AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene066583

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066583.t1 MTR_4g024550 100.000 108 0 0 4 111 33 140 4.02e-75 219
MS.gene066583.t1 MTR_5g011910 98.148 108 2 0 4 111 33 140 6.53e-74 216
MS.gene066583.t1 MTR_4g102170 96.296 108 4 0 4 111 33 140 2.13e-72 212
MS.gene066583.t1 MTR_4g024265 100.000 81 0 0 4 84 33 113 2.98e-53 171
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene066583.t1 AT4G00100 95.370 108 5 0 4 111 33 140 4.71e-72 211
MS.gene066583.t1 AT3G60770 95.370 108 5 0 4 111 33 140 5.68e-72 211

Find 31 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCCAAATTCAGGCTAATTT+TGG 0.149134 4.2:-78753791 MS.gene066583:CDS
GACCAAAATTAGCCTGAATT+TGG 0.223891 4.2:+78753789 None:intergenic
TATGCGCAAAATCTTGTTTC+CGG 0.257809 4.2:+78754030 None:intergenic
AGATGGAGTTAGACCTTTCT+TGG 0.271027 4.2:+78754108 None:intergenic
TACAGATCTTCAGGAATTTC+AGG 0.309178 4.2:+78753877 None:intergenic
ATCAGGTGATACAGATCTTC+AGG 0.338551 4.2:+78753868 None:intergenic
CAAAGAAGCTTCCACCAGTA+TGG 0.349985 4.2:-78753726 MS.gene066583:CDS
GGTCTAACTCCATCTCAAAT+TGG 0.359176 4.2:-78754100 MS.gene066583:CDS
GGAAGCATTTGGAGAGGAAC+AGG 0.374872 4.2:-78753825 MS.gene066583:CDS
TCAAGAAGGCTGTCTCAATT+AGG 0.379771 4.2:-78753846 MS.gene066583:CDS
AATACTTACTATTTCCATAC+TGG 0.381602 4.2:+78753712 None:intergenic
TTGAGACAGCCTTCTTGATC+AGG 0.385210 4.2:+78753851 None:intergenic
CCATGGAATTGCTCAGGTTA+AGG 0.405652 4.2:-78754059 MS.gene066583:CDS
TGTCTCAATTAGGAAGCATT+TGG 0.438327 4.2:-78753836 MS.gene066583:CDS
AGGACAAGGACTCCAAATTC+AGG 0.445955 4.2:-78753801 MS.gene066583:CDS
ATCTGCAAGTTTGCCAAGAA+AGG 0.457907 4.2:-78754121 MS.gene066583:CDS
GCTCAGGTTAAGGCTGTAAC+CGG 0.462422 4.2:-78754049 MS.gene066583:CDS
TGACTCCCATGGAATTGCTC+AGG 0.496575 4.2:-78754065 MS.gene066583:CDS
GTTATTCTTCGTGACTCCCA+TGG 0.508409 4.2:-78754076 MS.gene066583:CDS
CCTTAACCTGAGCAATTCCA+TGG 0.520963 4.2:+78754059 None:intergenic
TTTCTTGGCAAACTTGCAGA+TGG 0.531932 4.2:+78754123 None:intergenic
ACTTACTATTTCCATACTGG+TGG 0.562660 4.2:+78753715 None:intergenic
TATAGTAACGAGCAAGGCGA+TGG 0.565886 4.2:+78753755 None:intergenic
AGAATAACACCAATTTGAGA+TGG 0.576179 4.2:+78754091 None:intergenic
TCTTCTTATAGTAACGAGCA+AGG 0.583518 4.2:+78753749 None:intergenic
TCTGTATCACCTGATCAAGA+AGG 0.601322 4.2:-78753860 MS.gene066583:CDS
TTGCGCATATTGAAGGCGCA+TGG 0.612509 4.2:-78754016 MS.gene066583:intron
CAATTAGGAAGCATTTGGAG+AGG 0.640013 4.2:-78753831 MS.gene066583:CDS
CTTAACCTGAGCAATTCCAT+GGG 0.650971 4.2:+78754060 None:intergenic
GGAGAGGAACAGGAAGGACA+AGG 0.660004 4.2:-78753815 MS.gene066583:CDS
GCATTTGGAGAGGAACAGGA+AGG 0.678718 4.2:-78753821 MS.gene066583:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTTTTTTCATTAAAAA+AGG - chr4.2:78753746-78753765 MS.gene066583:CDS 10.0%
!! TATCATTAATATCTTCTTAT+AGG + chr4.2:78753827-78753846 None:intergenic 15.0%
!! TAATAGTATAACACTTAACA+TGG - chr4.2:78753724-78753743 MS.gene066583:CDS 20.0%
!!! TTTTGTCAATTTTCGTTTTT+TGG + chr4.2:78754020-78754039 None:intergenic 20.0%
!!! CTTTAATTTCTCTTTTCCTA+GGG - chr4.2:78754403-78754422 MS.gene066583:intron 25.0%
!!! TCTTTAATTTCTCTTTTCCT+AGG - chr4.2:78754402-78754421 MS.gene066583:intron 25.0%
AGAATAACACCAATTTGAGA+TGG + chr4.2:78754221-78754240 None:intergenic 30.0%
CATTAAAAAAGGTCTGCAAT+TGG - chr4.2:78753757-78753776 MS.gene066583:CDS 30.0%
GTGTTTACAGATCATAAAAG+TGG + chr4.2:78754074-78754093 None:intergenic 30.0%
! CCTAGTTAATCTTTTAGATC+CGG + chr4.2:78753865-78753884 None:intergenic 30.0%
! CTTTTATGATCTGTAAACAC+TGG - chr4.2:78754074-78754093 MS.gene066583:CDS 30.0%
