AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062050

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062050.t1 MTR_2g045700 88.764 178 20 0 1 178 94 271 5.37e-107 307
MS.gene062050.t1 MTR_2g045670 80.899 178 34 0 1 178 104 281 1.33e-96 281
MS.gene062050.t1 MTR_2g045630 76.842 190 27 2 1 177 92 277 1.07e-93 274
MS.gene062050.t1 MTR_1g034500 76.536 179 41 1 1 178 129 307 1.99e-89 264
MS.gene062050.t1 MTR_8g077950 41.250 80 47 0 93 172 200 279 2.06e-14 69.7
MS.gene062050.t1 MTR_8g077950 41.250 80 47 0 93 172 258 337 2.50e-14 69.7
MS.gene062050.t1 MTR_8g077950 41.250 80 47 0 93 172 260 339 2.70e-14 69.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062050.t1 AT4G36730 37.500 80 50 0 93 172 220 299 1.97e-13 67.4
MS.gene062050.t1 AT4G36730 37.500 80 50 0 93 172 222 301 2.10e-13 67.0

Find 26 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTGGGCTGGCTCAGAATT+TGG 0.128488 2.3:+44831777 MS.gene062050:CDS
TCTGGGCTGGCTCAGAATTT+GGG 0.215332 2.3:+44831778 MS.gene062050:CDS
CATAGATCTAACATGATTAT+TGG 0.266335 2.3:+44831624 MS.gene062050:CDS
GCTCAGCGAGCGTTTGTGTT+AGG 0.282879 2.3:-44833047 None:intergenic
CTCAATTAAATCGCTTTCAT+TGG 0.341910 2.3:-44833094 None:intergenic
TTCTTTGTAGAAAATCCATC+TGG 0.342852 2.3:+44831760 MS.gene062050:intron
GAAGAGCTAGTTAAAGAGTA+TGG 0.371404 2.3:+44833268 MS.gene062050:CDS
GATCTATGCTTCATACTTGA+AGG 0.385946 2.3:-44831609 None:intergenic
AAGATCAAAGATAAAGAAAC+AGG 0.437513 2.3:+44832863 MS.gene062050:CDS
CTTCTGCATCAAAACATGAC+AGG 0.499536 2.3:+44831280 MS.gene062050:CDS
CTGGGCTGGCTCAGAATTTG+GGG 0.503925 2.3:+44831779 MS.gene062050:CDS
CAATGAAAGCGATTTAATTG+AGG 0.517077 2.3:+44833095 MS.gene062050:CDS
AAATTCTGAGCCAGCCCAGA+TGG 0.526322 2.3:-44831775 None:intergenic
TGTAGAAAATCCATCTGGGC+TGG 0.535016 2.3:+44831765 MS.gene062050:intron
GAACAAATTGTACCTCATTG+AGG 0.556643 2.3:-44831310 None:intergenic
TCTAACATGATTATTGGTGA+TGG 0.561546 2.3:+44831630 MS.gene062050:CDS
CCGCGCAGGGCAGGAAGTGA+AGG 0.563398 2.3:+44831392 MS.gene062050:intron
TCTTTGTAGAAAATCCATCT+GGG 0.584157 2.3:+44831761 MS.gene062050:intron
AGCGAGCGTTTGTGTTAGGA+CGG 0.589890 2.3:-44833043 None:intergenic
GAAGGTAAGAGATCAACAGA+AGG 0.599437 2.3:+44831410 MS.gene062050:CDS
GCATCAAAACATGACAGGGA+TGG 0.609695 2.3:+44831285 MS.gene062050:CDS
CCATCACAAAAGATTCAAGT+AGG 0.623667 2.3:-44833325 None:intergenic
