AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene28771

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28771.t1 MTR_4g094332 91.556 225 18 1 1 225 1 224 2.42e-129 364
MS.gene28771.t1 MTR_4g094328 90.222 225 21 1 1 225 1 224 1.74e-126 357
MS.gene28771.t1 MTR_4g094330 90.222 225 21 1 1 225 1 224 1.74e-126 357
MS.gene28771.t1 MTR_1g099010 64.851 202 66 1 24 225 21 217 5.36e-89 261
MS.gene28771.t1 MTR_6g034975 66.500 200 62 2 26 225 16 210 8.71e-84 248
MS.gene28771.t1 MTR_4g094325 63.402 194 67 1 32 225 50 239 5.33e-82 244
MS.gene28771.t1 MTR_0119s0010 59.686 191 67 1 30 220 27 207 2.62e-71 216
MS.gene28771.t1 MTR_0119s0020 59.686 191 67 1 30 220 27 207 2.62e-71 216
MS.gene28771.t1 MTR_2g008110 59.686 191 67 1 30 220 27 207 3.48e-71 216
MS.gene28771.t1 MTR_4g094335 59.278 194 77 1 29 220 32 225 7.08e-70 214
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28771.t1 AT3G43660 62.121 198 65 2 29 225 10 198 1.71e-89 262
MS.gene28771.t1 AT1G21140 60.000 205 70 2 24 225 5 200 6.56e-80 238
MS.gene28771.t1 AT3G43630 60.500 200 69 2 24 222 4 194 3.34e-79 236
MS.gene28771.t1 AT1G76800 61.500 200 67 1 26 225 7 196 1.45e-77 232
MS.gene28771.t1 AT3G25190 62.085 211 75 2 18 225 9 217 1.05e-71 218

Find 50 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGCTATGGCCATTACTTT+TGG 0.296297 4.3:-19930846 MS.gene28771:CDS
ACCAAATTGATTGGCACTAC+TGG 0.296615 4.3:-19930819 MS.gene28771:CDS
TGTGGTTAGGTTTGCATTGT+TGG 0.312190 4.3:-19930946 MS.gene28771:CDS
TCTTGTGTTAGAGTTCTAAT+TGG 0.326616 4.3:-19930876 MS.gene28771:CDS
TCCAGTAGTGCCAATCAATT+TGG 0.330163 4.3:+19930818 None:intergenic
TTTGGTTTCACCAAATTGAT+TGG 0.341339 4.3:-19930828 MS.gene28771:CDS
TATCTCAATCTCAAAATTGC+TGG 0.375338 4.3:+19931427 None:intergenic
AGGTTTGCATTGTTGGTGTT+TGG 0.379958 4.3:-19930939 MS.gene28771:CDS
AGGGCTGCTTGAAATGGATT+TGG 0.388581 4.3:+19931065 None:intergenic
TGGCTTAGAGCAGCCATGTT+AGG 0.393100 4.3:-19931332 MS.gene28771:CDS
GTTTGGAGGAGTGGGTGCAT+TGG 0.412614 4.3:-19930922 MS.gene28771:CDS
GATGCTAGGGCTGCTTGAAA+TGG 0.413748 4.3:+19931059 None:intergenic
ACCGTTGCGTCGTTGATGAT+TGG 0.428147 4.3:-19931290 MS.gene28771:CDS
AGAGTACTACTGACATGAAT+AGG 0.444320 4.3:+19931404 None:intergenic
TGTGTTAGAGTTCTAATTGG+AGG 0.446628 4.3:-19930873 MS.gene28771:CDS
GGTTTCGCTGGTTTAGTAGC+AGG 0.462292 4.3:-19931224 MS.gene28771:CDS
CAACATTGATTACTTTCAAA+GGG 0.466059 4.3:-19931360 MS.gene28771:CDS
ATGCTCCGAGCTGGTTTCGC+TGG 0.471108 4.3:-19931236 MS.gene28771:CDS
TTGTTGGTGTTTGGAGGAGT+GGG 0.472009 4.3:-19930930 MS.gene28771:CDS
