AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene98410

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98410.t1 MTR_2g045630 88.421 190 17 2 1 189 92 277 2.66e-113 324
MS.gene98410.t1 MTR_2g045670 77.487 191 29 2 1 190 104 281 9.50e-95 277
MS.gene98410.t1 MTR_2g045700 77.487 191 29 2 1 190 94 271 4.11e-91 267
MS.gene98410.t1 MTR_1g034500 70.833 192 41 3 1 190 129 307 5.73e-81 243
MS.gene98410.t1 MTR_8g077950 43.750 80 44 1 106 184 258 337 1.53e-13 68.2
MS.gene98410.t1 MTR_8g077950 43.750 80 44 1 106 184 260 339 1.62e-13 67.8
MS.gene98410.t1 MTR_8g077950 43.750 80 44 1 106 184 200 279 3.28e-13 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene98410.t1 AT4G36730 40.000 80 47 1 106 184 220 299 4.73e-12 63.5
MS.gene98410.t1 AT4G36730 40.000 80 47 1 106 184 222 301 5.58e-12 63.5

Find 26 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATCTCTTCTTCATACTTAA+AGG 0.172932 2.4:-45039963 None:intergenic
CACTCTTAAGGATGAAAATT+TGG 0.215284 2.4:+45040679 MS.gene98410:CDS
ACTGGGGAATCCACTAAATA+TGG 0.264921 2.4:+45039567 MS.gene98410:CDS
AAGAGATCTAACATGATTAT+TGG 0.281485 2.4:+45039978 MS.gene98410:CDS
GTTCAGCGAGCATTTGTGTT+AGG 0.333023 2.4:-45040703 None:intergenic
GAACAAACTGTACCTCATTA+AGG 0.349941 2.4:-45039628 None:intergenic
TTCTTTGTAGAAAATCCATC+TGG 0.371434 2.4:+45040144 MS.gene98410:CDS
AAAGTTTCAAGTAGGCTTCA+TGG 0.384295 2.4:-45041234 None:intergenic
TCAAAAGATAAACACTCTTA+AGG 0.422261 2.4:+45040667 MS.gene98410:CDS
AAGATCAAAGATAAAGAAAC+AGG 0.437513 2.4:+45040446 MS.gene98410:CDS
AGACTGGTTTCCATATTTAG+TGG 0.453132 2.4:-45039577 None:intergenic
AAGTTTCAAGTAGGCTTCAT+GGG 0.491094 2.4:-45041233 None:intergenic
CTGGGATGGCTCAGAATTCG+TGG 0.491290 2.4:+45040163 MS.gene98410:CDS
CAATGAAAACGATTCTATTG+AGG 0.546332 2.4:+45040751 MS.gene98410:CDS
ACAGGAAGAGCTCGTTAAAG+AGG 0.547350 2.4:+45041184 MS.gene98410:intron
TCTAACATGATTATTGGTGA+TGG 0.571130 2.4:+45039984 MS.gene98410:CDS
GAATTCTGAGCCATCCCAGA+TGG 0.589461 2.4:-45040159 None:intergenic
TGTAGAAAATCCATCTGGGA+TGG 0.598950 2.4:+45040149 MS.gene98410:CDS
TCTTTGTAGAAAATCCATCT+GGG 0.602431 2.4:+45040145 MS.gene98410:CDS
CAGGAAGAGCTCGTTAAAGA+GGG 0.615515 2.4:+45041185 MS.gene98410:intron
CACATGAACTGCAGTTCACG+TGG 0.615775 2.4:+45040101 MS.gene98410:intron
GGAAGCATGAGATCAACAGA+TGG 0.622112 2.4:+45039728 MS.gene98410:CDS
