AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06175

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06175.t1 MTR_8g101880 98.347 121 2 0 1 121 1 121 2.34e-87 249
MS.gene06175.t1 MTR_8g101890 78.333 120 26 0 2 121 3 122 1.83e-70 207
MS.gene06175.t1 MTR_2g100380 61.667 120 46 0 2 121 98 217 8.90e-52 162
MS.gene06175.t1 MTR_5g062980 69.492 59 18 0 58 116 1 59 2.33e-26 95.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06175.t1 AT4G26210 73.950 119 31 0 2 120 3 121 5.23e-66 196
MS.gene06175.t1 AT4G26210 73.950 119 31 0 2 120 3 121 5.23e-66 196
MS.gene06175.t1 AT4G29480 73.950 119 31 0 2 120 3 121 9.15e-66 195
MS.gene06175.t1 AT2G19680 73.950 119 31 0 2 120 3 121 2.46e-65 194
MS.gene06175.t1 AT2G19680 73.950 119 31 0 2 120 3 121 2.46e-65 194

Find 23 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCATGCTTAGTTATAAAT+TGG 0.149886 4.2:+3296808 None:intergenic
TTGATTATGTCAAGCAAATA+TGG 0.268577 4.2:-3295075 MS.gene06175:CDS
TGAAAGGACTCGCAACGATT+TGG 0.343521 4.2:+3295106 None:intergenic
AAAACCATGCATAGCATTCC+AGG 0.362552 4.2:+3294999 None:intergenic
TCCATGCTTAGTTATAAATT+GGG 0.411328 4.2:+3296809 None:intergenic
GAAGAACAAGGAATACATTC+AGG 0.438061 4.2:-3296760 MS.gene06175:CDS
GGAAGGGGATTTACTTTCAC+AGG 0.448226 4.2:-3294959 MS.gene06175:CDS
TGGCATTTCTCTACTGTAGC+AGG 0.457610 4.2:+3296735 None:intergenic
TTCTTACCACAAGCAGCTGT+TGG 0.459464 4.2:-3296784 MS.gene06175:CDS
TCGTTGCGAGTCCTTTCATA+AGG 0.471623 4.2:-3295101 MS.gene06175:CDS
TGCTGGTCAGATTGTTGGAA+GGG 0.499361 4.2:-3294975 MS.gene06175:CDS
AGTAGAGAAATGCCAACTTC+TGG 0.523939 4.2:-3296727 MS.gene06175:CDS
ATAGTTGCTTGGCCAGAAGT+TGG 0.524773 4.2:+3296715 None:intergenic
TCCCAATTTATAACTAAGCA+TGG 0.525968 4.2:-3296810 MS.gene06175:CDS
ATAATCAAGTTCCTTATGAA+AGG 0.546893 4.2:+3295090 None:intergenic
GCTGGTCAGATTGTTGGAAG+GGG 0.563270 4.2:-3294974 MS.gene06175:CDS
GGTTAAAATAAAACCTAGCA+AGG 0.573767 4.2:+3296682 None:intergenic
GTGCTGGTCAGATTGTTGGA+AGG 0.577540 4.2:-3294976 MS.gene06175:CDS
GCGAGTGTAAAATAGTTGCT+TGG 0.582756 4.2:+3296704 None:intergenic
TCTTCTCCAACAGCTGCTTG+TGG 0.584533 4.2:+3296778 None:intergenic
TTGGCCTGGAATGCTATGCA+TGG 0.593962 4.2:-3295003 MS.gene06175:CDS
GATTTGAAGATTGAAGATGC+AGG 0.608817 4.2:-3295040 MS.gene06175:CDS