AACGGTGATTAGTCCATCAT+TGG 0.472628 4.3:+19931307 None:intergenic
GGAGGAGTGGGTGCATTGGT+TGG 0.478561 4.3:-19930918 MS.gene28771:CDS
GTGTTGTAGCTGCTGTGGTT+AGG 0.480340 4.3:-19930959 MS.gene28771:CDS
ACAACATTGATTACTTTCAA+AGG 0.489039 4.3:-19931361 MS.gene28771:CDS
TTTGCATTGTTGGTGTTTGG+AGG 0.490032 4.3:-19930936 MS.gene28771:CDS
GGAGCTTGTAGCATGGCAAT+TGG 0.492067 4.3:-19931203 MS.gene28771:CDS
AAAGAATCACAAAATCAGAA+TGG 0.497688 4.3:-19930982 MS.gene28771:CDS
AAGAATCACAAAATCAGAAT+GGG 0.499997 4.3:-19930981 MS.gene28771:CDS
TTCAATATGGCCTCCCACCT+TGG 0.500245 4.3:-19931473 None:intergenic
ATTGTTGGTGTTTGGAGGAG+TGG 0.501761 4.3:-19930931 MS.gene28771:CDS
AAAATGCAAGTGCTGATGCT+AGG 0.501770 4.3:+19931045 None:intergenic
AATTGGAGGTTGGATGGCTA+TGG 0.510325 4.3:-19930859 MS.gene28771:CDS
ATCTCAATCTCAAAATTGCT+GGG 0.516463 4.3:+19931428 None:intergenic
AGTTCTAATTGGAGGTTGGA+TGG 0.519543 4.3:-19930865 MS.gene28771:CDS
TTAGAGTTCTAATTGGAGGT+TGG 0.521312 4.3:-19930869 MS.gene28771:CDS
GCGTCGTTGATGATTGGTGT+TGG 0.527815 4.3:-19931284 MS.gene28771:CDS
TAAATGCAGCTGCTAGCAAT+GGG 0.531631 4.3:+19931006 None:intergenic
ATAAATGCAGCTGCTAGCAA+TGG 0.533922 4.3:+19931005 None:intergenic
AAATGCAAGTGCTGATGCTA+GGG 0.534060 4.3:+19931046 None:intergenic
TTTGGTGAAACCAAAAGTAA+TGG 0.542621 4.3:+19930836 None:intergenic
TCCATCATTGGCTCCTAACA+TGG 0.543290 4.3:+19931319 None:intergenic
ACCAATCATCAACGACGCAA+CGG 0.550619 4.3:+19931289 None:intergenic
ATCAAAGTAATGCTCCGAGC+TGG 0.567968 4.3:-19931245 MS.gene28771:CDS
GCCATGTTAGGAGCCAATGA+TGG 0.577904 4.3:-19931320 MS.gene28771:CDS
ATGATGATGAAAGTAGTGAA+AGG 0.610585 4.3:-19931097 MS.gene28771:CDS
TGATGATGAAAGTAGTGAAA+GGG 0.611622 4.3:-19931096 MS.gene28771:CDS
AATGGGTGTTGTAGCTGCTG+TGG 0.611775 4.3:-19930964 MS.gene28771:CDS
ATTACTTTCAAAGGGCACAA+TGG 0.615521 4.3:-19931352 MS.gene28771:CDS
CTAAACCAGCGAAACCAGCT+CGG 0.629821 4.3:+19931231 None:intergenic
AGTAGCAGGAGCTTGTAGCA+TGG 0.637161 4.3:-19931210 MS.gene28771:CDS
CTAACACAAGACCTCATCAG+AGG 0.675054 4.3:+19930888 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGAATCACAAAATCAGAA+TGG - chr4.3:19931297-19931316 MS.gene28771:CDS 25.0%
! AAGAATCACAAAATCAGAAT+GGG - chr4.3:19931298-19931317 MS.gene28771:CDS 25.0%
!! ACAACATTGATTACTTTCAA+AGG - chr4.3:19930918-19930937 MS.gene28771:CDS 25.0%
!! CAACATTGATTACTTTCAAA+GGG - chr4.3:19930919-19930938 MS.gene28771:CDS 25.0%
ATCTCAATCTCAAAATTGCT+GGG + chr4.3:19930854-19930873 None:intergenic 30.0%
TATCTCAATCTCAAAATTGC+TGG + chr4.3:19930855-19930874 None:intergenic 30.0%
TTTGGTGAAACCAAAAGTAA+TGG + chr4.3:19931446-19931465 None:intergenic 30.0%