GAATTCGTGGACAGTCGTCA+AGG 0.628246 2.4:+45040176 MS.gene98410:CDS
ATAGGGATGGAACCTTAATG+AGG 0.644156 2.4:+45039616 MS.gene98410:CDS
AGAGGGACTAGAATCAATTG+CGG 0.679585 2.4:+45041202 MS.gene98410:CDS
TGTGTGCGCAGTGCAGCAAG+TGG 0.681573 2.4:+45039707 MS.gene98410:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTATTTATTTTCCAAGAT+TGG + chr2.4:45041068-45041087 MS.gene98410:intron 15.0%
!! AAAATTGAACAAGTAAGAAA+GGG - chr2.4:45040792-45040811 None:intergenic 20.0%
!! AATAGAATCGTTTACATTAA+TGG - chr2.4:45040953-45040972 None:intergenic 20.0%
!! CAACATTTATAAATAGGAAA+TGG + chr2.4:45040497-45040516 MS.gene98410:intron 20.0%
!! GTACAGGTTATATAAAATTT+CGG + chr2.4:45039901-45039920 MS.gene98410:intron 20.0%
!! TAAAATTGAACAAGTAAGAA+AGG - chr2.4:45040793-45040812 None:intergenic 20.0%
!! TAAACTTCTTAAGATAAAAG+TGG - chr2.4:45039832-45039851 None:intergenic 20.0%
!! TACAAATATAGAAAACAAGA+TGG - chr2.4:45040878-45040897 None:intergenic 20.0%
!! TTTATAAATAGGAAATGGTT+TGG + chr2.4:45040502-45040521 MS.gene98410:intron 20.0%
!!! TTGAAATTTTTCTTTAGTAC+AGG + chr2.4:45039885-45039904 MS.gene98410:intron 20.0%
! AAACTTAGCAACATTAAGAA+GGG - chr2.4:45040312-45040331 None:intergenic 25.0%
! AAGAGATCTAACATGATTAT+TGG + chr2.4:45039978-45039997 MS.gene98410:CDS 25.0%
! AAGATCAAAGATAAAGAAAC+AGG + chr2.4:45040446-45040465 MS.gene98410:CDS 25.0%
! ACTTCTTTATAAACCAATCT+TGG - chr2.4:45041084-45041103 None:intergenic 25.0%
! CAAAAGAAATGCTACTAAAT+AGG - chr2.4:45040366-45040385 None:intergenic 25.0%
! CTATAATTTGAATGTTCAGA+AGG + chr2.4:45040064-45040083 MS.gene98410:intron 25.0%
! GCATTGCAACATTTATAAAT+AGG + chr2.4:45040491-45040510 MS.gene98410:intron 25.0%
! TAAACTTAGCAACATTAAGA+AGG - chr2.4:45040313-45040332 None:intergenic 25.0%
! TCAAAAGATAAACACTCTTA+AGG + chr2.4:45040667-45040686 MS.gene98410:CDS 25.0%
! TGATGCTCAACTAAAAAATA+TGG + chr2.4:45040221-45040240 MS.gene98410:CDS 25.0%
! TTGCTAATTTGAGTGTAATT+TGG + chr2.4:45041154-45041173 MS.gene98410:intron 25.0%
!!! TTAATGGACATCATGATTTT+TGG - chr2.4:45040937-45040956 None:intergenic 25.0%
AAAGAAAAAGACTGTCAAAC+AGG + chr2.4:45040412-45040431 MS.gene98410:CDS 30.0%
ACTCAAATTAGCAAGAATCT+TGG - chr2.4:45041148-45041167 None:intergenic 30.0%
CAATGAAAACGATTCTATTG+AGG + chr2.4:45040751-45040770 MS.gene98410:CDS 30.0%
CACTCTTAAGGATGAAAATT+TGG + chr2.4:45040679-45040698 MS.gene98410:CDS 30.0%
