AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene00836

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00836.t1 MTR_2g023100 97.403 77 2 0 1 77 1 77 5.65e-53 159
MS.gene00836.t1 MTR_4g046737 49.333 75 35 2 1 74 1 73 4.52e-20 76.3
MS.gene00836.t1 MTR_2g088730 59.184 49 20 0 27 75 32 80 1.14e-17 70.5
MS.gene00836.t1 MTR_5g009460 42.647 68 36 1 7 74 20 84 8.98e-15 63.2
MS.gene00836.t1 MTR_3g083540 51.111 45 22 0 28 72 98 142 2.27e-12 60.5
MS.gene00836.t1 MTR_4g100720 37.662 77 38 1 5 71 37 113 7.16e-12 57.8
MS.gene00836.t1 MTR_7g117730 51.163 43 21 0 30 72 71 113 1.51e-11 57.8
MS.gene00836.t1 MTR_0197s0010 47.727 44 23 0 29 72 59 102 1.52e-11 57.8
MS.gene00836.t1 MTR_8g060940 47.727 44 23 0 29 72 65 108 2.54e-11 57.0
MS.gene00836.t1 MTR_0247s0040 45.455 44 24 0 28 71 64 107 2.67e-11 56.2
MS.gene00836.t1 MTR_5g079670 48.837 43 22 0 29 71 69 111 3.78e-11 56.2
MS.gene00836.t1 MTR_0001s0360 46.000 50 24 1 18 67 57 103 7.38e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00836.t1 AT2G46410 63.636 44 16 0 27 70 36 79 1.64e-17 70.5
MS.gene00836.t1 AT4G01060 50.000 64 29 1 7 70 16 76 5.49e-16 65.9
MS.gene00836.t1 AT1G01380 56.818 44 19 0 27 70 32 75 1.45e-15 65.1
MS.gene00836.t1 AT5G53200 52.000 50 24 0 27 76 31 80 1.95e-15 65.5
MS.gene00836.t1 AT4G01060 60.000 45 18 0 26 70 29 73 2.02e-15 64.3
MS.gene00836.t1 AT4G01060 60.000 45 18 0 26 70 30 74 2.61e-15 64.3
MS.gene00836.t1 AT2G30420 36.111 72 43 1 1 72 15 83 1.68e-12 58.2
MS.gene00836.t1 AT2G30424 50.000 44 22 0 27 70 34 77 4.75e-12 56.6
MS.gene00836.t1 AT5G52600 45.455 44 24 0 29 72 70 113 1.05e-11 57.8
MS.gene00836.t1 AT5G14750 43.182 44 25 0 29 72 13 56 2.13e-11 55.8
MS.gene00836.t1 AT5G14750 43.182 44 25 0 29 72 13 56 2.13e-11 55.8
MS.gene00836.t1 AT2G30432 44.262 61 31 2 10 70 19 76 3.95e-11 53.9
MS.gene00836.t1 AT3G13540 52.500 40 19 0 30 69 82 121 7.78e-11 55.8