! ATGATGATGAAAGTAGTGAA+AGG - chr4.3:19931182-19931201 MS.gene28771:CDS 30.0%
! TCTTGTGTTAGAGTTCTAAT+TGG - chr4.3:19931403-19931422 MS.gene28771:CDS 30.0%
! TGATGATGAAAGTAGTGAAA+GGG - chr4.3:19931183-19931202 MS.gene28771:CDS 30.0%
! TTTGGTTTCACCAAATTGAT+TGG - chr4.3:19931451-19931470 MS.gene28771:CDS 30.0%
! AGAGTACTACTGACATGAAT+AGG + chr4.3:19930878-19930897 None:intergenic 35.0%
! ATTACTTTCAAAGGGCACAA+TGG - chr4.3:19930927-19930946 MS.gene28771:CDS 35.0%
! TCAGCACTTGCATTTTCTAT+TGG - chr4.3:19931241-19931260 MS.gene28771:CDS 35.0%
! TGTGTTAGAGTTCTAATTGG+AGG - chr4.3:19931406-19931425 MS.gene28771:CDS 35.0%
! TTAGAGTTCTAATTGGAGGT+TGG - chr4.3:19931410-19931429 MS.gene28771:CDS 35.0%
!!! ATTAGTTTTTGCTCCAAGGT+GGG + chr4.3:19930822-19930841 None:intergenic 35.0%
!!! TTCCATTAGTTTTTGCTCCA+AGG + chr4.3:19930826-19930845 None:intergenic 35.0%
ACCAAATTGATTGGCACTAC+TGG - chr4.3:19931460-19931479 MS.gene28771:CDS 40.0%
ATAAATGCAGCTGCTAGCAA+TGG + chr4.3:19931277-19931296 None:intergenic 40.0%
CACCTTGGAGCAAAAACTAA+TGG - chr4.3:19930821-19930840 MS.gene28771:CDS 40.0%
TAAATGCAGCTGCTAGCAAT+GGG + chr4.3:19931276-19931295 None:intergenic 40.0%
TCCAGTAGTGCCAATCAATT+TGG + chr4.3:19931464-19931483 None:intergenic 40.0%
TGTGGTTAGGTTTGCATTGT+TGG - chr4.3:19931333-19931352 MS.gene28771:CDS 40.0%
TTGGAAAAACTCCTCTGATG+AGG - chr4.3:19931380-19931399 MS.gene28771:CDS 40.0%
! AACGGTGATTAGTCCATCAT+TGG + chr4.3:19930975-19930994 None:intergenic 40.0%
! AGGTTTGCATTGTTGGTGTT+TGG - chr4.3:19931340-19931359 MS.gene28771:CDS 40.0%
! AGTTCTAATTGGAGGTTGGA+TGG - chr4.3:19931414-19931433 MS.gene28771:CDS 40.0%
! ATGGCTATGGCCATTACTTT+TGG - chr4.3:19931433-19931452 MS.gene28771:CDS 40.0%
! TTTGCATTGTTGGTGTTTGG+AGG - chr4.3:19931343-19931362 MS.gene28771:CDS 40.0%
!! AAAATGCAAGTGCTGATGCT+AGG + chr4.3:19931237-19931256 None:intergenic 40.0%
!! AAATGCAAGTGCTGATGCTA+GGG + chr4.3:19931236-19931255 None:intergenic 40.0%
!!! CATTAGTTTTTGCTCCAAGG+TGG + chr4.3:19930823-19930842 None:intergenic 40.0%
AATTGGAGGTTGGATGGCTA+TGG - chr4.3:19931420-19931439 MS.gene28771:CDS 45.0%
ACCAATCATCAACGACGCAA+CGG + chr4.3:19930993-19931012 None:intergenic 45.0%
ATCAAAGTAATGCTCCGAGC+TGG - chr4.3:19931034-19931053 MS.gene28771:CDS 45.0%
CTAACACAAGACCTCATCAG+AGG + chr4.3:19931394-19931413 None:intergenic 45.0%
! AGGGCTGCTTGAAATGGATT+TGG + chr4.3:19931217-19931236 None:intergenic 45.0%
! ATTGTTGGTGTTTGGAGGAG+TGG - chr4.3:19931348-19931367 MS.gene28771:CDS 45.0%
! TTGTTGGTGTTTGGAGGAGT+GGG - chr4.3:19931349-19931368 MS.gene28771:CDS 45.0%
