40170798-40170817 None:intergenic 35.0%
GCACACACATTGTTATCAAT+TGG - chr4.3:40170868-40170887 None:intergenic 35.0%
TCATCATTCATTTGGAGGAT+TGG - chr4.3:40170790-40170809 None:intergenic 35.0%
TTATTCCTCAAAGATGGCAT+AGG - chr4.3:40170730-40170749 None:intergenic 35.0%
TTGGTCTAGGAAAATTTGGT+TGG - chr4.3:40170567-40170586 None:intergenic 35.0%
! GAGATAATGAATCTGGAGTT+AGG + chr4.3:40170910-40170929 MS.gene021094:CDS 35.0%
!! AACAAAGCTTGTTGTTGTTG+TGG - chr4.3:40170643-40170662 None:intergenic 35.0%
AAGAAAACCTTGCCATGAGA+AGG + chr4.3:40170509-40170528 MS.gene021094:CDS 40.0%
AATCTCCTATGCCATCTTTG+AGG + chr4.3:40170722-40170741 MS.gene021094:CDS 40.0%
GATATGGTTATGCCTTCTCA+TGG - chr4.3:40170524-40170543 None:intergenic 40.0%
GTCTTCAATCGATGGAACAA+GGG + chr4.3:40170819-40170838 MS.gene021094:CDS 40.0%
TCATTCATTTGGAGGATTGG+GGG - chr4.3:40170787-40170806 None:intergenic 40.0%
TGTCTTCAATCGATGGAACA+AGG + chr4.3:40170818-40170837 MS.gene021094:CDS 40.0%
! GTACTCTTTGAGAGCTGATA+TGG - chr4.3:40170540-40170559 None:intergenic 40.0%
! TGCTGGAAATAGAGCTTTTC+AGG + chr4.3:40170615-40170634 MS.gene021094:CDS 40.0%
!! GTTGGAAGTTGGTGAAAACT+TGG - chr4.3:40170456-40170475 None:intergenic 40.0%
ATGTTGATGCAGGGAACTGA+TGG + chr4.3:40170586-40170605 MS.gene021094:CDS 45.0%
CCTAGACCAATGTTGATGCA+GGG + chr4.3:40170577-40170596 MS.gene021094:CDS 45.0%
GAAGCAACAACCTGAAAGCT+AGG - chr4.3:40170700-40170719 None:intergenic 45.0%
GGAACTGATGGAAACTTTGC+TGG + chr4.3:40170598-40170617 MS.gene021094:CDS 45.0%
TCAGTTCCCTGCATCAACAT+TGG - chr4.3:40170586-40170605 None:intergenic 45.0%
TCCTAGACCAATGTTGATGC+AGG + chr4.3:40170576-40170595 MS.gene021094:CDS 45.0%
!! ATGGAGGTGTCTTCAATCGA+TGG + chr4.3:40170811-40170830 MS.gene021094:CDS 45.0%
GGTTATGCCTTCTCATGGCA+AGG - chr4.3:40170519-40170538 None:intergenic 50.0%
! CCCTGCATCAACATTGGTCT+AGG - chr4.3:40170580-40170599 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 40170397 40170939 40170397 ID=MS.gene021094
chr4.3 mRNA 40170397 40170939 40170397 ID=MS.gene021094.t1;Parent=MS.gene021094
chr4.3 exon 40170397 40170939 40170397 ID=MS.gene021094.t1.exon1;Parent=MS.gene021094.t1
chr4.3 CDS 40170397 40170939 40170397 ID=cds.MS.gene021094.t1;Parent=MS.gene021094.t1
Gene Sequence

>MS.gene021094

ATGGCTACCATTGTTTCCATCTTCAATCAACTCTTTTTTGCTTGCAAATTTTGCAACCAAGTTTTCACCAACTTCCAACTATTCAAAACACATCATGATTCTCATTTCGTTCAAGAAAACCTTGCCATGAGAAGGCATAACCATATCAGCTCTCAAAGAGTACTTCACCAACCAAATTTTCCTAGACCAATGTTGATGCAGGGAACTGATGGAAACTTTGCTGGAAATAGAGCTTTTCAGGAACCACAACAACAACAAGCTTTGTTGATCTCTCAACCAAGAGTCAATCAATTTTCAAATCCTAGCTTTCAGGTTGTTGCTTCACAATCTCCTATGCCATCTTTGAGGAATAATGTCAATGTTACTAACATGACATCATCTGTAGCTCCCCCAATCCTCCAAATGAATGATGAAATGGAGGTGTCTTCAATCGATGGAACAAGGGAATATATCAATCAGTTGGATAAACCAATTGATAACAATGTGTGTGCTAATTCTGCTAATATCAATGATGAGATAATGAATCTGGAGTTAGGGCTCTAG
Protein sequence

>MS.gene021094.t1

MATIVSIFNQLFFACKFCNQVFTNFQLFKTHHDSHFVQENLAMRRHNHISSQRVLHQPNFPRPMLMQGTDGNFAGNRAFQEPQQQQALLISQPRVNQFSNPSFQVVASQSPMPSLRNNVNVTNMTSSVAPPILQMNDEMEVSSIDGTREYINQLDKPIDNNVCANSANINDEIMNLELGL