AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene61098

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene61098.t1 MTR_4g063510 92.308 182 12 1 1 180 1 182 2.17e-120 338
MS.gene61098.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 4.4:-42457488 None:intergenic
CATCATTCATTTGGAGGATT+GGG 0.266107 4.4:-42457706 None:intergenic
CCTCCATTTCATCATTCATT+TGG 0.297234 4.4:-42457715 None:intergenic
GTACTCTTTGAGAGCTGATA+TGG 0.314903 4.4:-42457457 None:intergenic
GAGATAATGAATCTGGAGTT+AGG 0.322546 4.4:+42457830 MS.gene61098:CDS
GGAACTGATGGAAACTTTGC+TGG 0.363889 4.4:+42457518 MS.gene61098:CDS
TCATCATTCATTTGGAGGAT+TGG 0.378564 4.4:-42457707 None:intergenic
GCACACACATTGTTATCAAT+TGG 0.381957 4.4:-42457785 None:intergenic
CAATGATGAGATAATGAATC+TGG 0.397042 4.4:+42457823 MS.gene61098:CDS
CCTCCAAATGAATGATGAAA+TGG 0.410720 4.4:+42457712 MS.gene61098:CDS
CCATTTCATCATTCATTTGG+AGG 0.421395 4.4:-42457712 None:intergenic
TCCTAGACCAATGTTGATGC+AGG 0.426807 4.4:+42457496 MS.gene61098:CDS
AATCTCCTATGCCATCTTTG+AGG 0.463913 4.4:+42457642 MS.gene61098:CDS
TTGACATTATTCCTCAAAGA+TGG 0.471350 4.4:-42457653 None:intergenic
GTTGGAAGTTGGTGAAAACT+TGG 0.482130 4.4:-42457373 None:intergenic
TTTGAAAATTGATTGACTCT+TGG 0.495953 4.4:-42457593 None:intergenic
CCCTGCATCAACATTGGTCT+AGG 0.502644 4.4:-42457497 None:intergenic
AACAAAGCTTGTTGTTGTTG+TGG 0.508962 4.4:-42457560 None:intergenic
AGATAATGAATCTGGAGTTA+GGG 0.518844 4.4:+42457831 MS.gene61098:CDS
ATCATTCATTTGGAGGATTG+GGG 0.520501 4.4:-42457705 None:intergenic
TTGGTCTAGGAAAATTTGGT+TGG 0.530130 4.4:-42457484 None:intergenic
GGTTATGCCTTCTCATGGCA+AGG 0.540608 4.4:-42457436 None:intergenic
GAGGGAATATATCAATCAGT+TGG 0.547285 4.4:+42457757 MS.gene61098:CDS
GAAGCAACAACCTGAAAGCT+AGG 0.549216 4.4:-42457617 None:intergenic
TTGATTGAAGATGGAAACAA+TGG 0.550348 4.4:-42457324 None:intergenic
AAGAAAACCTTGCCATGAGA+AGG 0.557385 4.4:+42457429 MS.gene61098:CDS
ATGTTGATGCAGGGAACTGA+TGG 0.564366 4.4:+42457506 MS.gene61098:CDS
CCTAGACCAATGTTGATGCA+GGG 0.568234 4.4:+42457497 MS.gene61098:CDS
ATGGAGGTGTCTTCAATCGA+TGG 0.576157 4.4:+42457731 MS.gene61098:CDS
TCAGTTCCCTGCATCAACAT+TGG 0.581528 4.4:-42457503 None:intergenic
TTATTCCTCAAAGATGGCAT+AGG 0.612129 4.4:-42457647 None:intergenic
TCATTCATTTGGAGGATTGG+GGG 0.612363 4.4:-42457704 None:intergenic
TGTCTTCAATCGATGGAACG+AGG 0.630329 4.4:+42457738 MS.gene61098:CDS
GTCTTCAATCGATGGAACGA+GGG 0.633013 4.4:+42457739 MS.gene61098:CDS
GATATGGTTATGCCTTCTCA+TGG 0.633947 4.4:-42457441 None:intergenic
CCAAATGAATGATGAAATGG+AGG 0.638819 4.4:+42457715 MS.gene61098:CDS
GATGGAAACAATGGTAGCCA+TGG 0.646684 4.4:-42457315 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAGAGTTGATTGAAGA+TGG - chr4.4:42457336-42457355 None:intergenic 25.0%
!! TTTGAAAATTGATTGACTCT+TGG - chr4.4:42457596-42457615 None:intergenic 25.0%
CAATGATGAGATAATGAATC+TGG + chr4.4:42457823-42457842 MS.gene61098:CDS 30.0%
TTGACATTATTCCTCAAAGA+TGG - chr4.4:42457656-42457675 None:intergenic 30.0%
TTGATTGAAGATGGAAACAA+TGG - chr4.4:42457327-42457346 None:intergenic 30.0%