GCAGCTGTTGGAGAAGAACA+AGG 0.648148 4.2:-3296772 MS.gene06175:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTTTAAAAAAAAAAAATTG+AGG + chr4.2:3295651-3295670 None:intergenic 10.0%
!! TAGATTTATTAATAAGGAAA+GGG + chr4.2:3295140-3295159 None:intergenic 15.0%
!! TCTTTAATTATTAAGTATGA+TGG - chr4.2:3295821-3295840 MS.gene06175:intron 15.0%
!!! GTTTTATTAAAGAGTTAAAA+GGG - chr4.2:3295671-3295690 MS.gene06175:intron 15.0%
!!! TGTTTTATTAAAGAGTTAAA+AGG - chr4.2:3295670-3295689 MS.gene06175:intron 15.0%
!! AAAAATCACTTACAATCAAT+AGG + chr4.2:3295207-3295226 None:intergenic 20.0%
!! AATAGAAACAAACTAAAAGT+AGG + chr4.2:3295756-3295775 None:intergenic 20.0%
!! CTAGATTTATTAATAAGGAA+AGG + chr4.2:3295141-3295160 None:intergenic 20.0%
!! TAGAAAAATACACGAAATTA+TGG + chr4.2:3295850-3295869 None:intergenic 20.0%
!! TATACAGTATAAAAGATGAT+CGG - chr4.2:3296008-3296027 MS.gene06175:intron 20.0%
!!! TTTTTTTTGCATTTTGATGT+CGG - chr4.2:3295227-3295246 MS.gene06175:intron 20.0%
! ATAATCAAGTTCCTTATGAA+AGG + chr4.2:3296711-3296730 None:intergenic 25.0%
! ATACAGTATAAAAGATGATC+GGG - chr4.2:3296009-3296028 MS.gene06175:intron 25.0%
! ATAGCTAAAAGAAGAAACTA+CGG + chr4.2:3296587-3296606 None:intergenic 25.0%
! GATTGAACAATCAGAATATT+AGG + chr4.2:3295332-3295351 None:intergenic 25.0%
! TCCAGCTAGATTTATTAATA+AGG + chr4.2:3295146-3295165 None:intergenic 25.0%
! TCCATGCTTAGTTATAAATT+GGG + chr4.2:3294992-3295011 None:intergenic 25.0%
! TCCTTATTAATAAATCTAGC+TGG - chr4.2:3295142-3295161 MS.gene06175:intron 25.0%
! TTCCATGCTTAGTTATAAAT+TGG + chr4.2:3294993-3295012 None:intergenic 25.0%
! TTGATTATGTCAAGCAAATA+TGG - chr4.2:3296723-3296742 MS.gene06175:CDS 25.0%
! TTGTACTAAATAGCTTATTG+TGG + chr4.2:3296166-3296185 None:intergenic 25.0%
!! ATATACCACTATAGCATTTT+AGG - chr4.2:3295935-3295954 MS.gene06175:intron 25.0%
!! TATACCACTATAGCATTTTA+GGG - chr4.2:3295936-3295955 MS.gene06175:intron 25.0%
!!! GTTTTGTTGTTTTGTACTTT+AGG - chr4.2:3295797-3295816 MS.gene06175:intron 25.0%
ACCATTAACTTTGTAGTTCA+GGG + chr4.2:3295373-3295392 None:intergenic 30.0%
GGTTAAAATAAAACCTAGCA+AGG + chr4.2:3295119-3295138 None:intergenic 30.0%
GTGAACTCTAAACTAACTAA+GGG + chr4.2:3296099-3296118 None:intergenic 30.0%
TAAGACTTCATTGCTAAGAA+AGG + chr4.2:3296057-3296076 None:intergenic 30.0%
TACAAAATACTGTGCAATAG+TGG - chr4.2:3296297-3296316 MS.gene06175:intron 30.0%