Find 16 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAACGATATCTTCCTCTTC+TGG 0.165562 2.3:-64999853 None:intergenic
ATATCTTCTGGGGTTCTTCC+AGG 0.255062 2.3:-65000065 None:intergenic
CAACGATATCTTCCTCTTCT+GGG 0.371629 2.3:-64999852 None:intergenic
TGTAGATGGCATCTCATTGC+TGG 0.392405 2.3:+65000035 MS.gene00836:intron
CTCATTGCTGGGAGAATCCC+TGG 0.434907 2.3:+65000047 MS.gene00836:CDS
CAGAAGATATTGAAAAGTAT+TGG 0.446559 2.3:+65000078 MS.gene00836:CDS
TATCTTCTGGGGTTCTTCCA+GGG 0.463656 2.3:-65000064 None:intergenic
GATGAAACGTGAGGCTGTGC+TGG 0.475255 2.3:+64999822 MS.gene00836:CDS
AATGGCCAGTATGTCTCTTC+AGG 0.479277 2.3:+64999615 MS.gene00836:CDS
TGTTTAGATTGGTCGGAAAG+AGG 0.513739 2.3:+64999881 MS.gene00836:CDS
TGGTACCTGAAGAGACATAC+TGG 0.523534 2.3:-64999620 None:intergenic
GTAGATGGCATCTCATTGCT+GGG 0.572643 2.3:+65000036 MS.gene00836:intron
AACGATATCTTCCTCTTCTG+GGG 0.611771 2.3:-64999851 None:intergenic
TATGCAACCACTGCAAACAA+TGG 0.637268 2.3:+64999597 MS.gene00836:CDS
ATACTGGCCATTGTTTGCAG+TGG 0.645184 2.3:-64999604 None:intergenic
CTCAGATCAGATGAAACGTG+AGG 0.650176 2.3:+64999813 MS.gene00836:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATATATATATATATATAT+AGG + chr2.3:64999661-64999680 MS.gene00836:intron 0.0%
!! TATATATATATATATATATA+GGG + chr2.3:64999660-64999679 MS.gene00836:intron 0.0%
!! ATATACAGATTCATATGATT+TGG - chr2.3:64999778-64999797 None:intergenic 20.0%
!! TATACAGATTCATATGATTT+GGG - chr2.3:64999777-64999796 None:intergenic 20.0%
!! TATATGTTAATTAACTTCGT+TGG + chr2.3:64999918-64999937 MS.gene00836:intron 20.0%
!!! AATACTTTTCAATATCTTCT+GGG - chr2.3:65000079-65000098 None:intergenic 20.0%
! TTTGACATGTTAATTGTAGA+TGG + chr2.3:65000021-65000040 MS.gene00836:intron 25.0%
!! ATACTTTTCAATATCTTCTG+GGG - chr2.3:65000078-65000097 None:intergenic 25.0%
!! CAATACTTTTCAATATCTTC+TGG - chr2.3:65000080-65000099 None:intergenic 25.0%
!! CAGAAGATATTGAAAAGTAT+TGG + chr2.3:65000078-65000097 MS.gene00836:CDS 25.0%
CGTTGCAAAAATGTTTAGAT+TGG + chr2.3:64999870-64999889 MS.gene00836:CDS 30.0%
GCAAAAATGTTTAGATTGGT+CGG + chr2.3:64999874-64999893 MS.gene00836:CDS 30.0%
TCATGTGTTTGTATTGTAGA+AGG + chr2.3:64999983-65000002 MS.gene00836:intron 30.0%
! AGATTCATATGATTTGGGAA+GGG - chr2.3:64999772-64999791 None:intergenic 30.0%
ATAAGATGGTCAACTTGAAG+TGG - chr2.3:64999643-64999662 None:intergenic 35.0%
ATCAAGTTTGTGCAAATGCA+AGG - chr2.3:64999950-64999969 None:intergenic 35.0%
! CAGATTCATATGATTTGGGA+AGG - chr2.3:64999773-64999792 None:intergenic 35.0%
! GATTCATATGATTTGGGAAG+GGG - chr2.3:64999771-64999790 None:intergenic 35.0%
AACGATATCTTCCTCTTCTG+GGG - chr2.3:64999854-64999873 None:intergenic 40.0%
CAACGATATCTTCCTCTTCT+GGG - chr2.3:64999855-64999874 None:intergenic 40.0%
GCATTTGCACAAACTTGATG+AGG + chr2.3:64999951-64999970 MS.gene00836:intron 40.0%
TATGCAACCACTGCAAACAA+TGG + chr2.3:64999597-64999616 MS.gene00836:CDS 40.0%
! TGTTTAGATTGGTCGGAAAG+AGG + chr2.3:64999881-64999900 MS.gene00836:CDS 40.0%
AATGGCCAGTATGTCTCTTC+AGG + chr2.3:64999615-64999634 MS.gene00836:CDS 45.0%
ATACTGGCCATTGTTTGCAG+TGG - chr2.3:64999607-64999626 None:intergenic 45.0%
CTCAGATCAGATGAAACGTG+AGG + chr2.3:64999813-64999832 MS.gene00836:intron 45.0%
GCAACGATATCTTCCTCTTC+TGG - chr2.3:64999856-64999875 None:intergenic 45.0%
GTAGATGGCATCTCATTGCT+GGG + chr2.3:65000036-65000055 MS.gene00836:intron 45.0%
TGGTACCTGAAGAGACATAC+TGG - chr2.3:64999623-64999642 None:intergenic 45.0%
TGTAGATGGCATCTCATTGC+TGG + chr2.3:65000035-65000054 MS.gene00836:intron 45.0%
!! ATATCTTCTGGGGTTCTTCC+AGG - chr2.3:65000068-65000087 None:intergenic 45.0%
!! TATCTTCTGGGGTTCTTCCA+GGG - chr2.3:65000067-65000086 None:intergenic 45.0%
!! ATATATATATATATATAAGA+TGG - chr2.3:64999657-64999676 None:intergenic 5.0%
! GCTGGAATTTTCCCCAGAAG+AGG + chr2.3:64999840-64999859 MS.gene00836:CDS 50.0%
CTCATTGCTGGGAGAATCCC+TGG + chr2.3:65000047-65000066 MS.gene00836:CDS 55.0%
GATGAAACGTGAGGCTGTGC+TGG + chr2.3:64999822-64999841 MS.gene00836:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 64999582 65000133 64999582 ID=MS.gene00836
chr2.3 mRNA 64999582 65000133 64999582 ID=MS.gene00836.t1;Parent=MS.gene00836
chr2.3 exon 64999582 64999636 64999582 ID=MS.gene00836.t1.exon1;Parent=MS.gene00836.t1
chr2.3 CDS 64999582 64999636 64999582 ID=cds.MS.gene00836.t1;Parent=MS.gene00836.t1
chr2.3 exon 64999818 64999902 64999818 ID=MS.gene00836.t1.exon2;Parent=MS.gene00836.t1
chr2.3 CDS 64999818 64999902 64999818 ID=cds.MS.gene00836.t1;Parent=MS.gene00836.t1
chr2.3 exon 65000040 65000133 65000040 ID=MS.gene00836.t1.exon3;Parent=MS.gene00836.t1
chr2.3 CDS 65000040 65000133 65000040 ID=cds.MS.gene00836.t1;Parent=MS.gene00836.t1
Gene Sequence

