AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35192

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35192.t1 MTR_4g094720 97.706 218 5 0 1 218 1 218 2.60e-162 447
MS.gene35192.t1 MTR_7g105830 30.556 180 115 3 6 180 74 248 1.54e-22 92.4
MS.gene35192.t1 MTR_1g105090 29.444 180 117 3 6 180 76 250 1.49e-21 90.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35192.t1 AT1G48130 71.818 220 55 2 1 218 1 215 3.14e-115 328
MS.gene35192.t1 AT5G06290 31.111 180 114 3 6 180 82 256 8.93e-24 95.9
MS.gene35192.t1 AT3G11630 31.667 180 113 3 6 180 75 249 5.25e-23 94.0
MS.gene35192.t1 AT5G06290 28.834 163 107 2 6 164 82 239 2.24e-19 83.6

Find 63 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGCTTGATGATTTCTCTTT+TGG 0.133784 4.4:-18880034 None:intergenic
TCCCCTGGCTTCCAGTTAGC+AGG 0.316622 4.4:-18880331 None:intergenic
ATGTTCCTCCCAGTTGTTGC+AGG 0.342538 4.4:-18880247 None:intergenic
CCATTGGAATCTTTCTCATC+AGG 0.347454 4.4:-18880072 None:intergenic
TATATATGTACCTTCTTATC+TGG 0.349549 4.4:-18880129 None:intergenic
CCAAGCTCAGTGGTACAAAC+TGG 0.350619 4.4:-18879773 None:intergenic
TTTCTGTACCCTGCAACAAC+TGG 0.357498 4.4:+18880238 MS.gene35192:CDS
CATATCCTTAGCTTGTTCAT+TGG 0.360719 4.4:-18880380 None:intergenic
AAATTGCAACCCCTGCTAAC+TGG 0.361486 4.4:+18880320 MS.gene35192:CDS
TGCAGATCTTCCATCCAAAA+AGG 0.376713 4.4:+18880423 MS.gene35192:CDS
CTTGTGTAGTATCAACTTCA+AGG 0.408006 4.4:-18879679 None:intergenic
GCTTGTTCATTGGTAACATC+AGG 0.425824 4.4:-18880370 None:intergenic
ACAATATGAAGAGCCCTTGA+TGG 0.428726 4.4:-18880102 None:intergenic
ACCCCTGCTAACTGGAAGCC+AGG 0.430708 4.4:+18880328 MS.gene35192:CDS
TACCACTGAGCTTGGTAAGA+TGG 0.430872 4.4:+18879781 MS.gene35192:CDS
CCCCTGGCTTCCAGTTAGCA+GGG 0.440132 4.4:-18880330 None:intergenic
TCCACTCATTGTGAGATTCA+AGG 0.461092 4.4:-18879865 None:intergenic
AAACGAGGAGTTATGCTGTT+AGG 0.461288 4.4:+18879827 MS.gene35192:CDS
AATATGCCAGGCCTTACTAT+AGG 0.481380 4.4:+18879641 None:intergenic
ACCATTCTCTTCTCTCATCC+AGG 0.497155 4.4:+18879740 MS.gene35192:CDS
CAATGGGAATTTACCATCAA+GGG 0.497458 4.4:+18880089 MS.gene35192:CDS
ATCACTTCTGTTCTGATACA+TGG 0.498086 4.4:+18879717 MS.gene35192:CDS
GTAGTATCAACTTCAAGGTC+AGG 0.507580 4.4:-18879674 None:intergenic
ATCAAGGGCTCTTCATATTG+TGG 0.511782 4.4:+18880104 MS.gene35192:CDS
CTGCAGTCTTAAAACCTTGA+GGG 0.516211 4.4:-18880405 None:intergenic
ACATCAGGAGAAATGACAAC+AGG 0.519996 4.4:-18880355 None:intergenic
CCAATGGGAATTTACCATCA+AGG 0.520641 4.4:+18880088 MS.gene35192:CDS