TTCTGCATCAAAACATGACA+GGG 0.624706 2.3:+44831281 MS.gene062050:CDS
GAATTTGGGGACAGTCGTCA+AGG 0.625862 2.3:+44831792 MS.gene062050:CDS
TCAAAAGATAGACACTCTCA+AGG 0.627438 2.3:+44833011 MS.gene062050:CDS
ACAGGGATGGAACCTCAATG+AGG 0.714168 2.3:+44831298 MS.gene062050:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATTTAAGAAAATAGAA+GGG + chr2.3:44832380-44832399 MS.gene062050:intron 10.0%
!! ATAAAATTGAACAATTAATA+AGG - chr2.3:44833138-44833157 None:intergenic 10.0%
!! TAAAATTGAACAATTAATAA+GGG - chr2.3:44833137-44833156 None:intergenic 10.0%
!! TAATAATTTAAGAAAATAGA+AGG + chr2.3:44832379-44832398 MS.gene062050:intron 10.0%
!!! CTATTTTCTTAAATTATTAT+TGG - chr2.3:44832378-44832397 None:intergenic 10.0%
!!! GATTAATTTTAATATAAATG+TGG + chr2.3:44831466-44831485 MS.gene062050:intron 10.0%
!! AAAATTGAACAATTAATAAG+GGG - chr2.3:44833136-44833155 None:intergenic 15.0%
!! AAGAAAGTTGGATTTATAAA+CGG - chr2.3:44832752-44832771 None:intergenic 20.0%
!! AAGTTAACTTAATAAAAGAC+TGG - chr2.3:44831943-44831962 None:intergenic 20.0%
!!! TATAGATTTTATTCAATGAC+TGG - chr2.3:44832043-44832062 None:intergenic 20.0%
! AACATATTTAGCTAGAAAGT+TGG - chr2.3:44832632-44832651 None:intergenic 25.0%
! AAGATCAAAGATAAAGAAAC+AGG + chr2.3:44832863-44832882 MS.gene062050:CDS 25.0%
! ACATGTTACAAACATGTTAT+AGG + chr2.3:44832110-44832129 MS.gene062050:intron 25.0%
! ATAGTACAAGTGAAAAATTG+AGG + chr2.3:44832430-44832449 MS.gene062050:intron 25.0%
! CATAGATCTAACATGATTAT+TGG + chr2.3:44831624-44831643 MS.gene062050:CDS 25.0%
! CTAAAATTTGAATGTTCAGA+AGG + chr2.3:44831718-44831737 MS.gene062050:intron 25.0%
! TGATGCTCAACTAAAAAATA+TGG + chr2.3:44831837-44831856 MS.gene062050:CDS 25.0%
!! ACGAATACTGATTATAACTA+TGG - chr2.3:44832603-44832622 None:intergenic 25.0%
!! GTAATTTTGCATAATAGCAT+AGG - chr2.3:44832470-44832489 None:intergenic 25.0%
!! GTACTATTTTCTTACACTTT+TGG - chr2.3:44832417-44832436 None:intergenic 25.0%
!!! ACTTTCTAGCTAAATATGTT+TGG + chr2.3:44832632-44832651 MS.gene062050:intron 25.0%
AAAGAAAAAGACTGTCAAAC+AGG + chr2.3:44832829-44832848 MS.gene062050:CDS 30.0%
AAAGTTGGATTTATAAACGG+TGG - chr2.3:44832749-44832768 None:intergenic 30.0%
AACTAAACTGAGCAACATTA+AGG - chr2.3:44832682-44832701 None:intergenic 30.0%
ACTAAACTGAGCAACATTAA+GGG - chr2.3:44832681-44832700 None:intergenic 30.0%
CAATGAAAGCGATTTAATTG+AGG + chr2.3:44833095-44833114 MS.gene062050:CDS 30.0%