TATAGTGGTATATCGAATAG+CGG + chr4.2:3295928-3295947 None:intergenic 30.0%
TCCCAATTTATAACTAAGCA+TGG - chr4.2:3294988-3295007 MS.gene06175:CDS 30.0%
TCGCTAATATATGTACTTGT+TGG - chr4.2:3295181-3295200 MS.gene06175:intron 30.0%
TGTGAACTCTAAACTAACTA+AGG + chr4.2:3296100-3296119 None:intergenic 30.0%
TGTTGAATTGAAACATCAGA+AGG - chr4.2:3296482-3296501 MS.gene06175:intron 30.0%
TGTTGAATTGAAACATCAGA+TGG - chr4.2:3296482-3296501 MS.gene06175:intron 30.0%
TTGTACTAAATAGCGTATTG+CGG + chr4.2:3296282-3296301 None:intergenic 30.0%
! ATACCACTATAGCATTTTAG+GGG - chr4.2:3295937-3295956 MS.gene06175:intron 30.0%
! ATTTTCTCCCTTGTCAATAA+AGG + chr4.2:3295281-3295300 None:intergenic 30.0%
! TTTTCTCCCTTGTCAATAAA+GGG + chr4.2:3295280-3295299 None:intergenic 30.0%
AATATGACACTGTTGCATAG+TGG - chr4.2:3296330-3296349 MS.gene06175:intron 35.0%
AATCCCCTAAAATGCTATAG+TGG + chr4.2:3295943-3295962 None:intergenic 35.0%
ACACTGTGAACTCTAAACTA+AGG + chr4.2:3296104-3296123 None:intergenic 35.0%
AGCCAATTACAGTGAATTTG+CGG - chr4.2:3295579-3295598 MS.gene06175:intron 35.0%
ATAGTGGTATATCGAATAGC+GGG + chr4.2:3295927-3295946 None:intergenic 35.0%
ATCACATGAACCCTAATTCA+TGG + chr4.2:3296434-3296453 None:intergenic 35.0%
CACTGTGAACTCTAAACTAA+GGG + chr4.2:3296103-3296122 None:intergenic 35.0%
CCATTAACTTTGTAGTTCAG+GGG + chr4.2:3295372-3295391 None:intergenic 35.0%
GAAGAACAAGGAATACATTC+AGG - chr4.2:3295038-3295057 MS.gene06175:CDS 35.0%
GACCATTAACTTTGTAGTTC+AGG + chr4.2:3295374-3295393 None:intergenic 35.0%
GATTTGAAGATTGAAGATGC+AGG - chr4.2:3296758-3296777 MS.gene06175:CDS 35.0%
TATTGATCAGAATTCCCATG+TGG - chr4.2:3296543-3296562 MS.gene06175:intron 35.0%
TGTTGGATATCATAGAGTTC+AGG - chr4.2:3296408-3296427 MS.gene06175:intron 35.0%
!! ACTATAGCATTTTAGGGGAT+TGG - chr4.2:3295942-3295961 MS.gene06175:intron 35.0%
AAAACCATGCATAGCATTCC+AGG + chr4.2:3296802-3296821 None:intergenic 40.0%
AGAGTTCAGGCCATGAATTA+GGG - chr4.2:3296421-3296440 MS.gene06175:intron 40.0%
AGTAGAGAAATGCCAACTTC+TGG - chr4.2:3295071-3295090 MS.gene06175:CDS 40.0%
ATTGACAAGGGAGAAAATCC+TGG - chr4.2:3295283-3295302 MS.gene06175:intron 40.0%
CCCCTGAACTACAAAGTTAA+TGG - chr4.2:3295369-3295388 MS.gene06175:intron 40.0%
GCGAGTGTAAAATAGTTGCT+TGG + chr4.2:3295097-3295116 None:intergenic 40.0%
TAGAGTTCAGGCCATGAATT+AGG - chr4.2:3296420-3296439 MS.gene06175:intron 40.0%