CTAATTTGAGTGTAATTTGG+TGG + chr2.4:45041157-45041176 MS.gene98410:intron 30.0%
CTTCTAATGTGTTTGTTTGA+TGG + chr2.4:45040573-45040592 MS.gene98410:intron 30.0%
GATCTCTTCTTCATACTTAA+AGG - chr2.4:45039966-45039985 None:intergenic 30.0%
GTCTAATTACATCCTTTCTT+TGG + chr2.4:45039931-45039950 MS.gene98410:intron 30.0%
TCTAACATGATTATTGGTGA+TGG + chr2.4:45039984-45040003 MS.gene98410:CDS 30.0%
TCTTCATATTCTTTCTGACA+AGG - chr2.4:45040641-45040660 None:intergenic 30.0%
TCTTTGTAGAAAATCCATCT+GGG + chr2.4:45040145-45040164 MS.gene98410:CDS 30.0%
TTCTGCACCAAAAAATGATA+GGG + chr2.4:45039599-45039618 MS.gene98410:CDS 30.0%
TTCTTTGTAGAAAATCCATC+TGG + chr2.4:45040144-45040163 MS.gene98410:CDS 30.0%
! CTCAATAGAATCGTTTTCAT+TGG - chr2.4:45040753-45040772 None:intergenic 30.0%
! TTAGTAGCATTTCTTTTGAC+AGG + chr2.4:45040368-45040387 MS.gene98410:intron 30.0%
AATTACATCCTTTCTTTGGC+AGG + chr2.4:45039935-45039954 MS.gene98410:intron 35.0%
CTTCTGCACCAAAAAATGAT+AGG + chr2.4:45039598-45039617 MS.gene98410:CDS 35.0%
GAACAAACTGTACCTCATTA+AGG - chr2.4:45039631-45039650 None:intergenic 35.0%
TAATTCTCCGTATTGTGTTG+TGG + chr2.4:45041104-45041123 MS.gene98410:intron 35.0%
TCCATTTAACAAGATGAACC+TGG - chr2.4:45041048-45041067 None:intergenic 35.0%
TTGAGAACCACAACACAATA+CGG - chr2.4:45041114-45041133 None:intergenic 35.0%
! ACAGTTTGTTCTTGATCTTC+TGG + chr2.4:45039640-45039659 MS.gene98410:intron 35.0%
! ATTTGAGTGTAATTTGGTGG+TGG + chr2.4:45041160-45041179 MS.gene98410:intron 35.0%
!! AGACTGGTTTCCATATTTAG+TGG - chr2.4:45039580-45039599 None:intergenic 35.0%
!!! GTTCCATCCCTATCATTTTT+TGG - chr2.4:45039609-45039628 None:intergenic 35.0%
AACCTGGCTACATTCATGTT+AGG - chr2.4:45041032-45041051 None:intergenic 40.0%
ACTGGGGAATCCACTAAATA+TGG + chr2.4:45039567-45039586 MS.gene98410:CDS 40.0%
AGAGGGACTAGAATCAATTG+CGG + chr2.4:45041202-45041221 MS.gene98410:CDS 40.0%
ATAGGGATGGAACCTTAATG+AGG + chr2.4:45039616-45039635 MS.gene98410:CDS 40.0%
GCACCAAAAAATGATAGGGA+TGG + chr2.4:45039603-45039622 MS.gene98410:CDS 40.0%
GCCAGGTTCATCTTGTTAAA+TGG + chr2.4:45041044-45041063 MS.gene98410:intron 40.0%
TACCTAACATGAATGTAGCC+AGG + chr2.4:45041027-45041046 MS.gene98410:intron 40.0%
TGTAGAAAATCCATCTGGGA+TGG + chr2.4:45040149-45040168 MS.gene98410:CDS 40.0%
! AAAGGATTTTGTTCGGGCTT+TGG - chr2.4:45039688-45039707 None:intergenic 40.0%
! CGCACACAAAGGATTTTGTT+CGG - chr2.4:45039695-45039714 None:intergenic 40.0%
! GCACACAAAGGATTTTGTTC+GGG - chr2.4:45039694-45039713 None:intergenic 40.0%
!!! CATTTTTTGGTGCAGAAGAC+TGG - chr2.4:45039596-45039615 None:intergenic 40.0%
ACAGGAAGAGCTCGTTAAAG+AGG + chr2.4:45041184-45041203 MS.gene98410:intron 45.0%
AGGAGAATCCTGCCAAAGAA+AGG - chr2.4:45039946-45039965 None:intergenic 45.0%
CAGGAAGAGCTCGTTAAAGA+GGG + chr2.4:45041185-45041204 MS.gene98410:intron 45.0%
GGTACGTACATGACCATGAT+CGG + chr2.4:45040467-45040486 MS.gene98410:intron 45.0%
GTTCAGCGAGCATTTGTGTT+AGG - chr2.4:45040706-45040725 None:intergenic 45.0%
! ATGTTGCAATGCACCGATCA+TGG - chr2.4:45040483-45040502 None:intergenic 45.0%
! GGAAGCATGAGATCAACAGA+TGG + chr2.4:45039728-45039747 MS.gene98410:CDS 45.0%
!! GTGTAATTTGGTGGTGGAAC+AGG + chr2.4:45041166-45041185 MS.gene98410:intron 45.0%
CACATGAACTGCAGTTCACG+TGG + chr2.4:45040101-45040120 MS.gene98410:intron 50.0%
GAATTCGTGGACAGTCGTCA+AGG + chr2.4:45040176-45040195 MS.gene98410:CDS 50.0%
GAATTCTGAGCCATCCCAGA+TGG - chr2.4:45040162-45040181 None:intergenic 50.0%
CTGGGATGGCTCAGAATTCG+TGG + chr2.4:45040163-45040182 MS.gene98410:CDS 55.0%
TTGCTGCACTGCGCACACAA+AGG - chr2.4:45039706-45039725 None:intergenic 55.0%
TGTGTGCGCAGTGCAGCAAG+TGG + chr2.4:45039707-45039726 MS.gene98410:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 45039564 45041250 45039564 ID=MS.gene98410
chr2.4 mRNA 45039564 45041250 45039564 ID=MS.gene98410.t1;Parent=MS.gene98410
chr2.4 exon 45039564 45039637 45039564 ID=MS.gene98410.t1.exon1;Parent=MS.gene98410.t1
chr2.4 CDS 45039564 45039637 45039564 ID=cds.MS.gene98410.t1;Parent=MS.gene98410.t1
chr2.4 exon 45039718 45039772 45039718 ID=MS.gene98410.t1.exon2;Parent=MS.gene98410.t1
chr2.4 CDS 45039718 45039772 45039718 ID=cds.MS.gene98410.t1;Parent=MS.gene98410.t1
chr2.4 exon 45039957 45040005 45039957 ID=MS.gene98410.t1.exon3;Parent=MS.gene98410.t1
chr2.4 CDS 45039957 45040005 45039957 ID=cds.MS.gene98410.t1;Parent=MS.gene98410.t1
chr2.4 exon 45040115 45040242 45040115 ID=MS.gene98410.t1.exon4;Parent=MS.gene98410.t1
chr2.4 CDS 45040115 45040242 45040115 ID=cds.MS.gene98410.t1;Parent=MS.gene98410.t1
chr2.4 exon 45040390 45040467 45040390 ID=MS.gene98410.t1.exon5;Parent=MS.gene98410.t1
chr2.4 CDS 45040390 45040467 45040390 ID=cds.MS.gene98410.t1;Parent=MS.gene98410.t1
