AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene78406


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78406.t1 MTR_2g097680 92.398 171 7 4 1 170 18 183 1.30e-80 237
MS.gene78406.t1 MTR_1g071380 90.643 171 8 6 1 170 1 164 1.79e-77 228
MS.gene78406.t1 MTR_2g097680 89.831 118 6 4 1 117 18 130 6.72e-58 177
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78406.t1 AT2G29180 41.772 158 75 5 20 163 5 159 6.02e-24 92.4

Find 29 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGCTTATCCGTTATCACTAT+TGG 0.245133 2.3:+5423148 MS.gene78406:CDS
GCTTATCCGTTATCACTATT+GGG 0.260636 2.3:+5423149 MS.gene78406:CDS
TCTGGTTGTAGTAGTGATAA+TGG 0.300412 2.3:-5422954 None:intergenic
GAAAGGAAGGTTGCAATCTT+TGG 0.300675 2.3:-5422857 None:intergenic
GCTGTAGCAGCAACAGGATT+TGG 0.334339 2.3:-5423013 None:intergenic
TTCAAAGGAAGTCCAAACTA+TGG 0.343791 2.3:+5422990 MS.gene78406:CDS
CATTGATGCTTCGGAGCAAT+TGG 0.360695 2.3:+5423057 MS.gene78406:CDS
CTGGTTGTAGTAGTGATAAT+GGG 0.369858 2.3:-5422953 None:intergenic
AACAGGATTTGGCCATAGTT+TGG 0.372494 2.3:-5423002 None:intergenic
AAAAGAAAAGAAAAGTAGTA+AGG 0.384781 2.3:+5424152 MS.gene78406:CDS
AGGGCAGGACCTAAAGGATT+TGG 0.404020 2.3:+5424172 MS.gene78406:CDS
GAGAAAGATGAAGAAGTTGT+TGG 0.423658 2.3:-5422929 None:intergenic
TGCTACAGCCATTGATGCTT+CGG 0.431580 2.3:+5423048 MS.gene78406:CDS
TCAACAGCTGTAGCAGCAAC+AGG 0.437132 2.3:-5423019 None:intergenic
CAATTGCTCCGAAGCATCAA+TGG 0.447559 2.3:-5423056 None:intergenic
AGAAGATGATGTTGAAAGGA+AGG 0.478894 2.3:-5422870 None:intergenic
TCATCAACTACCACTGATGA+TGG 0.480753 2.3:+5423082 MS.gene78406:CDS
AAAGAAAAGAAAAGTAGTAA+GGG 0.491413 2.3:+5424153 MS.gene78406:CDS
AAGAAGAAGATGATGTTGAA+AGG 0.496918 2.3:-5422874 None:intergenic
GTAGTAAGGGCAGGACCTAA+AGG 0.510055 2.3:+5424166 MS.gene78406:CDS
CTTATCCGTTATCACTATTG+GGG 0.525510 2.3:+5423150 MS.gene78406:CDS
CATCAACTACCACTGATGAT+GGG 0.525641 2.3:+5423083 MS.gene78406:CDS
AAAAGAAAAGTAGTAAGGGC+AGG 0.536130 2.3:+5424157 MS.gene78406:CDS
ATATACCCCAATAGTGATAA+CGG 0.550650 2.3:-5423155 None:intergenic
TTTCTTGACAAAGAGAGAGA+AGG 0.571247 2.3:+5424090 MS.gene78406:CDS
ATCAACTACCACTGATGATG+GGG 0.608198 2.3:+5423084 MS.gene78406:CDS
AAGAGACACCCCATCATCAG+TGG 0.647668 2.3:-5423092 None:intergenic
GAGAAAGAAGAAGCAGCTAG+CGG 0.687353 2.3:+5424121 MS.gene78406:CDS
TGATGATGCAAATAATGCAG+TGG 0.718262 2.3:-5422825 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTCTATATTAATAAAAGAAT+TGG - chr2.3:5423215-5423234 None:intergenic 15.0%
!! TATTCAAAATGAACTAATTA+GGG - chr2.3:5423574-5423593 None:intergenic 15.0%
!!! AAATGATTATGAACTAATTT+TGG - chr2.3:5423547-5423566 None:intergenic 15.0%
!!! AATAGAATTTTACAATATTG+AGG + chr2.3:5423590-5423609 MS.gene78406:intron 15.0%
!!! CAATTCTTTTATTAATATAG+AGG + chr2.3:5423213-5423232 MS.gene78406:intron 15.0%