ATCATCGCATCAAACATGAT+TGG + chr4.2:78753907-78753926 None:intergenic 35.0%
CCGGATCTAAAAGATTAACT+AGG - chr4.2:78753862-78753881 MS.gene066583:CDS 35.0%
CTGAATTATTGTTGTGATGC+AGG + chr4.2:78753949-78753968 None:intergenic 35.0%
GATAATAGTCGATGAACAAC+CGG - chr4.2:78753843-78753862 MS.gene066583:CDS 35.0%
TACAGATCTTCAGGAATTTC+AGG + chr4.2:78754435-78754454 None:intergenic 35.0%
TCTTCTTATAGTAACGAGCA+AGG + chr4.2:78754563-78754582 None:intergenic 35.0%
! CAAGATTTTGCGCATATTGA+AGG - chr4.2:78754286-78754305 MS.gene066583:intron 35.0%
! CTCCAAATTCAGGCTAATTT+TGG - chr4.2:78754518-78754537 MS.gene066583:intron 35.0%
! GACCAAAATTAGCCTGAATT+TGG + chr4.2:78754523-78754542 None:intergenic 35.0%
! TATGCGCAAAATCTTGTTTC+CGG + chr4.2:78754282-78754301 None:intergenic 35.0%
!! TGTCTCAATTAGGAAGCATT+TGG - chr4.2:78754473-78754492 MS.gene066583:intron 35.0%
AGATGGAGTTAGACCTTTCT+TGG + chr4.2:78754204-78754223 None:intergenic 40.0%
ATCAGGTGATACAGATCTTC+AGG + chr4.2:78754444-78754463 None:intergenic 40.0%
ATCTGCAAGTTTGCCAAGAA+AGG - chr4.2:78754188-78754207 MS.gene066583:intron 40.0%
CTGATGTTCATGAATTGCAC+AGG - chr4.2:78754154-78754173 MS.gene066583:intron 40.0%
CTTAACCTGAGCAATTCCAT+GGG + chr4.2:78754252-78754271 None:intergenic 40.0%
GGTCTAACTCCATCTCAAAT+TGG - chr4.2:78754209-78754228 MS.gene066583:intron 40.0%
TCAAGAAGGCTGTCTCAATT+AGG - chr4.2:78754463-78754482 MS.gene066583:intron 40.0%
TCTGTATCACCTGATCAAGA+AGG - chr4.2:78754449-78754468 MS.gene066583:intron 40.0%
TTTCTTGGCAAACTTGCAGA+TGG + chr4.2:78754189-78754208 None:intergenic 40.0%
!! CAATTAGGAAGCATTTGGAG+AGG - chr4.2:78754478-78754497 MS.gene066583:intron 40.0%
AGGACAAGGACTCCAAATTC+AGG - chr4.2:78754508-78754527 MS.gene066583:intron 45.0%
CAAAGAAGCTTCCACCAGTA+TGG - chr4.2:78754583-78754602 MS.gene066583:intron 45.0%
CCATGGAATTGCTCAGGTTA+AGG - chr4.2:78754250-78754269 MS.gene066583:intron 45.0%
CCTTAACCTGAGCAATTCCA+TGG + chr4.2:78754253-78754272 None:intergenic 45.0%
GTTATTCTTCGTGACTCCCA+TGG - chr4.2:78754233-78754252 MS.gene066583:intron 45.0%
TATAGTAACGAGCAAGGCGA+TGG + chr4.2:78754557-78754576 None:intergenic 45.0%
TTGAGACAGCCTTCTTGATC+AGG + chr4.2:78754461-78754480 None:intergenic 45.0%
! GTGATGCAGGACAACGTTTT+CGG + chr4.2:78753936-78753955 None:intergenic 45.0%
GAATTTCAGGAGCAAGCCCT+AGG + chr4.2:78754422-78754441 None:intergenic 50.0%
GCATTTGGAGAGGAACAGGA+AGG - chr4.2:78754488-78754507 MS.gene066583:intron 50.0%
GCTCAGGTTAAGGCTGTAAC+CGG - chr4.2:78754260-78754279 MS.gene066583:intron 50.0%
TGACTCCCATGGAATTGCTC+AGG - chr4.2:78754244-78754263 MS.gene066583:intron 50.0%
! TTGCGCATATTGAAGGCGCA+TGG - chr4.2:78754293-78754312 MS.gene066583:intron 50.0%
!! GGAAGCATTTGGAGAGGAAC+AGG - chr4.2:78754484-78754503 MS.gene066583:intron 50.0%
!! GGCTAATTTTGGTCGAGAGC+AGG - chr4.2:78754529-78754548 MS.gene066583:intron 50.0%
GGAGAGGAACAGGAAGGACA+AGG - chr4.2:78754494-78754513 MS.gene066583:intron 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 78753720 78754611 78753720 ID=MS.gene066583
chr4.2 mRNA 78753720 78754611 78753720 ID=MS.gene066583.t1;Parent=MS.gene066583
chr4.2 exon 78754603 78754611 78754603 ID=MS.gene066583.t1.exon1;Parent=MS.gene066583.t1
chr4.2 CDS 78754603 78754611 78754603 ID=cds.MS.gene066583.t1;Parent=MS.gene066583.t1
chr4.2 exon 78754017 78754155 78754017 ID=MS.gene066583.t1.exon2;Parent=MS.gene066583.t1
chr4.2 CDS 78754017 78754155 78754017 ID=cds.MS.gene066583.t1;Parent=MS.gene066583.t1
chr4.2 exon 78753720 78753907 78753720 ID=MS.gene066583.t1.exon3;Parent=MS.gene066583.t1
chr4.2 CDS 78753720 78753907 78753720 ID=cds.MS.gene066583.t1;Parent=MS.gene066583.t1
Gene Sequence