TGATATCCAACACTGAACAC+AGG + chr4.2:3296400-3296419 None:intergenic 40.0%
TTCCCTCCCTTTATTGACAA+GGG - chr4.2:3295271-3295290 MS.gene06175:intron 40.0%
TTGTCAATAAAGGGAGGGAA+GGG + chr4.2:3295271-3295290 None:intergenic 40.0%
TTGTCAATAGCGTGCTATAG+CGG - chr4.2:3295470-3295489 MS.gene06175:intron 40.0%
! TATTGCTGACTGTGGTTTGT+GGG + chr4.2:3295545-3295564 None:intergenic 40.0%
! TATTTTACACTCGCCTTGCT+AGG - chr4.2:3295103-3295122 MS.gene06175:CDS 40.0%
!! TTTTGTGCTGGTCAGATTGT+TGG - chr4.2:3296818-3296837 MS.gene06175:CDS 40.0%
!!! GCAGGTATTGCTGTTTTGTT+TGG - chr4.2:3296776-3296795 MS.gene06175:CDS 40.0%
!!! TATTGCTGTTTTGTTTGGCC+TGG - chr4.2:3296781-3296800 MS.gene06175:CDS 40.0%
AACACAGGTGTAGTCAACTG+TGG + chr4.2:3296385-3296404 None:intergenic 45.0%
AACGTATCCGTGGTAGGATT+TGG - chr4.2:3295496-3295515 MS.gene06175:intron 45.0%
ACAAGGGAGAAAATCCTGGA+GGG - chr4.2:3295287-3295306 MS.gene06175:intron 45.0%
ACTACACCTGTGTTCAGTGT+TGG - chr4.2:3296391-3296410 MS.gene06175:intron 45.0%
AGCAGACACGATAGCAGTTA+GGG + chr4.2:3295606-3295625 None:intergenic 45.0%
ATAGTTGCTTGGCCAGAAGT+TGG + chr4.2:3295086-3295105 None:intergenic 45.0%
ATCCGTGGTAGGATTTGGAA+CGG - chr4.2:3295501-3295520 MS.gene06175:intron 45.0%
CAAACCACAGTCAGCAATAG+TGG - chr4.2:3295546-3295565 MS.gene06175:intron 45.0%
CTCCCTTGTCAATAAAGGGA+GGG + chr4.2:3295276-3295295 None:intergenic 45.0%
CTGTGCAATAGTGGCTATAG+CGG - chr4.2:3296306-3296325 MS.gene06175:intron 45.0%
CTTCCCTCCCTTTATTGACA+AGG - chr4.2:3295270-3295289 MS.gene06175:intron 45.0%
CTTGTCAATAAAGGGAGGGA+AGG + chr4.2:3295272-3295291 None:intergenic 45.0%
GGAAGGGGATTTACTTTCAC+AGG - chr4.2:3296839-3296858 MS.gene06175:CDS 45.0%
GGCCGCAAATTCACTGTAAT+TGG + chr4.2:3295584-3295603 None:intergenic 45.0%
TAGCAGACACGATAGCAGTT+AGG + chr4.2:3295607-3295626 None:intergenic 45.0%
TCGTTGCGAGTCCTTTCATA+AGG - chr4.2:3296697-3296716 MS.gene06175:CDS 45.0%
TCTCCCTTGTCAATAAAGGG+AGG + chr4.2:3295277-3295296 None:intergenic 45.0%
TGAAAGGACTCGCAACGATT+TGG + chr4.2:3296695-3296714 None:intergenic 45.0%
TGCTGGTCAGATTGTTGGAA+GGG - chr4.2:3296823-3296842 MS.gene06175:CDS 45.0%
TGGCATTTCTCTACTGTAGC+AGG + chr4.2:3295066-3295085 None:intergenic 45.0%
TTCTTACCACAAGCAGCTGT+TGG - chr4.2:3295014-3295033 MS.gene06175:CDS 45.0%