!!! TTTTATAAATGTAAATGACT+TGG + chr2.3:5423938-5423957 MS.gene78406:intron 15.0%
!!! TTTTTCGTTTTGTAATTTTA+TGG + chr2.3:5423794-5423813 MS.gene78406:intron 15.0%
!! AAAAGAAAAGAAAAGTAGTA+AGG + chr2.3:5424152-5424171 MS.gene78406:CDS 20.0%
!! AAAGAAAAGAAAAGTAGTAA+GGG + chr2.3:5424153-5424172 MS.gene78406:CDS 20.0%
!! CTAAATTGATTATGAAAGTT+AGG - chr2.3:5423488-5423507 None:intergenic 20.0%
!! CTATTCAAAATGAACTAATT+AGG - chr2.3:5423575-5423594 None:intergenic 20.0%
!!! GAAAATCCATATTTTTTCAA+AGG + chr2.3:5422975-5422994 MS.gene78406:CDS 20.0%
!!! TATTGACATTACATGTTTTA+GGG + chr2.3:5423407-5423426 MS.gene78406:intron 20.0%
!!! TTATTGACATTACATGTTTT+AGG + chr2.3:5423406-5423425 MS.gene78406:intron 20.0%
!!! TTGAAAAAATATGGATTTTC+TGG - chr2.3:5422975-5422994 None:intergenic 20.0%
!!! TTGCGATTTTAATACATTAA+GGG - chr2.3:5423758-5423777 None:intergenic 20.0%
!!! TTTGCGATTTTAATACATTA+AGG - chr2.3:5423759-5423778 None:intergenic 20.0%
! TTACTTAGCATTAGTATTCA+GGG + chr2.3:5424012-5424031 MS.gene78406:intron 25.0%
! TTAGTGAAAATTATTTCCCT+TGG + chr2.3:5423323-5423342 MS.gene78406:intron 25.0%
!! TTTTGATCTTTGAATATGTG+AGG - chr2.3:5423904-5423923 None:intergenic 25.0%
AAGAAGAAGATGATGTTGAA+AGG - chr2.3:5422877-5422896 None:intergenic 30.0%
AGTAAAAACGTGTGTTGAAA+TGG - chr2.3:5422904-5422923 None:intergenic 30.0%
ATATACCCCAATAGTGATAA+CGG - chr2.3:5423158-5423177 None:intergenic 30.0%
CACATATTTAGAGACCTAAA+TGG - chr2.3:5423717-5423736 None:intergenic 30.0%
CTAGTTTATACTTTGTAGTG+TGG - chr2.3:5423381-5423400 None:intergenic 30.0%
GTTACTTAGCATTAGTATTC+AGG + chr2.3:5424011-5424030 MS.gene78406:intron 30.0%
TTTAGGTCTCTAAATATGTG+AGG + chr2.3:5423717-5423736 MS.gene78406:intron 30.0%
! ATCTTTTGACCAAATCCTTT+AGG - chr2.3:5424184-5424203 None:intergenic 30.0%
! CCTCCTATCTAAAACTATTT+CGG + chr2.3:5423987-5424006 MS.gene78406:intron 30.0%
! CTTTTCTTCATTGCTTTCAT+TGG + chr2.3:5423127-5423146 MS.gene78406:CDS 30.0%
! GGACTTCCTTTGAAAAAATA+TGG - chr2.3:5422984-5423003 None:intergenic 30.0%
! TTTAAAGCAAACAGCCATTT+AGG + chr2.3:5423700-5423719 MS.gene78406:intron 30.0%
!! TTTTTGTTTGTTTGTGTTGC+AGG + chr2.3:5424045-5424064 MS.gene78406:intron 30.0%
!!! ACACCGAAATAGTTTTAGAT+AGG - chr2.3:5423993-5424012 None:intergenic 30.0%
AAAAGAAAAGTAGTAAGGGC+AGG + chr2.3:5424157-5424176 MS.gene78406:CDS 35.0%
AGAAGATGATGTTGAAAGGA+AGG - chr2.3:5422873-5422892 None:intergenic 35.0%
ATTCCATGTCATATTGTCCA+AGG - chr2.3:5423343-5423362 None:intergenic 35.0%
CTGGTTGTAGTAGTGATAAT+GGG - chr2.3:5422956-5422975 None:intergenic 35.0%
CTTATCCGTTATCACTATTG+GGG + chr2.3:5423150-5423169 MS.gene78406:CDS 35.0%
GAGAAAGATGAAGAAGTTGT+TGG - chr2.3:5422932-5422951 None:intergenic 35.0%
GCTTATCCGTTATCACTATT+GGG + chr2.3:5423149-5423168 MS.gene78406:CDS 35.0%
TCTGGTTGTAGTAGTGATAA+TGG - chr2.3:5422957-5422976 None:intergenic 35.0%