TCAAGGGCTCTTCATATTGT+GGG 0.523725 4.4:+18880105 MS.gene35192:CDS
TGTTCCTCCCAGTTGTTGCA+GGG 0.527210 4.4:-18880246 None:intergenic
TTCTGTACCCTGCAACAACT+GGG 0.528210 4.4:+18880239 MS.gene35192:CDS
CTGATGAGAAAGATTCCAAT+GGG 0.528282 4.4:+18880073 MS.gene35192:CDS
GAATTGTGTCACCTATAGTA+AGG 0.528944 4.4:-18879652 None:intergenic
CAAGCTCAGTGGTACAAACT+GGG 0.530027 4.4:-18879772 None:intergenic
TCAAAACTAGAAAATATGCC+AGG 0.532876 4.4:+18879629 None:intergenic
CCAGTTTGTACCACTGAGCT+TGG 0.535145 4.4:+18879773 MS.gene35192:CDS
GTAAATGCAGCCAGGTGCTA+AGG 0.544504 4.4:+18879987 MS.gene35192:intron
CCCCTGCTAACTGGAAGCCA+GGG 0.547614 4.4:+18880329 MS.gene35192:CDS
GTGTCACCTATAGTAAGGCC+TGG 0.556059 4.4:-18879647 None:intergenic
CAAACTGGGGTAAAATCACC+TGG 0.556076 4.4:-18879758 None:intergenic
CCCTGGCTTCCAGTTAGCAG+GGG 0.564511 4.4:-18880329 None:intergenic
ATGTATCAGAACAGAAGTGA+TGG 0.570051 4.4:-18879715 None:intergenic
ACCTTGAATCTCACAATGAG+TGG 0.571324 4.4:+18879864 MS.gene35192:CDS
CCTGATGAGAAAGATTCCAA+TGG 0.571797 4.4:+18880072 MS.gene35192:CDS
TGTTACCAATGAACAAGCTA+AGG 0.572171 4.4:+18880375 MS.gene35192:CDS
TATTGTGGGACCAGATAAGA+AGG 0.572882 4.4:+18880119 MS.gene35192:CDS
CCTTGATGGTAAATTCCCAT+TGG 0.577339 4.4:-18880088 None:intergenic
GAAATGACAACAGGTTCCCC+TGG 0.579339 4.4:-18880346 None:intergenic
TGCAACAACTGGGAGGAACA+TGG 0.585961 4.4:+18880249 MS.gene35192:CDS
GGATAGTTCACCTTAGCACC+TGG 0.589170 4.4:-18879997 None:intergenic
TCTGCAGTCTTAAAACCTTG+AGG 0.590174 4.4:-18880406 None:intergenic
GCTAAGGATATGTTCCCTCA+AGG 0.596047 4.4:+18880391 MS.gene35192:CDS
ACCTGGATGAGAGAAGAGAA+TGG 0.604374 4.4:-18879741 None:intergenic
AATCATCAAGCAACTCAACA+TGG 0.618819 4.4:+18880044 MS.gene35192:CDS
GCAGGCACATTATCAAACAT+TGG 0.624118 4.4:-18880461 None:intergenic
GAACATGGATGAAGTGCTGA+GGG 0.626828 4.4:+18880264 MS.gene35192:CDS
GGAACATGGATGAAGTGCTG+AGG 0.641851 4.4:+18880263 MS.gene35192:CDS
CTTGAAGTTGATACTACACA+AGG 0.656492 4.4:+18879680 MS.gene35192:CDS
GCTTCTGAGTTTAACAAACG+AGG 0.664933 4.4:+18879812 MS.gene35192:CDS
AGCCATCTTACCAAGCTCAG+TGG 0.696126 4.4:-18879783 None:intergenic
CCCTGCTAACTGGAAGCCAG+GGG 0.697213 4.4:+18880330 MS.gene35192:CDS
CATGGATGAAGTGCTGAGGG+TGG 0.707751 4.4:+18880267 MS.gene35192:CDS
AAGCTCAGTGGTACAAACTG+GGG 0.719818 4.4:-18879771 None:intergenic
TGTACCCTGCAACAACTGGG+AGG 0.722121 4.4:+18880242 MS.gene35192:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAAATTAAACAAACATTT+AGG - chr4.4:18880202-18880221 None:intergenic 15.0%
!! ACAAATTAAACAAACATTTA+GGG - chr4.4:18880201-18880220 None:intergenic 15.0%
! GAAACATGCATACAAAATTA+TGG - chr4.4:18879946-18879965 None:intergenic 25.0%
! TATATATGTACCTTCTTATC+TGG - chr4.4:18880132-18880151 None:intergenic 25.0%
GTGGAAAATAGGAAAACTTA+CGG - chr4.4:18879912-18879931 None:intergenic 30.0%
!! TGCTTGATGATTTCTCTTTT+GGG - chr4.4:18880036-18880055 None:intergenic 30.0%
!! TTGCTTGATGATTTCTCTTT+TGG - chr4.4:18880037-18880056 None:intergenic 30.0%
!!! CTTTTGGGATCAGTAATTAT+TGG - chr4.4:18880021-18880040 None:intergenic 30.0%
AATCATCAAGCAACTCAACA+TGG + chr4.4:18880044-18880063 MS.gene35192:CDS 35.0%
ATCACTTCTGTTCTGATACA+TGG + chr4.4:18879717-18879736 MS.gene35192:CDS 35.0%
ATGTATCAGAACAGAAGTGA+TGG - chr4.4:18879718-18879737 None:intergenic 35.0%
CAATGGGAATTTACCATCAA+GGG + chr4.4:18880089-18880108 MS.gene35192:CDS 35.0%
CTGATGAGAAAGATTCCAAT+GGG + chr4.4:18880073-18880092 MS.gene35192:CDS 35.0%
CTTGTGTAGTATCAACTTCA+AGG - chr4.4:18879682-18879701 None:intergenic 35.0%
GAATTGTGTCACCTATAGTA+AGG - chr4.4:18879655-18879674 None:intergenic 35.0%
TGTTACCAATGAACAAGCTA+AGG + chr4.4:18880375-18880394 MS.gene35192:CDS 35.0%
! CTAAGATACTCCTTTTTGGA+TGG - chr4.4:18880436-18880455 None:intergenic 35.0%
! GAACCTAAGATACTCCTTTT+TGG - chr4.4:18880440-18880459 None:intergenic 35.0%
!! CATATCCTTAGCTTGTTCAT+TGG - chr4.4:18880383-18880402 None:intergenic 35.0%
!! CATCCAAAAAGGAGTATCTT+AGG + chr4.4:18880434-18880453 MS.gene35192:CDS 35.0%
!! CTTGAAGTTGATACTACACA+AGG + chr4.4:18879680-18879699 MS.gene35192:CDS 35.0%
AAACGAGGAGTTATGCTGTT+AGG + chr4.4:18879827-18879846 MS.gene35192:CDS 40.0%
AATTATGGTGTGCATGCATG+TGG - chr4.4:18879931-18879950 None:intergenic 40.0%
ACAATATGAAGAGCCCTTGA+TGG - chr4.4:18880105-18880124 None:intergenic 40.0%
ACATCAGGAGAAATGACAAC+AGG - chr4.4:18880358-18880377 None:intergenic 40.0%
ACCTTGAATCTCACAATGAG+TGG + chr4.4:18879864-18879883 MS.gene35192:CDS 40.0%
ATCAAGGGCTCTTCATATTG+TGG + chr4.4:18880104-18880123 MS.gene35192:CDS 40.0%
CCAATGGGAATTTACCATCA+AGG + chr4.4:18880088-18880107 MS.gene35192:CDS 40.0%
CCATTGGAATCTTTCTCATC+AGG - chr4.4:18880075-18880094 None:intergenic 40.0%
CCTGATGAGAAAGATTCCAA+TGG + chr4.4:18880072-18880091 MS.gene35192:CDS 40.0%
CTGCAGTCTTAAAACCTTGA+GGG - chr4.4:18880408-18880427 None:intergenic 40.0%
GCTTCTGAGTTTAACAAACG+AGG + chr4.4:18879812-18879831 MS.gene35192:CDS 40.0%
GTAGTATCAACTTCAAGGTC+AGG - chr4.4:18879677-18879696 None:intergenic 40.0%