CTAACTTCTTAAGATAACAC+TGG - chr2.3:44831514-44831533 None:intergenic 30.0%
CTCAATTAAATCGCTTTCAT+TGG - chr2.3:44833097-44833116 None:intergenic 30.0%
CTTAAGAAGTTAGAACACTT+GGG + chr2.3:44831521-44831540 MS.gene062050:intron 30.0%
CTTAGCAACATTAAGAAAGT+TGG - chr2.3:44832764-44832783 None:intergenic 30.0%
GTTACAAACATGTTATAGGA+AGG + chr2.3:44832114-44832133 MS.gene062050:intron 30.0%
TCTAACATGATTATTGGTGA+TGG + chr2.3:44831630-44831649 MS.gene062050:CDS 30.0%
TCTTAAGAAGTTAGAACACT+TGG + chr2.3:44831520-44831539 MS.gene062050:intron 30.0%
TCTTCATATTCTTTCTGTCA+AGG - chr2.3:44832985-44833004 None:intergenic 30.0%
TCTTTGTAGAAAATCCATCT+GGG + chr2.3:44831761-44831780 MS.gene062050:intron 30.0%
TTATAATCAGTATTCGTGAG+TGG + chr2.3:44832606-44832625 MS.gene062050:intron 30.0%
TTCTTTGTAGAAAATCCATC+TGG + chr2.3:44831760-44831779 MS.gene062050:intron 30.0%
! AAACGGTGGTAACATTTTAT+AGG - chr2.3:44832735-44832754 None:intergenic 30.0%
! CTTTAGTACATCCTTTTCTT+TGG + chr2.3:44831577-44831596 MS.gene062050:intron 30.0%
! GGATTTTCTACAAAGAAACA+AGG - chr2.3:44831757-44831776 None:intergenic 30.0%
! TTAGTTGCATTTCTTTTGAC+AGG + chr2.3:44832785-44832804 MS.gene062050:intron 30.0%
!! TATTGGTGATGGTAAGATTA+TGG + chr2.3:44831641-44831660 MS.gene062050:intron 30.0%
ACATGGTTGTCTAGACTTAT+TGG - chr2.3:44832307-44832326 None:intergenic 35.0%
ACTCAAATTAGGAGCAATCT+TGG - chr2.3:44833228-44833247 None:intergenic 35.0%
CACCAAATCACACTCAAATT+AGG - chr2.3:44833239-44833258 None:intergenic 35.0%
CATCATTATATCGCCTATAG+CGG - chr2.3:44832195-44832214 None:intergenic 35.0%
CTAAGCATATCTAGCAAGAT+TGG - chr2.3:44832568-44832587 None:intergenic 35.0%
CTCCTAATTTGAGTGTGATT+TGG + chr2.3:44833234-44833253 MS.gene062050:intron 35.0%
GAACAAATTGTACCTCATTG+AGG - chr2.3:44831313-44831332 None:intergenic 35.0%
GAAGAGCTAGTTAAAGAGTA+TGG + chr2.3:44833268-44833287 MS.gene062050:CDS 35.0%
GATCTATGCTTCATACTTGA+AGG - chr2.3:44831612-44831631 None:intergenic 35.0%
GTACAAGTGAAAAATTGAGG+TGG + chr2.3:44832433-44832452 MS.gene062050:intron 35.0%
GTCTAACAAAGAGAGATCAA+AGG - chr2.3:44833189-44833208 None:intergenic 35.0%
TCAAAAGATAGACACTCTCA+AGG + chr2.3:44833011-44833030 MS.gene062050:CDS 35.0%
TTCTGCATCAAAACATGACA+GGG + chr2.3:44831281-44831300 MS.gene062050:CDS 35.0%
! AAACGATTTTGTTCAGGCTT+TGG - chr2.3:44831370-44831389 None:intergenic 35.0%