! ATAGCGGAATAACGTATCCG+TGG - chr4.2:3295486-3295505 MS.gene06175:intron 45.0%
! CTATTGCTGACTGTGGTTTG+TGG + chr4.2:3295546-3295565 None:intergenic 45.0%
!! GCCTCTAAAAAGCACCACAT+GGG + chr4.2:3296560-3296579 None:intergenic 45.0%
!! TCCCATGTGGTGCTTTTTAG+AGG - chr4.2:3296556-3296575 MS.gene06175:intron 45.0%
!! TGCCTCTAAAAAGCACCACA+TGG + chr4.2:3296561-3296580 None:intergenic 45.0%
!!! TGCTATGCATGGTTTTGTGC+TGG - chr4.2:3296806-3296825 MS.gene06175:CDS 45.0%
AACTTGAAACCTCACCCTCC+AGG + chr4.2:3295304-3295323 None:intergenic 50.0%
AAGATGATCGGGTGATCGTG+TGG - chr4.2:3296020-3296039 MS.gene06175:intron 50.0%
ACCACAGTCAGCAATAGTGG+TGG - chr4.2:3295549-3295568 MS.gene06175:intron 50.0%
CGGAATAACGTATCCGTGGT+AGG - chr4.2:3295490-3295509 MS.gene06175:intron 50.0%
CTGCTATCGTGTCTGCTAGT+AGG - chr4.2:3295609-3295628 MS.gene06175:intron 50.0%
GACAAGGGAGAAAATCCTGG+AGG - chr4.2:3295286-3295305 MS.gene06175:intron 50.0%
GCAGACACGATAGCAGTTAG+GGG + chr4.2:3295605-3295624 None:intergenic 50.0%
GCAGCTGTTGGAGAAGAACA+AGG - chr4.2:3295026-3295045 MS.gene06175:CDS 50.0%
GCTGGTCAGATTGTTGGAAG+GGG - chr4.2:3296824-3296843 MS.gene06175:CDS 50.0%
GTCCGTTCCAAATCCTACCA+CGG + chr4.2:3295506-3295525 None:intergenic 50.0%
TCTTCTCCAACAGCTGCTTG+TGG + chr4.2:3295023-3295042 None:intergenic 50.0%
TTGGCCTGGAATGCTATGCA+TGG - chr4.2:3296795-3296814 MS.gene06175:CDS 50.0%
! ACCACCACTATTGCTGACTG+TGG + chr4.2:3295553-3295572 None:intergenic 50.0%
! GGGATTGGTGCATGCTATCT+GGG - chr4.2:3295957-3295976 MS.gene06175:intron 50.0%
! GTGCTGGTCAGATTGTTGGA+AGG - chr4.2:3296822-3296841 MS.gene06175:CDS 50.0%
GGAGAAAATCCTGGAGGGTG+AGG - chr4.2:3295292-3295311 MS.gene06175:intron 55.0%
! AGGATTTGGAACGGACCGCA+CGG - chr4.2:3295510-3295529 MS.gene06175:intron 55.0%
! GGGGATTGGTGCATGCTATC+TGG - chr4.2:3295956-3295975 MS.gene06175:intron 55.0%
! AACGGACCGCACGGTGCTTT+TGG - chr4.2:3295519-3295538 MS.gene06175:intron 60.0%
!! TGTGGGCCAAAAGCACCGTG+CGG + chr4.2:3295528-3295547 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 3294946 3296874 3294946 ID=MS.gene06175
chr4.2 mRNA 3294946 3296874 3294946 ID=MS.gene06175.t1;Parent=MS.gene06175
chr4.2 exon 3296696 3296874 3296696 ID=MS.gene06175.t1.exon1;Parent=MS.gene06175.t1
chr4.2 CDS 3296696 3296874 3296696 ID=cds.MS.gene06175.t1;Parent=MS.gene06175.t1