TTCAAAGGAAGTCCAAACTA+TGG + chr2.3:5422990-5423009 MS.gene78406:CDS 35.0%
TTCCATGTCATATTGTCCAA+GGG - chr2.3:5423342-5423361 None:intergenic 35.0%
TTGAGACATGCTTGCAATTT+CGG - chr2.3:5423250-5423269 None:intergenic 35.0%
TTTCTTGACAAAGAGAGAGA+AGG + chr2.3:5424090-5424109 MS.gene78406:CDS 35.0%
! TGATGATGCAAATAATGCAG+TGG - chr2.3:5422828-5422847 None:intergenic 35.0%
!!! CCGAAATAGTTTTAGATAGG+AGG - chr2.3:5423990-5424009 None:intergenic 35.0%
AACAGGATTTGGCCATAGTT+TGG - chr2.3:5423005-5423024 None:intergenic 40.0%
AATCGCAAACACATCTCTAG+TGG + chr2.3:5423770-5423789 MS.gene78406:intron 40.0%
ACACATGCAGTCAACTTACT+AGG - chr2.3:5423513-5423532 None:intergenic 40.0%
CACATGCAGTCAACTTACTA+GGG - chr2.3:5423512-5423531 None:intergenic 40.0%
CATCAACTACCACTGATGAT+GGG + chr2.3:5423083-5423102 MS.gene78406:CDS 40.0%
CTTAGCATTAGTATTCAGGG+AGG + chr2.3:5424015-5424034 MS.gene78406:intron 40.0%
GAAAGGAAGGTTGCAATCTT+TGG - chr2.3:5422860-5422879 None:intergenic 40.0%
GGCAAATGGTCACGATTTAA+AGG + chr2.3:5423650-5423669 MS.gene78406:intron 40.0%
GGCTTATCCGTTATCACTAT+TGG + chr2.3:5423148-5423167 MS.gene78406:CDS 40.0%
TCATCAACTACCACTGATGA+TGG + chr2.3:5423082-5423101 MS.gene78406:CDS 40.0%
TTCCCTTGGACAATATGACA+TGG + chr2.3:5423337-5423356 MS.gene78406:intron 40.0%
! AGTAAGTTGACTGCATGTGT+TGG + chr2.3:5423513-5423532 MS.gene78406:intron 40.0%
! ATCAACTACCACTGATGATG+GGG + chr2.3:5423084-5423103 MS.gene78406:CDS 40.0%
CATTGATGCTTCGGAGCAAT+TGG + chr2.3:5423057-5423076 MS.gene78406:CDS 45.0%
GAGAAAGAAGAAGCAGCTAG+CGG + chr2.3:5424121-5424140 MS.gene78406:CDS 45.0%
TGCTACAGCCATTGATGCTT+CGG + chr2.3:5423048-5423067 MS.gene78406:CDS 45.0%
! CAATTGCTCCGAAGCATCAA+TGG - chr2.3:5423059-5423078 None:intergenic 45.0%
! GCCAAAACGAGTGACTAGTT+TGG + chr2.3:5423629-5423648 MS.gene78406:intron 45.0%
! GCCAAACTAGTCACTCGTTT+TGG - chr2.3:5423633-5423652 None:intergenic 45.0%
!! CGAGTGACTAGTTTGGCAAA+TGG + chr2.3:5423636-5423655 MS.gene78406:intron 45.0%
AAGAGACACCCCATCATCAG+TGG - chr2.3:5423095-5423114 None:intergenic 50.0%
AGGGCAGGACCTAAAGGATT+TGG + chr2.3:5424172-5424191 MS.gene78406:CDS 50.0%
GCTGTAGCAGCAACAGGATT+TGG - chr2.3:5423016-5423035 None:intergenic 50.0%
GTAGTAAGGGCAGGACCTAA+AGG + chr2.3:5424166-5424185 MS.gene78406:CDS 50.0%
TCAACAGCTGTAGCAGCAAC+AGG - chr2.3:5423022-5423041 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 5422821 5424228 5422821 ID=MS.gene78406
chr2.3 mRNA 5422821 5424228 5422821 ID=MS.gene78406.t1;Parent=MS.gene78406
chr2.3 exon 5422821 5423171 5422821 ID=MS.gene78406.t1.exon1;Parent=MS.gene78406.t1
chr2.3 CDS 5422821 5423171 5422821 ID=cds.MS.gene78406.t1;Parent=MS.gene78406.t1
chr2.3 exon 5424067 5424228 5424067 ID=MS.gene78406.t1.exon2;Parent=MS.gene78406.t1
chr2.3 CDS 5424067 5424228 5424067 ID=cds.MS.gene78406.t1;Parent=MS.gene78406.t1
Gene Sequence