!! TCCATCATTGGCTCCTAACA+TGG + chr4.3:19930963-19930982 None:intergenic 45.0%
AGTAGCAGGAGCTTGTAGCA+TGG - chr4.3:19931069-19931088 MS.gene28771:CDS 50.0%
CTAAACCAGCGAAACCAGCT+CGG + chr4.3:19931051-19931070 None:intergenic 50.0%
GATGCTAGGGCTGCTTGAAA+TGG + chr4.3:19931223-19931242 None:intergenic 50.0%
GCCATGTTAGGAGCCAATGA+TGG - chr4.3:19930959-19930978 MS.gene28771:CDS 50.0%
GGAGCTTGTAGCATGGCAAT+TGG - chr4.3:19931076-19931095 MS.gene28771:CDS 50.0%
GTGTTGTAGCTGCTGTGGTT+AGG - chr4.3:19931320-19931339 MS.gene28771:CDS 50.0%
TGGCTTAGAGCAGCCATGTT+AGG - chr4.3:19930947-19930966 MS.gene28771:CDS 50.0%
! AATGGGTGTTGTAGCTGCTG+TGG - chr4.3:19931315-19931334 MS.gene28771:CDS 50.0%
! AGTTTTTGCTCCAAGGTGGG+AGG + chr4.3:19930819-19930838 None:intergenic 50.0%
!! ACCGTTGCGTCGTTGATGAT+TGG - chr4.3:19930989-19931008 MS.gene28771:CDS 50.0%
!! GCGTCGTTGATGATTGGTGT+TGG - chr4.3:19930995-19931014 MS.gene28771:CDS 50.0%
!! GGTTTCGCTGGTTTAGTAGC+AGG - chr4.3:19931055-19931074 MS.gene28771:CDS 50.0%
GTTTGGAGGAGTGGGTGCAT+TGG - chr4.3:19931357-19931376 MS.gene28771:CDS 55.0%
! ATGCTCCGAGCTGGTTTCGC+TGG - chr4.3:19931043-19931062 MS.gene28771:CDS 60.0%
! GGAGGAGTGGGTGCATTGGT+TGG - chr4.3:19931361-19931380 MS.gene28771:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 19930812 19931489 19930812 ID=MS.gene28771
chr4.3 mRNA 19930812 19931489 19930812 ID=MS.gene28771.t1;Parent=MS.gene28771
chr4.3 exon 19930812 19931489 19930812 ID=MS.gene28771.t1.exon1;Parent=MS.gene28771.t1
chr4.3 CDS 19930812 19931489 19930812 ID=cds.MS.gene28771.t1;Parent=MS.gene28771.t1
Gene Sequence

>MS.gene28771

ATGGCCTCCCACCTTGGAGCAAAAACTAATGGAATTTCACCCAGCAATTTTGAGATTGAGATACCTATTCATGTCAGTAGTACTCTCAAAATTGAAAAAGAGAGCAACAACATTGATTACTTTCAAAGGGCACAATGGCTTAGAGCAGCCATGTTAGGAGCCAATGATGGACTAATCACCGTTGCGTCGTTGATGATTGGTGTTGGAGCTATAAAAGAAGACATCAAAGTAATGCTCCGAGCTGGTTTCGCTGGTTTAGTAGCAGGAGCTTGTAGCATGGCAATTGGTGAGTTTGTGTCTGTTTATACTCAATATGACATTGAGATAGCTCAGATAAATAGAGAAAGTGAAGCTAATAATAATAATGATGATGATGATGAAAGTAGTGAAAGGGAGAAATTGCCAAATCCATTTCAAGCAGCCCTAGCATCAGCACTTGCATTTTCTATTGGTGCAGTGATCCCATTGCTAGCAGCTGCATTTATAAAGAATCACAAAATCAGAATGGGTGTTGTAGCTGCTGTGGTTAGGTTTGCATTGTTGGTGTTTGGAGGAGTGGGTGCATTGGTTGGAAAAACTCCTCTGATGAGGTCTTGTGTTAGAGTTCTAATTGGAGGTTGGATGGCTATGGCCATTACTTTTGGTTTCACCAAATTGATTGGCACTACTGGACTTTGA
Protein sequence

>MS.gene28771.t1

MASHLGAKTNGISPSNFEIEIPIHVSSTLKIEKESNNIDYFQRAQWLRAAMLGANDGLITVASLMIGVGAIKEDIKVMLRAGFAGLVAGACSMAIGEFVSVYTQYDIEIAQINRESEANNNNDDDDESSEREKLPNPFQAALASALAFSIGAVIPLLAAAFIKNHKIRMGVVAAVVRFALLVFGGVGALVGKTPLMRSCVRVLIGGWMAMAITFGFTKLIGTTGL