! CTAATTTGAGTGTGATTTGG+TGG + chr2.3:44833237-44833256 MS.gene062050:intron 35.0%
!! AAAGTCTTGTTCCTAACACA+TGG - chr2.3:44832324-44832343 None:intergenic 35.0%
!! CTAGATATGCTTAGCTTTGT+TGG + chr2.3:44832574-44832593 MS.gene062050:intron 35.0%
AGAAACAGGTACATACGACA+AGG + chr2.3:44832877-44832896 MS.gene062050:intron 40.0%
AGTAGACTACACAAAACGAC+TGG - chr2.3:44832241-44832260 None:intergenic 40.0%
AGTCTAGACAACCATGTGTT+AGG + chr2.3:44832310-44832329 MS.gene062050:intron 40.0%
CTATTGACAACACCAGTTAC+AGG + chr2.3:44832259-44832278 MS.gene062050:intron 40.0%
CTTCTGCATCAAAACATGAC+AGG + chr2.3:44831280-44831299 MS.gene062050:CDS 40.0%
GAAGGTAAGAGATCAACAGA+AGG + chr2.3:44831410-44831429 MS.gene062050:CDS 40.0%
! AGTACATCCTTTTCTTTGGC+AGG + chr2.3:44831581-44831600 MS.gene062050:intron 40.0%
! GATGCGTAGTGGAATTTGAA+TGG + chr2.3:44832211-44832230 MS.gene062050:intron 40.0%
! GCGGATAAACGATTTTGTTC+AGG - chr2.3:44831376-44831395 None:intergenic 40.0%
!!! CATGTTTTGATGCAGAAGAC+AGG - chr2.3:44831278-44831297 None:intergenic 40.0%
ACAAAATCGTTTATCCGCGC+AGG + chr2.3:44831378-44831397 MS.gene062050:intron 45.0%
ACACATACCTAGTGTGTCAG+TGG - chr2.3:44832507-44832526 None:intergenic 45.0%
AGGTACATACGACAAGGCTT+TGG + chr2.3:44832883-44832902 MS.gene062050:intron 45.0%
CAAAATCGTTTATCCGCGCA+GGG + chr2.3:44831379-44831398 MS.gene062050:intron 45.0%
GCATCAAAACATGACAGGGA+TGG + chr2.3:44831285-44831304 MS.gene062050:CDS 45.0%
GGCGATATAATGATGCGTAG+TGG + chr2.3:44832200-44832219 MS.gene062050:intron 45.0%
GTCAGTGGCGCATATCATAT+GGG - chr2.3:44832492-44832511 None:intergenic 45.0%
TGTAGAAAATCCATCTGGGC+TGG + chr2.3:44831765-44831784 MS.gene062050:intron 45.0%
TGTCAGTGGCGCATATCATA+TGG - chr2.3:44832493-44832512 None:intergenic 45.0%
AAATTCTGAGCCAGCCCAGA+TGG - chr2.3:44831778-44831797 None:intergenic 50.0%
ACAGGGATGGAACCTCAATG+AGG + chr2.3:44831298-44831317 MS.gene062050:CDS 50.0%
AGCGAGCGTTTGTGTTAGGA+CGG - chr2.3:44833046-44833065 None:intergenic 50.0%
ATATGCGCCACTGACACACT+AGG + chr2.3:44832497-44832516 MS.gene062050:intron 50.0%
GAATTTGGGGACAGTCGTCA+AGG + chr2.3:44831792-44831811 MS.gene062050:CDS 50.0%
GGAGAGTCCTGCCAAAGAAA+AGG - chr2.3:44831591-44831610 None:intergenic 50.0%
TGTGATACGCTAGCCGCTAT+AGG + chr2.3:44832179-44832198 MS.gene062050:intron 50.0%
!! ATCTGGGCTGGCTCAGAATT+TGG + chr2.3:44831777-44831796 MS.gene062050:CDS 50.0%
!! GTGTGATTTGGTGGTCGAAC+AGG + chr2.3:44833246-44833265 MS.gene062050:intron 50.0%
!! TCTGGGCTGGCTCAGAATTT+GGG + chr2.3:44831778-44831797 MS.gene062050:CDS 50.0%
ACACCAGTTACAGGCGCTCT+TGG + chr2.3:44832268-44832287 MS.gene062050:intron 55.0%
CACCAGTTACAGGCGCTCTT+GGG + chr2.3:44832269-44832288 MS.gene062050:intron 55.0%
GCTCAGCGAGCGTTTGTGTT+AGG - chr2.3:44833050-44833069 None:intergenic 55.0%
TTACAGGCGCTCTTGGGACT+TGG + chr2.3:44832275-44832294 MS.gene062050:intron 55.0%
!! CTGGGCTGGCTCAGAATTTG+GGG + chr2.3:44831779-44831798 MS.gene062050:CDS 55.0%
ATCGTTTATCCGCGCAGGGC+AGG + chr2.3:44831383-44831402 MS.gene062050:intron 60.0%
!! GTCCCAAGAGCGCCTGTAAC+TGG - chr2.3:44832274-44832293 None:intergenic 60.0%
CCTTCACTTCCTGCCCTGCG+CGG - chr2.3:44831395-44831414 None:intergenic 65.0%
CCGCGCAGGGCAGGAAGTGA+AGG + chr2.3:44831392-44831411 MS.gene062050:intron 70.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 44831246 44833333 44831246 ID=MS.gene062050
chr2.3 mRNA 44831246 44833333 44831246 ID=MS.gene062050.t1;Parent=MS.gene062050
chr2.3 exon 44831246 44831319 44831246 ID=MS.gene062050.t1.exon1;Parent=MS.gene062050.t1
chr2.3 CDS 44831246 44831319 44831246 ID=cds.MS.gene062050.t1;Parent=MS.gene062050.t1
chr2.3 exon 44831400 44831454 44831400 ID=MS.gene062050.t1.exon2;Parent=MS.gene062050.t1
chr2.3 CDS 44831400 44831454 44831400 ID=cds.MS.gene062050.t1;Parent=MS.gene062050.t1
chr2.3 exon 44831603 44831651 44831603 ID=MS.gene062050.t1.exon3;Parent=MS.gene062050.t1
chr2.3 CDS 44831603 44831651 44831603 ID=cds.MS.gene062050.t1;Parent=MS.gene062050.t1
chr2.3 exon 44831770 44831858 44831770 ID=MS.gene062050.t1.exon4;Parent=MS.gene062050.t1
chr2.3 CDS 44831770 44831858 44831770 ID=cds.MS.gene062050.t1;Parent=MS.gene062050.t1
chr2.3 exon 44832807 44832884 44832807 ID=MS.gene062050.t1.exon5;Parent=MS.gene062050.t1
chr2.3 CDS 44832807 44832884 44832807 ID=cds.MS.gene062050.t1;Parent=MS.gene062050.t1
chr2.3 exon 44832991 44833116 44832991 ID=MS.gene062050.t1.exon6;Parent=MS.gene062050.t1
chr2.3 CDS 44832991 44833116 44832991 ID=cds.MS.gene062050.t1;Parent=MS.gene062050.t1
chr2.3 exon 44833268 44833333 44833268 ID=MS.gene062050.t1.exon7;Parent=MS.gene062050.t1
chr2.3 CDS 44833268 44833333 44833268 ID=cds.MS.gene062050.t1;Parent=MS.gene062050.t1
Gene Sequence

>MS.gene062050

