AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004081

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004081.t1 MTR_7g117590 69.872 156 26 3 56 191 18 172 1.13e-68 207
MS.gene004081.t1 MTR_1g054470 48.649 185 36 5 1 180 3 133 3.62e-48 154
MS.gene004081.t1 MTR_2g012700 37.273 110 68 1 83 191 11 120 9.60e-28 101
MS.gene004081.t1 MTR_2g062330 39.316 117 66 3 76 191 27 139 1.90e-26 99.0
MS.gene004081.t1 MTR_5g071400 70.213 47 8 2 56 97 14 59 2.16e-14 66.2
MS.gene004081.t1 MTR_0010s0310 33.333 90 57 1 95 181 151 240 1.42e-13 67.4
MS.gene004081.t1 MTR_6g477950 36.275 102 61 3 90 190 46 144 3.55e-12 63.9
MS.gene004081.t1 MTR_6g087720 29.915 117 81 1 63 178 182 298 8.65e-12 62.8
MS.gene004081.t1 MTR_5g078270 31.461 89 58 1 96 181 210 298 3.46e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATCAACAATTCGAATTT+TGG 0.069208 4.2:-41996624 None:intergenic
CCATCGACTTCTTCTTCATT+TGG 0.249648 4.2:-41996349 None:intergenic
GTGGATGGTTTGAGTTTGTT+AGG 0.273672 4.2:+41996714 MS.gene004081:CDS
TGAAGATCGGGTCATTTGAT+TGG 0.360270 4.2:+41996028 MS.gene004081:CDS
CGAATTGTTGATGATGAAAC+TGG 0.373851 4.2:+41996632 MS.gene004081:CDS
GAATGTGAAGTTCGTGATAA+AGG 0.381874 4.2:+41996665 MS.gene004081:CDS
AAGTTCGTGATAAAGGAAAT+TGG 0.388847 4.2:+41996672 MS.gene004081:CDS
GGCTGCTGGACGAAGAGTTC+TGG 0.395341 4.2:+41996447 MS.gene004081:CDS
TTTGAAATTGTGCAAATACT+TGG 0.402550 4.2:-41996372 None:intergenic
ATTAGTTCTGCTACGGCTGC+TGG 0.408831 4.2:+41996433 MS.gene004081:CDS
GAAGATCGGGTCATTTGATT+GGG 0.427759 4.2:+41996029 MS.gene004081:CDS
ATGAAATGTGCGGCGGATGC+AGG 0.449012 4.2:+41995965 MS.gene004081:CDS
CGAAGAAGAAGATGAAGATC+GGG 0.478220 4.2:+41996016 MS.gene004081:CDS
TGGATGGTTTGAGTTTGTTA+GGG 0.484898 4.2:+41996715 MS.gene004081:CDS
CTGCAGCGATGTAATTGATC+CGG 0.509939 4.2:+41996294 MS.gene004081:intron
CTTCTTCGTCCATCTCAAAA+CGG 0.536060 4.2:-41996001 None:intergenic
ACGAAGAAGAAGATGAAGAT+CGG 0.540825 4.2:+41996015 MS.gene004081:CDS
CGATGTAATTGATCCGGAGT+TGG 0.544205 4.2:+41996300 MS.gene004081:CDS
CAATCTTATTGCCGTCAAAA+CGG 0.544280 4.2:-41996061 None:intergenic
TTATTGCCGTCAAAACGGTT+CGG 0.545486 4.2:-41996056 None:intergenic
CTTTGAATTGCAATCTTCCG+AGG 0.557056 4.2:-41996584 None:intergenic
TCGTGATAAAGGAAATTGGA+TGG 0.565929 4.2:+41996676 MS.gene004081:CDS
TGAATGTGTAGCGTATTCCT+CGG 0.575387 4.2:+41996567 MS.gene004081:intron
AGAAATACGTTGGAAGTGGA+TGG 0.575514 4.2:+41996699 MS.gene004081:CDS
ATGGAGAAATACGTTGGAAG+TGG 0.576439 4.2:+41996695 MS.gene004081:CDS
GCATAGTATTAGTTCTGCTA+CGG 0.580120 4.2:+41996426 MS.gene004081:CDS
AATTGGATGGAGAAATACGT+TGG 0.583531 4.2:+41996689 MS.gene004081:CDS
CCATCTCAAAACGGCGACGA+TGG 0.584489 4.2:-41995992 None:intergenic
AGGGCAAAAGAACTCAAAGA+AGG 0.584629 4.2:+41996734 MS.gene004081:CDS
GCATCCGCCGCACATTTCAT+CGG 0.590420 4.2:-41995962 None:intergenic
GGTATCAATTCGTCCAACTC+CGG 0.591453 4.2:-41996313 None:intergenic
GATACAAATAATTTGTGTGG+AGG 0.593345 4.2:-41996785 None:intergenic
ACTGATACAAATAATTTGTG+TGG 0.607437 4.2:-41996788 None:intergenic
CCAAATGAAGAAGAAGTCGA+TGG 0.658231 4.2:+41996349 MS.gene004081:CDS
ATGGCGACCGATGAAATGTG+CGG 0.726557 4.2:+41995955 MS.gene004081:CDS
GCGACCGATGAAATGTGCGG+CGG 0.753822 4.2:+41995958 MS.gene004081:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAATTTCAAAATTTTCAAAA+CGG + chr4.2:41996385-41996404 MS.gene004081:CDS 15.0%
!!! GTTGGTTTTTATTTTATTTT+TGG + chr4.2:41996469-41996488 MS.gene004081:intron 15.0%
!!! GTTTTTTATTTTATTTTTGC+TGG + chr4.2:41996491-41996510 MS.gene004081:intron 15.0%
!!! TGTTGTTTTTTTTAATCATC+TGG + chr4.2:41996248-41996267 MS.gene004081:intron 20.0%
! CTTAAAATAGCCTTCTAAAT+GGG - chr4.2:41996129-41996148 None:intergenic 25.0%
!! ACTGATACAAATAATTTGTG+TGG - chr4.2:41996791-41996810 None:intergenic 25.0%
!! ATCATCAACAATTCGAATTT+TGG - chr4.2:41996627-41996646 None:intergenic 25.0%
!! TTTGAAATTGTGCAAATACT+TGG - chr4.2:41996375-41996394 None:intergenic 25.0%
!!! CATTTAGAAGGCTATTTTAA+GGG + chr4.2:41996128-41996147 MS.gene004081:intron 25.0%
AAGTTCGTGATAAAGGAAAT+TGG + chr4.2:41996672-41996691 MS.gene004081:CDS 30.0%
CCTTAAAATAGCCTTCTAAA+TGG - chr4.2:41996130-41996149 None:intergenic 30.0%
! AAAACGGTGATCATACTTTT+TGG + chr4.2:41996401-41996420 MS.gene004081:CDS 30.0%
! GATACAAATAATTTGTGTGG+AGG - chr4.2:41996788-41996807 None:intergenic 30.0%
!! CCATTTAGAAGGCTATTTTA+AGG + chr4.2:41996127-41996146 MS.gene004081:intron 30.0%
AATTGGATGGAGAAATACGT+TGG + chr4.2:41996689-41996708 MS.gene004081:CDS 35.0%
ACGAAGAAGAAGATGAAGAT+CGG + chr4.2:41996015-41996034 MS.gene004081:CDS 35.0%
ACGTCTGAGAAGAAAATTCT+AGG + chr4.2:41996175-41996194 MS.gene004081:intron 35.0%
CAATCTTATTGCCGTCAAAA+CGG - chr4.2:41996064-41996083 None:intergenic 35.0%
CGTCTGAGAAGAAAATTCTA+GGG + chr4.2:41996176-41996195 MS.gene004081:intron 35.0%
GAATGTGAAGTTCGTGATAA+AGG + chr4.2:41996665-41996684 MS.gene004081:CDS 35.0%
TCGTGATAAAGGAAATTGGA+TGG + chr4.2:41996676-41996695 MS.gene004081:CDS 35.0%
TGAAAATGTCTTCTTCTAGC+AGG + chr4.2:41996207-41996226 MS.gene004081:intron 35.0%
TTAAGGGTTGTTGTGAATCT+TGG + chr4.2:41996144-41996163 MS.gene004081:intron 35.0%
! TCATTTGGATTTTCGTCTAC+AGG - chr4.2:41996337-41996356 None:intergenic 35.0%