>MS.gene066583

ATGCTAATAGTATAACACTTAACATGGTTTTTTTTTTCATTAAAAAAGGTCTGCAATTGGTTCACTTGTACTGCATGATTAATATCATATTTTGATCAAACTCTCCTATAAGAAGATATTAATGATAATAGTCGATGAACAACCGGATCTAAAAGATTAACTAGGTTTTTGTTGTTCATCACAACCAATCATGTTTGATGCGATGATTAAAGACCGAAAACGTTGTCCTGCATCACAACAATAATTCAGTATCACAACAAAAATGATGCAATAAAGTTTCTACAACAAAATTTAACACCAAAAAACGAAAATTGACAAAAAAATCAAATTTAAAAACATTGTTCAAACAAGCCACTTTTATGATCTGTAAACACTGGTTTTGATTGTATATTATTAATTTTCAATTTCTTTTAGATTATCATGATTTTTATGTTCTGATGTTCATGAATTGCACAGGTTGACGAGACCATCTGCAAGTTTGCCAAGAAAGGTCTAACTCCATCTCAAATTGGTGTTATTCTTCGTGACTCCCATGGAATTGCTCAGGTTAAGGCTGTAACCGGAAACAAGATTTTGCGCATATTGAAGGCGCATGGTATGCTTGACTTGTTTGTTTTGTTTCTCTGTTTGTTTGTTTTAACTTGACTTGTGTATAGTGTTTTGAATTTGATGACTTAACTATTCTTTAATTTCTCTTTTCCTAGGGCTTGCTCCTGAAATTCCTGAAGATCTGTATCACCTGATCAAGAAGGCTGTCTCAATTAGGAAGCATTTGGAGAGGAACAGGAAGGACAAGGACTCCAAATTCAGGCTAATTTTGGTCGAGAGCAGGATCCATCGCCTTGCTCGTTACTATAAGAAGACAAAGAAGCTTCCACCAGTATGGAAATAG
Protein sequence

>MS.gene066583.t1

MLIVDETICKFAKKGLTPSQIGVILRDSHGIAQVKAVTGNKILRILKAHGLAPEIPEDLYHLIKKAVSIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTKKLPPVWK