AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028403

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028403.t1 MTR_4g094332 94.643 224 12 0 1 224 1 224 2.75e-136 381
MS.gene028403.t1 MTR_4g094328 93.304 224 15 0 1 224 1 224 1.37e-132 372
MS.gene028403.t1 MTR_4g094330 93.304 224 15 0 1 224 1 224 1.37e-132 372
MS.gene028403.t1 MTR_1g099010 66.169 201 64 1 24 224 21 217 9.89e-90 263
MS.gene028403.t1 MTR_6g034975 65.550 209 69 2 16 224 5 210 9.76e-87 255
MS.gene028403.t1 MTR_4g094325 62.857 210 74 2 15 224 34 239 3.03e-84 250
MS.gene028403.t1 MTR_0119s0010 61.579 190 64 1 30 219 27 207 1.26e-72 220
MS.gene028403.t1 MTR_0119s0020 61.579 190 64 1 30 219 27 207 1.26e-72 220
MS.gene028403.t1 MTR_2g008110 61.579 190 64 1 30 219 27 207 1.60e-72 219
MS.gene028403.t1 MTR_4g094335 57.073 205 79 2 18 219 27 225 1.95e-70 215
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028403.t1 AT3G43660 63.959 197 62 2 29 224 10 198 5.03e-91 266
MS.gene028403.t1 AT3G43630 62.312 199 66 2 24 221 4 194 1.82e-80 239
MS.gene028403.t1 AT1G21140 62.827 191 63 1 34 224 18 200 6.05e-80 238
MS.gene028403.t1 AT1G76800 62.500 200 66 1 25 224 6 196 2.29e-79 236
MS.gene028403.t1 AT3G25190 64.455 211 69 2 18 224 9 217 1.07e-74 225

Find 52 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGCTATGGCCATTACTTT+TGG 0.296297 4.2:+18618277 MS.gene028403:CDS
TCTTGTGTTAGAGTGCTTAT+TGG 0.298679 4.2:+18618247 MS.gene028403:CDS
TGTGGTTAGCTTTGCATTGT+TGG 0.307872 4.2:+18618177 MS.gene028403:CDS
TCCAGTAGAACCAATCAATT+TGG 0.330667 4.2:-18618305 None:intergenic
AGCTTTGCATTGTTGGTGTT+TGG 0.347559 4.2:+18618184 MS.gene028403:CDS
TTCAAAGGGCACAGTGGCTT+AGG 0.366043 4.2:+18617780 MS.gene028403:CDS
TGGCTTAGGGCAGCCATGTT+AGG 0.370873 4.2:+18617794 MS.gene028403:CDS
ACCAAATTGATTGGTTCTAC+TGG 0.370878 4.2:+18618304 MS.gene028403:CDS
TTTGGTTTCACCAAATTGAT+TGG 0.383690 4.2:+18618295 MS.gene028403:CDS
ATCTCAACCTCAAAATTGTT+TGG 0.384795 4.2:-18617698 None:intergenic
AGGGCTGCTTGAAATGGATT+TGG 0.388581 4.2:-18618058 None:intergenic
ATCAAAGTAATGCTCCTTGC+TGG 0.393708 4.2:+18617881 MS.gene028403:CDS
GATGCTAGGGCTGCTTGAAA+TGG 0.413748 4.2:-18618064 None:intergenic
ATGCTCCTTGCTGGTTTCGC+TGG 0.425505 4.2:+18617890 MS.gene028403:CDS
GTTTGGAGGAGTGGGAGCAT+TGG 0.437850 4.2:+18618201 MS.gene028403:CDS
TCCTTCATGGCCTCCCACCT+TGG 0.453012 4.2:+18617653 None:intergenic
CAACATTGATTACTTTCAAA+GGG 0.466059 4.2:+18617766 MS.gene028403:CDS
GGTTTCGCTGGTTTAGTAGC+CGG 0.470478 4.2:+18617902 MS.gene028403:CDS
TCAAAGGGCACAGTGGCTTA+GGG 0.472665 4.2:+18617781 MS.gene028403:CDS
AACAGTGATTAGTCCATCAT+TGG 0.482821 4.2:-18617819 None:intergenic
TTAGAGTGCTTATTGGTGGT+TGG 0.485640 4.2:+18618254 MS.gene028403:CDS
TTGTTGGTGTTTGGAGGAGT+GGG 0.488776 4.2:+18618193 MS.gene028403:CDS
TGATGATGAAAGTACTGAAA+AGG 0.488855 4.2:+18618027 MS.gene028403:CDS
ACAACATTGATTACTTTCAA+AGG 0.489039 4.2:+18617765 MS.gene028403:CDS
AAGAATCACAAAATCAGAAT+GGG 0.491528 4.2:+18618142 MS.gene028403:CDS
AAAATGCCAGTGCTGATGCT+AGG 0.492361 4.2:-18618078 None:intergenic
AAAGAATCACAAAATCAGAA+TGG 0.497277 4.2:+18618141 MS.gene028403:CDS
TTTGCATTGTTGGTGTTTGG+AGG 0.499902 4.2:+18618187 MS.gene028403:CDS
GGAGGAGTGGGAGCATTGGT+TGG 0.501548 4.2:+18618205 MS.gene028403:CDS
ATTGTTGGTGTTTGGAGGAG+TGG 0.501761 4.2:+18618192 MS.gene028403:CDS
AGAAAACTATTAGCATGGAT+AGG 0.502706 4.2:-18617722 None:intergenic
TGTGTTAGAGTGCTTATTGG+TGG 0.506211 4.2:+18618250 MS.gene028403:CDS
GCATCGTTGATGATTGGTGT+TGG 0.506584 4.2:+18617842 MS.gene028403:CDS
TATTGGTGGTTGGATGGCTA+TGG 0.515341 4.2:+18618264 MS.gene028403:CDS
ACTGTTGCATCGTTGATGAT+TGG 0.516876 4.2:+18617836 MS.gene028403:CDS
AACCTCAAAATTGTTTGGTG+AGG 0.527938 4.2:-18617693 None:intergenic
GAAAACTATTAGCATGGATA+GGG 0.536330 4.2:-18617721 None:intergenic
AGTGCTTATTGGTGGTTGGA+TGG 0.539553 4.2:+18618258 MS.gene028403:CDS
TTTGGTGAAACCAAAAGTAA+TGG 0.542621 4.2:-18618287 None:intergenic
TCCATCATTGGCTCCTAACA+TGG 0.543290 4.2:-18617807 None:intergenic
CTTTGAGAAAACTATTAGCA+TGG 0.548309 4.2:-18617727 None:intergenic
GGTGCTTGTAGCATGGCAAT+TGG 0.557712 4.2:+18617923 MS.gene028403:CDS
AGCAGCCCTAGCATCAGCAC+TGG 0.559205 4.2:+18618072 MS.gene028403:CDS
ATAAATGCAGCTGCTAGCAA+TGG 0.565330 4.2:-18618118 None:intergenic
AAATGCCAGTGCTGATGCTA+GGG 0.565337 4.2:-18618077 None:intergenic
AATTGCCATGCTACAAGCAC+CGG 0.567135 4.2:-18617921 None:intergenic
AGTAGCCGGTGCTTGTAGCA+TGG 0.572629 4.2:+18617916 MS.gene028403:CDS
GCCATGTTAGGAGCCAATGA+TGG 0.577904 4.2:+18617806 MS.gene028403:CDS
CTAACACAAGACCTCATCAA+AGG 0.611245 4.2:-18618235 None:intergenic
AATGGGAGTTGTAGCTGCTG+TGG 0.646963 4.2:+18618159 MS.gene028403:CDS
CTAAACCAGCGAAACCAGCA+AGG 0.672858 4.2:-18617895 None:intergenic
ATTACTTTCAAAGGGCACAG+TGG 0.699406 4.2:+18617774 MS.gene028403:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAGAATCACAAAATCAGAA+TGG + chr4.2:18618141-18618160 MS.gene028403:CDS 25.0%
! AAGAATCACAAAATCAGAAT+GGG + chr4.2:18618142-18618161 MS.gene028403:CDS 25.0%
!! ACAACATTGATTACTTTCAA+AGG + chr4.2:18617765-18617784 MS.gene028403:CDS 25.0%
!! CAACATTGATTACTTTCAAA+GGG + chr4.2:18617766-18617785 MS.gene028403:CDS 25.0%
AGAAAACTATTAGCATGGAT+AGG - chr4.2:18617725-18617744 None:intergenic 30.0%
ATCTCAACCTCAAAATTGTT+TGG - chr4.2:18617701-18617720 None:intergenic 30.0%
GAAAACTATTAGCATGGATA+GGG - chr4.2:18617724-18617743 None:intergenic 30.0%
TTTGGTGAAACCAAAAGTAA+TGG - chr4.2:18618290-18618309 None:intergenic 30.0%
! CTTTGAGAAAACTATTAGCA+TGG - chr4.2:18617730-18617749 None:intergenic 30.0%
! TTTGGTTTCACCAAATTGAT+TGG + chr4.2:18618295-18618314 MS.gene028403:CDS 30.0%
!! TGATGATGAAAGTACTGAAA+AGG + chr4.2:18618027-18618046 MS.gene028403:CDS 30.0%
CACCTTGGAGAAAAAACTAA+CGG + chr4.2:18617668-18617687 MS.gene028403:CDS 35.0%
TCCAGTAGAACCAATCAATT+TGG - chr4.2:18618308-18618327 None:intergenic 35.0%
TTGGAAAAACTCCTTTGATG+AGG + chr4.2:18618224-18618243 MS.gene028403:CDS 35.0%
! AACAGTGATTAGTCCATCAT+TGG - chr4.2:18617822-18617841 None:intergenic 35.0%
! AACCTCAAAATTGTTTGGTG+AGG - chr4.2:18617696-18617715 None:intergenic 35.0%
! AACCTCACCAAACAATTTTG+AGG + chr4.2:18617691-18617710 MS.gene028403:CDS 35.0%
! TCTTGTGTTAGAGTGCTTAT+TGG + chr4.2:18618247-18618266 MS.gene028403:CDS 35.0%
!! ACCAAATTGATTGGTTCTAC+TGG + chr4.2:18618304-18618323 MS.gene028403:CDS 35.0%
!!! GTTAGTTTTTTCTCCAAGGT+GGG - chr4.2:18617669-18617688 None:intergenic 35.0%
!!! TTCCGTTAGTTTTTTCTCCA+AGG - chr4.2:18617673-18617692 None:intergenic 35.0%
ATAAATGCAGCTGCTAGCAA+TGG - chr4.2:18618121-18618140 None:intergenic 40.0%
ATCAAAGTAATGCTCCTTGC+TGG + chr4.2:18617881-18617900 MS.gene028403:CDS 40.0%
CTAACACAAGACCTCATCAA+AGG - chr4.2:18618238-18618257 None:intergenic 40.0%
! AGCTTTGCATTGTTGGTGTT+TGG + chr4.2:18618184-18618203 MS.gene028403:CDS 40.0%
! ATGGCTATGGCCATTACTTT+TGG + chr4.2:18618277-18618296 MS.gene028403:CDS 40.0%
! ATTACTTTCAAAGGGCACAG+TGG + chr4.2:18617774-18617793 MS.gene028403:CDS 40.0%
! TGTGTTAGAGTGCTTATTGG+TGG + chr4.2:18618250-18618269 MS.gene028403:CDS 40.0%
! TTAGAGTGCTTATTGGTGGT+TGG + chr4.2:18618254-18618273 MS.gene028403:CDS 40.0%
! TTTGCATTGTTGGTGTTTGG+AGG + chr4.2:18618187-18618206 MS.gene028403:CDS 40.0%
!! ACTGTTGCATCGTTGATGAT+TGG + chr4.2:18617836-18617855 MS.gene028403:CDS 40.0%
!! TGTGGTTAGCTTTGCATTGT+TGG + chr4.2:18618177-18618196 MS.gene028403:CDS 40.0%
!!! CGTTAGTTTTTTCTCCAAGG+TGG - chr4.2:18617670-18617689 None:intergenic 40.0%
AATTGCCATGCTACAAGCAC+CGG - chr4.2:18617924-18617943 None:intergenic 45.0%
! AGGGCTGCTTGAAATGGATT+TGG - chr4.2:18618061-18618080 None:intergenic 45.0%
! AGTGCTTATTGGTGGTTGGA+TGG + chr4.2:18618258-18618277 MS.gene028403:CDS 45.0%
! ATTGTTGGTGTTTGGAGGAG+TGG + chr4.2:18618192-18618211 MS.gene028403:CDS 45.0%
! TATTGGTGGTTGGATGGCTA+TGG + chr4.2:18618264-18618283 MS.gene028403:CDS 45.0%
! TTGTTGGTGTTTGGAGGAGT+GGG + chr4.2:18618193-18618212 MS.gene028403:CDS 45.0%
!! AAAATGCCAGTGCTGATGCT+AGG - chr4.2:18618081-18618100 None:intergenic 45.0%
!! AAATGCCAGTGCTGATGCTA+GGG - chr4.2:18618080-18618099 None:intergenic 45.0%
!! GCATCGTTGATGATTGGTGT+TGG + chr4.2:18617842-18617861 MS.gene028403:CDS 45.0%
!! TCCATCATTGGCTCCTAACA+TGG - chr4.2:18617810-18617829 None:intergenic 45.0%
!!! AGTTTTTTCTCCAAGGTGGG+AGG - chr4.2:18617666-18617685 None:intergenic 45.0%
!!! TCAGCACTGGCATTTTCTGT+TGG + chr4.2:18618085-18618104 MS.gene028403:CDS 45.0%
AATGGGAGTTGTAGCTGCTG+TGG + chr4.2:18618159-18618178 MS.gene028403:CDS 50.0%
CTAAACCAGCGAAACCAGCA+AGG - chr4.2:18617898-18617917 None:intergenic 50.0%
GATGCTAGGGCTGCTTGAAA+TGG - chr4.2:18618067-18618086 None:intergenic 50.0%
GCCATGTTAGGAGCCAATGA+TGG + chr4.2:18617806-18617825 MS.gene028403:CDS 50.0%
GGTGCTTGTAGCATGGCAAT+TGG + chr4.2:18617923-18617942 MS.gene028403:CDS 50.0%
! TCAAAGGGCACAGTGGCTTA+GGG + chr4.2:18617781-18617800 MS.gene028403:CDS 50.0%
! TTCAAAGGGCACAGTGGCTT+AGG + chr4.2:18617780-18617799 MS.gene028403:CDS 50.0%
!! GGTTTCGCTGGTTTAGTAGC+CGG + chr4.2:18617902-18617921 MS.gene028403:CDS 50.0%
AGTAGCCGGTGCTTGTAGCA+TGG + chr4.2:18617916-18617935 MS.gene028403:CDS 55.0%
TGGCTTAGGGCAGCCATGTT+AGG + chr4.2:18617794-18617813 MS.gene028403:CDS 55.0%
! GTTTGGAGGAGTGGGAGCAT+TGG + chr4.2:18618201-18618220 MS.gene028403:CDS 55.0%
!! ATGCTCCTTGCTGGTTTCGC+TGG + chr4.2:18617890-18617909 MS.gene028403:CDS 55.0%
AGCAGCCCTAGCATCAGCAC+TGG + chr4.2:18618072-18618091 MS.gene028403:CDS 60.0%
!! GGAGGAGTGGGAGCATTGGT+TGG + chr4.2:18618205-18618224 MS.gene028403:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 18617659 18618333 18617659 ID=MS.gene028403
chr4.2 mRNA 18617659 18618333 18617659 ID=MS.gene028403.t1;Parent=MS.gene028403
chr4.2 exon 18617659 18618333 18617659 ID=MS.gene028403.t1.exon1;Parent=MS.gene028403.t1
chr4.2 CDS 18617659 18618333 18617659 ID=cds.MS.gene028403.t1;Parent=MS.gene028403.t1
Gene Sequence

>MS.gene028403

ATGGCCTCCCACCTTGGAGAAAAAACTAACGGAACCTCACCAAACAATTTTGAGGTTGAGATCCCTATCCATGCTAATAGTTTTCTCAAAGTTGAAAAAGAGAGCAACAACATTGATTACTTTCAAAGGGCACAGTGGCTTAGGGCAGCCATGTTAGGAGCCAATGATGGACTAATCACTGTTGCATCGTTGATGATTGGTGTTGGAGCTATAAAAGAAGACATCAAAGTAATGCTCCTTGCTGGTTTCGCTGGTTTAGTAGCCGGTGCTTGTAGCATGGCAATTGGTGAGTTTGTTTCTGTTTATACTCAATATGACATTGAGATAGCTCAGATAAATAGAGAAAGAGAAGCTAATAATAATGACAATGATGATGAAAGTACTGAAAAGGAGAAATTGCCAAATCCATTTCAAGCAGCCCTAGCATCAGCACTGGCATTTTCTGTTGGTGCAGTGATGCCATTGCTAGCAGCTGCATTTATAAAGAATCACAAAATCAGAATGGGAGTTGTAGCTGCTGTGGTTAGCTTTGCATTGTTGGTGTTTGGAGGAGTGGGAGCATTGGTTGGAAAAACTCCTTTGATGAGGTCTTGTGTTAGAGTGCTTATTGGTGGTTGGATGGCTATGGCCATTACTTTTGGTTTCACCAAATTGATTGGTTCTACTGGACTTTGA
Protein sequence

>MS.gene028403.t1

MASHLGEKTNGTSPNNFEVEIPIHANSFLKVEKESNNIDYFQRAQWLRAAMLGANDGLITVASLMIGVGAIKEDIKVMLLAGFAGLVAGACSMAIGEFVSVYTQYDIEIAQINREREANNNDNDDESTEKEKLPNPFQAALASALAFSVGAVMPLLAAAFIKNHKIRMGVVAAVVSFALLVFGGVGALVGKTPLMRSCVRVLIGGWMAMAITFGFTKLIGSTGL