!! CGAATTGTTGATGATGAAAC+TGG + chr4.2:41996632-41996651 MS.gene004081:CDS 35.0%
!! GCATAGTATTAGTTCTGCTA+CGG + chr4.2:41996426-41996445 MS.gene004081:CDS 35.0%
!! GTTTTGACGGCAATAAGATT+GGG + chr4.2:41996063-41996082 MS.gene004081:CDS 35.0%
!! TGGATGGTTTGAGTTTGTTA+GGG + chr4.2:41996715-41996734 MS.gene004081:CDS 35.0%
!!! TGGGCTTTTTAGTTATTGAC+CGG + chr4.2:41996082-41996101 MS.gene004081:CDS 35.0%
AGAAATACGTTGGAAGTGGA+TGG + chr4.2:41996699-41996718 MS.gene004081:CDS 40.0%
AGGGCAAAAGAACTCAAAGA+AGG + chr4.2:41996734-41996753 MS.gene004081:CDS 40.0%
ATGGAGAAATACGTTGGAAG+TGG + chr4.2:41996695-41996714 MS.gene004081:CDS 40.0%
ATTGACCGGGCAAAAATGAA+TGG + chr4.2:41996096-41996115 MS.gene004081:CDS 40.0%
CCAAATGAAGAAGAAGTCGA+TGG + chr4.2:41996349-41996368 MS.gene004081:CDS 40.0%
CGAAGAAGAAGATGAAGATC+GGG + chr4.2:41996016-41996035 MS.gene004081:CDS 40.0%
CTTCTTCGTCCATCTCAAAA+CGG - chr4.2:41996004-41996023 None:intergenic 40.0%
CTTTGAATTGCAATCTTCCG+AGG - chr4.2:41996587-41996606 None:intergenic 40.0%
GAAGATCGGGTCATTTGATT+GGG + chr4.2:41996029-41996048 MS.gene004081:CDS 40.0%
TGAAGATCGGGTCATTTGAT+TGG + chr4.2:41996028-41996047 MS.gene004081:CDS 40.0%
TGAATGTGTAGCGTATTCCT+CGG + chr4.2:41996567-41996586 MS.gene004081:intron 40.0%
TTATTGCCGTCAAAACGGTT+CGG - chr4.2:41996059-41996078 None:intergenic 40.0%
TTGACCGGGCAAAAATGAAT+GGG + chr4.2:41996097-41996116 MS.gene004081:CDS 40.0%
! GTGGATGGTTTGAGTTTGTT+AGG + chr4.2:41996714-41996733 MS.gene004081:CDS 40.0%
! TTGCTGGAGTATTTGCACAT+GGG + chr4.2:41996507-41996526 MS.gene004081:intron 40.0%
! TTTGCTGGAGTATTTGCACA+TGG + chr4.2:41996506-41996525 MS.gene004081:intron 40.0%
!! CCATCGACTTCTTCTTCATT+TGG - chr4.2:41996352-41996371 None:intergenic 40.0%
!! CGTTTTGACGGCAATAAGAT+TGG + chr4.2:41996062-41996081 MS.gene004081:CDS 40.0%
!!! GGGCTTTTTAGTTATTGACC+GGG + chr4.2:41996083-41996102 MS.gene004081:CDS 40.0%
CGATGTAATTGATCCGGAGT+TGG + chr4.2:41996300-41996319 MS.gene004081:CDS 45.0%
CTGCAGCGATGTAATTGATC+CGG + chr4.2:41996294-41996313 MS.gene004081:intron 45.0%
GGGCAAAAATGAATGGGTCA+CGG + chr4.2:41996103-41996122 MS.gene004081:intron 45.0%
GGTATCAATTCGTCCAACTC+CGG - chr4.2:41996316-41996335 None:intergenic 45.0%
! GGTTTTCCGAACCGTTTTGA+CGG + chr4.2:41996050-41996069 MS.gene004081:CDS 45.0%
!! GTGACCCATTCATTTTTGCC+CGG - chr4.2:41996104-41996123 None:intergenic 45.0%
ATGGCGACCGATGAAATGTG+CGG + chr4.2:41995955-41995974 MS.gene004081:CDS 50.0%
GAGTATTTGCACATGGGTGG+TGG + chr4.2:41996513-41996532 MS.gene004081:intron 50.0%
! CTGGAGTATTTGCACATGGG+TGG + chr4.2:41996510-41996529 MS.gene004081:intron 50.0%