! AACATTGGTCTAGGAAAATT+TGG - chr4.4:42457491-42457510 None:intergenic 30.0%
! AGATAATGAATCTGGAGTTA+GGG + chr4.4:42457831-42457850 MS.gene61098:CDS 30.0%
!! ATTTTCAAATCCTAGCTTTC+AGG + chr4.4:42457607-42457626 MS.gene61098:CDS 30.0%
!! CATGATGTGTTTTGAATAGT+TGG - chr4.4:42457394-42457413 None:intergenic 30.0%
!! TGTTTTGAATAGTTGGAAGT+TGG - chr4.4:42457387-42457406 None:intergenic 30.0%
ATCATTCATTTGGAGGATTG+GGG - chr4.4:42457708-42457727 None:intergenic 35.0%
CATCATTCATTTGGAGGATT+GGG - chr4.4:42457709-42457728 None:intergenic 35.0%
CCAAATGAATGATGAAATGG+AGG + chr4.4:42457715-42457734 MS.gene61098:CDS 35.0%
CCATTTCATCATTCATTTGG+AGG - chr4.4:42457715-42457734 None:intergenic 35.0%
CCTCCAAATGAATGATGAAA+TGG + chr4.4:42457712-42457731 MS.gene61098:CDS 35.0%
CCTCCATTTCATCATTCATT+TGG - chr4.4:42457718-42457737 None:intergenic 35.0%
GAGGGAATATATCAATCAGT+TGG + chr4.4:42457757-42457776 MS.gene61098:CDS 35.0%
GCACACACATTGTTATCAAT+TGG - chr4.4:42457788-42457807 None:intergenic 35.0%
TCATCATTCATTTGGAGGAT+TGG - chr4.4:42457710-42457729 None:intergenic 35.0%
TTATTCCTCAAAGATGGCAT+AGG - chr4.4:42457650-42457669 None:intergenic 35.0%
TTGGTCTAGGAAAATTTGGT+TGG - chr4.4:42457487-42457506 None:intergenic 35.0%
! GAGATAATGAATCTGGAGTT+AGG + chr4.4:42457830-42457849 MS.gene61098:CDS 35.0%
!! AACAAAGCTTGTTGTTGTTG+TGG - chr4.4:42457563-42457582 None:intergenic 35.0%
AAGAAAACCTTGCCATGAGA+AGG + chr4.4:42457429-42457448 MS.gene61098:CDS 40.0%
AATCTCCTATGCCATCTTTG+AGG + chr4.4:42457642-42457661 MS.gene61098:CDS 40.0%
GATATGGTTATGCCTTCTCA+TGG - chr4.4:42457444-42457463 None:intergenic 40.0%
TCATTCATTTGGAGGATTGG+GGG - chr4.4:42457707-42457726 None:intergenic 40.0%
! GTACTCTTTGAGAGCTGATA+TGG - chr4.4:42457460-42457479 None:intergenic 40.0%
! TGCTGGAAATAGAGCTTTTC+AGG + chr4.4:42457535-42457554 MS.gene61098:CDS 40.0%
!! GTTGGAAGTTGGTGAAAACT+TGG - chr4.4:42457376-42457395 None:intergenic 40.0%
ATGTTGATGCAGGGAACTGA+TGG + chr4.4:42457506-42457525 MS.gene61098:CDS 45.0%
CCTAGACCAATGTTGATGCA+GGG + chr4.4:42457497-42457516 MS.gene61098:CDS 45.0%
GAAGCAACAACCTGAAAGCT+AGG - chr4.4:42457620-42457639 None:intergenic 45.0%
GGAACTGATGGAAACTTTGC+TGG + chr4.4:42457518-42457537 MS.gene61098:CDS 45.0%
GTCTTCAATCGATGGAACGA+GGG + chr4.4:42457739-42457758 MS.gene61098:CDS 45.0%
TCAGTTCCCTGCATCAACAT+TGG - chr4.4:42457506-42457525 None:intergenic 45.0%
TCCTAGACCAATGTTGATGC+AGG + chr4.4:42457496-42457515 MS.gene61098:CDS 45.0%
TGTCTTCAATCGATGGAACG+AGG + chr4.4:42457738-42457757 MS.gene61098:CDS 45.0%
!! ATGGAGGTGTCTTCAATCGA+TGG + chr4.4:42457731-42457750 MS.gene61098:CDS 45.0%
GGTTATGCCTTCTCATGGCA+AGG - chr4.4:42457439-42457458 None:intergenic 50.0%
! CCCTGCATCAACATTGGTCT+AGG - chr4.4:42457500-42457519 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 42457317 42457859 42457317 ID=MS.gene61098
chr4.4 mRNA 42457317 42457859 42457317 ID=MS.gene61098.t1;Parent=MS.gene61098
chr4.4 exon 42457317 42457859 42457317 ID=MS.gene61098.t1.exon1;Parent=MS.gene61098.t1
chr4.4 CDS 42457317 42457859 42457317 ID=cds.MS.gene61098.t1;Parent=MS.gene61098.t1
Gene Sequence