>MS.gene78406

ATGGCCACTGCATTATTTGCATCATCATCATCATCTCCAAAGATTGCAACCTTCCTTTCAACATCATCTTCTTCTTCTTTCCATTTCAACACACGTTTTTACTCACTTCCAACAACTTCTTCATCTTTCTCTCCCATTATCACTACTACAACCAGAAAATCCATATTTTTTCAAAGGAAGTCCAAACTATGGCCAAATCCTGTTGCTGCTACAGCTGTTGAAGATGCTGCTACAGCCATTGATGCTTCGGAGCAATTGGTTTCATCAACTACCACTGATGATGGGGTGTCTCTTATCGTATCAGCTCTTTTCTTCATTGCTTTCATTGGCTTATCCGTTATCACTATTGGGGTATATTCGTCATTTTCTTCTATTCTCACTTTTTTGTTTTCCAATTCTTTTATTAATATAGAGGTAAATTATCATCCGAAATTGCAAGCATGTCTCAAAATAGTGTTTGATTTTTGTGAATTGACAAACATATTTGTGAAATTGTAAAATGTTAGTGAAAATTATTTCCCTTGGACAATATGACATGGAATCTAACATCAATGTTACCACACTACAAAGTATAAACTAGTTTGTTTATTGACATTACATGTTTTAGGGACTAATTTGTCAATAATTAATTAGTTCATGTATATTTGTAATTATTGATAAATTACCTAACTTTCATAATCAATTTAGTCCCTAGTAAGTTGACTGCATGTGTTGGATCAACGTCCAAAATTAGTTCATAATCATTTTAGTCCCTAATTAGTTCATTTTGAATAGAATTTTACAATATTGAGGATGTATATGTCAATTCGCCAAAACGAGTGACTAGTTTGGCAAATGGTCACGATTTAAAGGATCAATTTGACTATGCGCACTCATTTGTTTAAAGCAAACAGCCATTTAGGTCTCTAAATATGTGAGGTGTTGTTAGTACAGTCCCTTAATGTATTAAAATCGCAAACACATCTCTAGTGGCTTTTTCGTTTTGTAATTTTATGGATTATATTGACTAACGAATAAAAAAAAAAAAAAACATGTTGATGTGCTTGTAATTCGATTCACTCAGTGACTATAGTGACAACACCTCACATATTCAAAGATCAAAATGATTGATTATCGTTTTTATAAATGTAAATGACTTGGTAAGTTAGTAGTATTTGAACTTTTGACCTCCTATCTAAAACTATTTCGGTGTTACTTAGCATTAGTATTCAGGGAGGTTCTGTATTTTTGTTTGTTTGTGTTGCAGGTTATCTATTTAGCAGTAACAGATTTCTTGACAAAGAGAGAGAAGGAAAAATTTGAGAAAGAAGAAGCAGCTAGCGGAAAGAAGAAAAAGAAAAGAAAAGTAGTAAGGGCAGGACCTAAAGGATTTGGTCAAAAGATTGTTCAAACTGAAGATGATGATTGA

Protein sequence

>MS.gene78406.t1

MATALFASSSSSPKIATFLSTSSSSSFHFNTRFYSLPTTSSSFSPIITTTTRKSIFFQRKSKLWPNPVAATAVEDAATAIDASEQLVSSTTTDDGVSLIVSALFFIAFIGLSVITIGVIYLAVTDFLTKREKEKFEKEEAASGKKKKKRKVVRAGPKGFGQKIVQTEDDD