>MS.gene00836

ATGAGTGACTCAAAGTATGCAACCACTGCAAACAATGGCCAGTATGTCTCTTCAGGTACCACTTCAAGTTGACCATCTTATATATATATATATATATATATATATATATATATATATATATATATATAGGGTTTTTCTATCATGTTTTTAATTAATCAATATATGTTTCAATCGATATATTTTTCACCCCTTCCCAAATCATATGAATCTGTATATGTTTCTGCTTGCTGTCTCAGATCAGATGAAACGTGAGGCTGTGCTGGAATTTTCCCCAGAAGAGGAAGATATCGTTGCAAAAATGTTTAGATTGGTCGGAAAGAGGTTAGCTTTGTCATATATATGTTAATTAACTTCGTTGGTATCTTCCTTGCATTTGCACAAACTTGATGAGGCAATTAGTATCATGTGTTTGTATTGTAGAAGGTCTAATTAAAGTTTGTTTGACATGTTAATTGTAGATGGCATCTCATTGCTGGGAGAATCCCTGGAAGAACCCCAGAAGATATTGAAAAGTATTGGACATCAAAGTTCTCATCATCAACTGCATGCTAA
Protein sequence

>MS.gene00836.t1

MSDSKYATTANNGQYVSSDQMKREAVLEFSPEEEDIVAKMFRLVGKRWHLIAGRIPGRTPEDIEKYWTSKFSSSTAC