chr2.4 exon 45040647 45040772 45040647 ID=MS.gene98410.t1.exon6;Parent=MS.gene98410.t1
chr2.4 CDS 45040647 45040772 45040647 ID=cds.MS.gene98410.t1;Parent=MS.gene98410.t1
chr2.4 exon 45041188 45041250 45041188 ID=MS.gene98410.t1.exon7;Parent=MS.gene98410.t1
chr2.4 CDS 45041188 45041250 45041188 ID=cds.MS.gene98410.t1;Parent=MS.gene98410.t1
Gene Sequence

>MS.gene98410

ATGACTGGGGAATCCACTAAATATGGAAACCAGTCTTCTGCACCAAAAAATGATAGGGATGGAACCTTAATGAGGTACAGTTTGTTCTTGATCTTCTGGTAAATTTGTTAATAGCATTTTTCCAAAGCCCGAACAAAATCCTTTGTGTGCGCAGTGCAGCAAGTGGAAGCATGAGATCAACAGATGGAGATCAAGATGATAGTAACAAAGTATGTTTATCGATTAATTTTTATATAAATGTTGTTGATGAATGTAATGTGTTCTGCCACTTTTATCTTAAGAAGTTTAGAAGACTTAAGAAATGAATAGTTTATTAAAGCTTTGAAATTTTTCTTTAGTACAGGTTATATAAAATTTCGGCAAAAATGTCTAATTACATCCTTTCTTTGGCAGGATTCTCCTTTAAGTATGAAGAAGAGATCTAACATGATTATTGGTGATGGTAAGATTTCGATTTTTCTTTTGATTATTTTATAATAAGAATTTATGCTTTATTTGATCTATAATTTGAATGTTCAGAAGGTGACTAATACAAAGCACATGAACTGCAGTTCACGTGGCTAACAGTCTTGCATCTTGTTTCTTTGTAGAAAATCCATCTGGGATGGCTCAGAATTCGTGGACAGTCGTCAAGGAATCTGACACTGACATTGATGTTGATGCTCAACTAAAAAATATGGTATTATAAAGTTTTTTGTGTTTTCGTAGCTAAATATGTATAGTAAATACACTTCAGAAAGTAAATCCCTTCTTAATGTTGCTAAGTTTAGTTGCATTTCTTGCACAATGTCTAGCATTTCCTATTTAGTAGCATTTCTTTTGACAGGAAGTTGATGAAATAAGAAAAGAAAGAAAAAGACTGTCAAACAGGAAATCAGCTCAAAGATCAAAGATAAAGAAACAGGTACGTACATGACCATGATCGGTGCATTGCAACATTTATAAATAGGAAATGGTTTGGTTGCATATGATTAAAATGTAAAAAGAAAAAGATGATCTGATTATCTAACTTCTAATGTGTTTGTTTGATGGTCTATTTAACTTGTATTTCATTCGATGTTATCATTATTTGTGCCTTGTCAGAAAGAATATGAAGAGCAATGTCAAAAGATAAACACTCTTAAGGATGAAAATTTGGTCCTAACACAAATGCTCGCTGAACTTTCAGAGAAATGTCTCGAGCTCACCAATGAAAACGATTCTATTGAGGTCAATCATTTTAATTCCCTTTCTTACTTGTTCAATTTTATATCATTCAATAAACAAGATACTTGTTTGATTTGAGAAATATTTTTTTCAATTAAAAAAATTCCATCTTGTTTTCTATATTTGTATGAGAAACAATTAAATAAACTAAGATGCTTATGAATCCAAAAATCATGATGTCCATTAATGTAAACGATTCTATTGATCTCTCTTTGTAACAAACTTTCTAATAAACTAGTGCAACAAATTATCTAAGTTACCTAACATGAATGTAGCCAGGTTCATCTTGTTAAATGGAAATTATTTATTTTCCAAGATTGGTTTATAAAGAAGTTAATTCTCCGTATTGTGTTGTGGTTCTCAATGCTCTATTTTCCAAGATTCTTGCTAATTTGAGTGTAATTTGGTGGTGGAACAGGAAGAGCTCGTTAAAGAGGGACTAGAATCAATTGCGGATCTATTGCCCATGAAGCCTACTTGA
Protein sequence

>MS.gene98410.t1

MTGESTKYGNQSSAPKNDRDGTLMSAASGSMRSTDGDQDDSNKDSPLSMKKRSNMIIGDVHVANSLASCFFVENPSGMAQNSWTVVKESDTDIDVDAQLKNMEVDEIRKERKRLSNRKSAQRSKIKKQKEYEEQCQKINTLKDENLVLTQMLAELSEKCLELTNENDSIEEELVKEGLESIADLLPMKPT