!! ATTAGTTCTGCTACGGCTGC+TGG + chr4.2:41996433-41996452 MS.gene004081:CDS 50.0%
ATGAAATGTGCGGCGGATGC+AGG + chr4.2:41995965-41995984 MS.gene004081:CDS 55.0%
CCATCTCAAAACGGCGACGA+TGG - chr4.2:41995995-41996014 None:intergenic 55.0%
GCATCCGCCGCACATTTCAT+CGG - chr4.2:41995965-41995984 None:intergenic 55.0%
TGGGTCACGGCCCATTTAGA+AGG + chr4.2:41996116-41996135 MS.gene004081:intron 55.0%
! GCTGGACGAAGAGTTCTGGT+TGG + chr4.2:41996451-41996470 MS.gene004081:intron 55.0%
!!! CCATCGTCGCCGTTTTGAGA+TGG + chr4.2:41995992-41996011 MS.gene004081:CDS 55.0%
GCGACCGATGAAATGTGCGG+CGG + chr4.2:41995958-41995977 MS.gene004081:CDS 60.0%
GGCTGCTGGACGAAGAGTTC+TGG + chr4.2:41996447-41996466 MS.gene004081:CDS 60.0%
! GCACATGGGTGGTGGCTTTC+TGG + chr4.2:41996521-41996540 MS.gene004081:intron 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 41995955 41996820 41995955 ID=MS.gene004081
chr4.2 mRNA 41995955 41996820 41995955 ID=MS.gene004081.t1;Parent=MS.gene004081
chr4.2 exon 41995955 41996118 41995955 ID=MS.gene004081.t1.exon1;Parent=MS.gene004081.t1
chr4.2 CDS 41995955 41996118 41995955 ID=cds.MS.gene004081.t1;Parent=MS.gene004081.t1
chr4.2 exon 41996300 41996468 41996300 ID=MS.gene004081.t1.exon2;Parent=MS.gene004081.t1
chr4.2 CDS 41996300 41996468 41996300 ID=cds.MS.gene004081.t1;Parent=MS.gene004081.t1
chr4.2 exon 41996578 41996820 41996578 ID=MS.gene004081.t1.exon3;Parent=MS.gene004081.t1
chr4.2 CDS 41996578 41996820 41996578 ID=cds.MS.gene004081.t1;Parent=MS.gene004081.t1
Gene Sequence

>MS.gene004081

ATGGCGACCGATGAAATGTGCGGCGGATGCAGGTCTGCCATCGTCGCCGTTTTGAGATGGACGAAGAAGAAGATGAAGATCGGGTCATTTGATTGGGTTTTCCGAACCGTTTTGACGGCAATAAGATTGGGCTTTTTAGTTATTGACCGGGCAAAAATGAATGGGTCACGGCCCATTTAGAAGGCTATTTTAAGGGTTGTTGTGAATCTTGGCATTGTCGACGTCTGAGAAGAAAATTCTAGGGTTTGAATTTGAAAATGTCTTCTTCTAGCAGGTAACTTCAATGTTTGAGTTGTTGTTTTTTTTAATCATCTGGTTATTTATTAGATGTTGTTGAAACTGCAGCGATGTAATTGATCCGGAGTTGGACGAATTGATACCTGTAGACGAAAATCCAAATGAAGAAGAAGTCGATGGCCAAGTATTTGCACAATTTCAAAATTTTCAAAACGGTGATCATACTTTTTGGATGCATAGTATTAGTTCTGCTACGGCTGCTGGACGAAGAGTTCTGGTTGGTTTTTATTTTATTTTTGGTTTTTTATTTTATTTTTGCTGGAGTATTTGCACATGGGTGGTGGCTTTCTGGTTGAAAAGTAATATTATTTGTTTTGAATGTGTAGCGTATTCCTCGGAAGATTGCAATTCAAAGTATGTATGTGAATCAATCCAAAATTCGAATTGTTGATGATGAAACTGGAGAAGAATATGAATGTGAAGTTCGTGATAAAGGAAATTGGATGGAGAAATACGTTGGAAGTGGATGGTTTGAGTTTGTTAGGGCAAAAGAACTCAAAGAAGGAGATTCTTTGTTCTTCACTATTGATAATCCTCCACACAAATTATTTGTATCAGTGATTAGATAG
Protein sequence

>MS.gene004081.t1

MATDEMCGGCRSAIVAVLRWTKKKMKIGSFDWVFRTVLTAIRLGFLVIDRAKMNGDVIDPELDELIPVDENPNEEEVDGQVFAQFQNFQNGDHTFWMHSISSATAAGRRVLRIPRKIAIQSMYVNQSKIRIVDDETGEEYECEVRDKGNWMEKYVGSGWFEFVRAKELKEGDSLFFTIDNPPHKLFVSVIR