chr4.2 exon 3294946 3295132 3294946 ID=MS.gene06175.t1.exon2;Parent=MS.gene06175.t1
chr4.2 CDS 3294946 3295132 3294946 ID=cds.MS.gene06175.t1;Parent=MS.gene06175.t1
Gene Sequence

>MS.gene06175

ATGTCGAAGTTGCAGCAGTTGACATCAAAAGCGTGTCAAGCGTCCCAATTTATAACTAAGCATGGAACTTCTTACCACAAGCAGCTGTTGGAGAAGAACAAGGAATACATTCAGGATCCTGCTACAGTAGAGAAATGCCAACTTCTGGCCAAGCAACTATTTTACACTCGCCTTGCTAGGTTTTATTTTAACCCTTTCCTTATTAATAAATCTAGCTGGATTTAGTGTTTAATATTCGCTAATATATGTACTTGTTGGCCTATTGATTGTAAGTGATTTTTTTTTTTTTGCATTTTGATGTCGGTACATTTCTAACTGTCTACCCTTCCCTCCCTTTATTGACAAGGGAGAAAATCCTGGAGGGTGAGGTTTCAAGTTTTGAACCTAATATTCTGATTGTTCAATCATATTAGTTGAAACTTACCCCTGAACTACAAAGTTAATGGTCAAATACTCAGTGTTATTGTGAAACATATTACTTTTGTATTAGATTAACATCAATATTTTAGTATTTGCTAGCTATGTTGTCAATAGCGTGCTATAGCGGAATAACGTATCCGTGGTAGGATTTGGAACGGACCGCACGGTGCTTTTGGCCCACAAACCACAGTCAGCAATAGTGGTGGTTGCAGCAGCCAATTACAGTGAATTTGCGGCCCCTAACTGCTATCGTGTCTGCTAGTAGGATTTTAGAGCAAAATTCCTCAATTTTTTTTTTTTAAACTGTTTTATTAAAGAGTTAAAAGGGTAGTGTTCTGTTCTTCATTTTGTTGTGTTATGCGCACAAACAATCGTTATGTTCTTCTGCCTACTTTTAGTTTGTTTCTATTATGTTTTTCTTCTCTTTTTAAGTTTTGTTGTTTTGTACTTTAGGTTCTTTAATTATTAAGTATGATGGTCTCCATAATTTCGTGTATTTTTCTATTTTTGAATATTTATGCTTACTTTGTACACTGATTTTTAGTCATTAGCAGCTATCCCGCTATTCGATATACCACTATAGCATTTTAGGGGATTGGTGCATGCTATCTGGGATTAACAACACAGTTTGCTAGTTATTATTATACAGTATAAAAGATGATCGGGTGATCGTGTGGTCGACATGAATCCTTTCTTAGCAATGAAGTCTTAGTAATGTAGTGTGATGCAGCCCTTAGTTAGTTTAGAGTTCACAGTGTTGTTAATGCATAGCTGAATTTGACAAATCGTTGCTGTTTCCACAATAAGCTATTTAGTACAAAATACTGTGAAATAGCAATGCAGTGTTAGTAATGTAGTGTGATGCAGCCCTTAGTTTAGAGTTCACAGTGTATTTGACAAATCGCTACTGTTTCCGCAATACGCTATTTAGTACAAAATACTGTGCAATAGTGGCTATAGCGGCAATATGACACTGTTGCATAGTGGAACTTGAACAAACTGCTATTTTTCACTATCCACAGTTGACTACACCTGTGTTCAGTGTTGGATATCATAGAGTTCAGGCCATGAATTAGGGTTCATGTGATCTGATATATGATCAGAATTCTGATACTATGTTGAATTGAAACATCAGAAGGTATATGTTGAATTGAAACATCAGATGGTATATTCTTAATATTGATCAGAATTCCCATGTGGTGCTTTTTAGAGGCATTTCCGTAGTTTCTTCTTTTAGCTATATGTATAGCAAATCTATTTTATTTTGTGCTAATTCAGTTCTTGTGCGTTCATATAAGTTATAACTCATCAATCTTTTGCAGTATTCCAAATCGTTGCGAGTCCTTTCATAAGGAACTTGATTATGTCAAGCAAATATGGAAGAATAAGCAAGATTTGAAGATTGAAGATGCAGGTATTGCTGTTTTGTTTGGCCTGGAATGCTATGCATGGTTTTGTGCTGGTCAGATTGTTGGAAGGGGATTTACTTTCACAGGATACTATGTCTGA
Protein sequence

>MS.gene06175.t1

MSKLQQLTSKACQASQFITKHGTSYHKQLLEKNKEYIQDPATVEKCQLLAKQLFYTRLASIPNRCESFHKELDYVKQIWKNKQDLKIEDAGIAVLFGLECYAWFCAGQIVGRGFTFTGYYV