ATGACTGGTGAATCAAGAGAATATGCAAACCTGTCTTCTGCATCAAAACATGACAGGGATGGAACCTCAATGAGGTACAATTTGTTCTTGTTCTTCTGATAAACTTGTTAATAGCATTTTTCCAAAGCCTGAACAAAATCGTTTATCCGCGCAGGGCAGGAAGTGAAGGTAAGAGATCAACAGAAGGAGATCAAGATGATAGTAACAAAGTATGTTTATCGATTAATTTTAATATAAATGTGGTTGATGAATGTATTGTTTTCTGCCAGTGTTATCTTAAGAAGTTAGAACACTTGGGAATGAGAGTAGTTTATTAAAGCTTTAAAATTTTCTTTAGTACATCCTTTTCTTTGGCAGGACTCTCCTTCAAGTATGAAGCATAGATCTAACATGATTATTGGTGATGGTAAGATTATGGATTTTTCTTTTGATTATCTTATAATAAGAATTCATGTTTTTATTTTTTTTTAATCTAAAATTTGAATGTTCAGAAGGTGACAGTCTTGCTCCTTGTTTCTTTGTAGAAAATCCATCTGGGCTGGCTCAGAATTTGGGGACAGTCGTCAAGGAATCTGACACTGACATTGATGTTGATGCTCAACTAAAAAATATGGTATTATAAAGTTTTATGCGTTTTTGTAGCATAAATGATTTTTTTTTTTTTTTTTGTGAATTAGCTAAACTAGAAGAACAACCAGTCTTTTATTAAGTTAACTTGCGTTCTCTTTTGAATCATTATATTGTGCACATACAAACATATTCTCTCATACAAACATGTTCTCTCATACAAACAACCAGTCATTGAATAAAATCTATATTATTAAGTTAACTTGTTAATTAGCTAAACTTGAAAATCTCAATTCAACATGTTACAAACATGTTATAGGAAGGAAGTGTTCTTAAGTTGAATTTTTTTAAAAAATCACTAATGTTTGTGATACGCTAGCCGCTATAGGCGATATAATGATGCGTAGTGGAATTTGAATGGACTGCCAGTCGTTTTGTGTAGTCTACTATTGACAACACCAGTTACAGGCGCTCTTGGGACTTGGTCTTTTCCAATAAGTCTAGACAACCATGTGTTAGGAACAAGACTTTTTTAGAACTATAAAACACAAACATGTAGACACCAATAATAATTTAAGAAAATAGAAGGGACTAAATGTAACCAAAAGTGTAAGAAAATAGTACAAGTGAAAAATTGAGGTGGCAAAAATAAAACCTATGCTATTATGCAAAATTACCCATATGATATGCGCCACTGACACACTAGGTATGTGTGTGTGTGTGTGTGTATTTAAATTGTTTATTTTCTATCTCCAATCTTGCTAGATATGCTTAGCTTTGTTGGCTGCCATAGTTATAATCAGTATTCGTGAGTGGCCAACTTTCTAGCTAAATATGTTTGGTGTATACATTTCAGAAAGTAAATCCCTTAATGTTGCTCAGTTTAGTTACATTTCTTGCACAATATTGTCTAGCATTTCCTATAAAATGTTACCACCGTTTATAAATCCAACTTTCTTAATGTTGCTAAGTTTAGTTGCATTTCTTTTGACAGGAAGTTGATGAAATAAGAAAAGAAAGAAAAAGACTGTCAAACAGGAAATCAGCTAAAAGATCAAAGATAAAGAAACAGGTACATACGACAAGGCTTTGGTTGAGTATGATTAAAGTTTAAAAATAAAACAGATGTGTTTGTTTGATAATCTATTTATCTTTGTATTTCATTTGTGCCTTGACAGAAAGAATATGAAGAGCTGTGTCAAAAGATAGACACTCTCAAGGATGAAAATTCCGTCCTAACACAAACGCTCGCTGAGCTTTCTGAGAAATGTCTTGAGCTCACCAATGAAAGCGATTTAATTGAGGTCAATCATTTTAACTCCCCTTATTAATTGTTCAATTTTATATCAGTCATTAAACTAAGATACTTATATCCTTTGATCTCTCTTTGTTAGACGACAATTATTTATTTTCCAAGATTGCTCCTAATTTGAGTGTGATTTGGTGGTCGAACAGGAAGAGCTAGTTAAAGAGTATGGAACAGAATCAATTGCAGATATATTGCACATGAAGCCTACTTGA
Protein sequence

>MS.gene062050.t1

MTGESREYANLSSASKHDRDGTSMRAGSEGKRSTEGDQDDSNKDSPSSMKHRSNMIIGDENPSGLAQNLGTVVKESDTDIDVDAQLKNMEVDEIRKERKRLSNRKSAKRSKIKKQKEYEELCQKIDTLKDENSVLTQTLAELSEKCLELTNESDLIEEELVKEYGTESIADILHMKPT