>MS.gene61098

ATGGCTACCATTGTTTCCATCTTCAATCAACTCTTTTTTGCTTGCAAATTTTGCAACCAAGTTTTCACCAACTTCCAACTATTCAAAACACATCATGATTCTCATTTCGTTCAAGAAAACCTTGCCATGAGAAGGCATAACCATATCAGCTCTCAAAGAGTACTTCACCAACCAAATTTTCCTAGACCAATGTTGATGCAGGGAACTGATGGAAACTTTGCTGGAAATAGAGCTTTTCAGGAACCACAACAACAACAAGCTTTGTTGATCTCTCAACCAAGAGTCAATCAATTTTCAAATCCTAGCTTTCAGGTTGTTGCTTCACAATCTCCTATGCCATCTTTGAGGAATAATGTCAATGTTACTAACATGACATCATCTGTAGCTCCCCCAATCCTCCAAATGAATGATGAAATGGAGGTGTCTTCAATCGATGGAACGAGGGAATATATCAATCAGTTGGATAAACCAATTGATAACAATGTGTGTGCTAATTCTGCTAATATCAATGATGAGATAATGAATCTGGAGTTAGGGCTCTAG
Protein sequence

>MS.gene61098.t1

MATIVSIFNQLFFACKFCNQVFTNFQLFKTHHDSHFVQENLAMRRHNHISSQRVLHQPNFPRPMLMQGTDGNFAGNRAFQEPQQQQALLISQPRVNQFSNPSFQVVASQSPMPSLRNNVNVTNMTSSVAPPILQMNDEMEVSSIDGTREYINQLDKPIDNNVCANSANINDEIMNLELGL