TATTGTGGGACCAGATAAGA+AGG + chr4.4:18880119-18880138 MS.gene35192:CDS 40.0%
TCAAGGGCTCTTCATATTGT+GGG + chr4.4:18880105-18880124 MS.gene35192:CDS 40.0%
TCCACTCATTGTGAGATTCA+AGG - chr4.4:18879868-18879887 None:intergenic 40.0%
TCTGCAGTCTTAAAACCTTG+AGG - chr4.4:18880409-18880428 None:intergenic 40.0%
TGCAGATCTTCCATCCAAAA+AGG + chr4.4:18880423-18880442 MS.gene35192:CDS 40.0%
TGTGCATGCATGTGGAAAAT+AGG - chr4.4:18879923-18879942 None:intergenic 40.0%
TTGCAATTGTAAATGCAGCC+AGG + chr4.4:18879979-18879998 MS.gene35192:intron 40.0%
! CCTTGATGGTAAATTCCCAT+TGG - chr4.4:18880091-18880110 None:intergenic 40.0%
! GCTTGTTCATTGGTAACATC+AGG - chr4.4:18880373-18880392 None:intergenic 40.0%
AAATTGCAACCCCTGCTAAC+TGG + chr4.4:18880320-18880339 MS.gene35192:CDS 45.0%
AAGCTCAGTGGTACAAACTG+GGG - chr4.4:18879774-18879793 None:intergenic 45.0%
ACCATTCTCTTCTCTCATCC+AGG + chr4.4:18879740-18879759 MS.gene35192:CDS 45.0%
ACCTGGATGAGAGAAGAGAA+TGG - chr4.4:18879744-18879763 None:intergenic 45.0%
CAAACTGGGGTAAAATCACC+TGG - chr4.4:18879761-18879780 None:intergenic 45.0%
CAAGCTCAGTGGTACAAACT+GGG - chr4.4:18879775-18879794 None:intergenic 45.0%
GCTAAGGATATGTTCCCTCA+AGG + chr4.4:18880391-18880410 MS.gene35192:CDS 45.0%
TACCACTGAGCTTGGTAAGA+TGG + chr4.4:18879781-18879800 MS.gene35192:CDS 45.0%
TTCTGTACCCTGCAACAACT+GGG + chr4.4:18880239-18880258 MS.gene35192:CDS 45.0%
TTTCTGTACCCTGCAACAAC+TGG + chr4.4:18880238-18880257 MS.gene35192:CDS 45.0%
!! GAACATGGATGAAGTGCTGA+GGG + chr4.4:18880264-18880283 MS.gene35192:CDS 45.0%
AGCCATCTTACCAAGCTCAG+TGG - chr4.4:18879786-18879805 None:intergenic 50.0%
ATGTTCCTCCCAGTTGTTGC+AGG - chr4.4:18880250-18880269 None:intergenic 50.0%
CCAAGCTCAGTGGTACAAAC+TGG - chr4.4:18879776-18879795 None:intergenic 50.0%
CCAGTTTGTACCACTGAGCT+TGG + chr4.4:18879773-18879792 MS.gene35192:CDS 50.0%
GAAATGACAACAGGTTCCCC+TGG - chr4.4:18880349-18880368 None:intergenic 50.0%
GGATAGTTCACCTTAGCACC+TGG - chr4.4:18880000-18880019 None:intergenic 50.0%
GTAAATGCAGCCAGGTGCTA+AGG + chr4.4:18879987-18880006 MS.gene35192:intron 50.0%
GTGTCACCTATAGTAAGGCC+TGG - chr4.4:18879650-18879669 None:intergenic 50.0%
TGCAACAACTGGGAGGAACA+TGG + chr4.4:18880249-18880268 MS.gene35192:CDS 50.0%
TGTTCCTCCCAGTTGTTGCA+GGG - chr4.4:18880249-18880268 None:intergenic 50.0%
!! GGAACATGGATGAAGTGCTG+AGG + chr4.4:18880263-18880282 MS.gene35192:CDS 50.0%
TGTACCCTGCAACAACTGGG+AGG + chr4.4:18880242-18880261 MS.gene35192:CDS 55.0%
!! CATGGATGAAGTGCTGAGGG+TGG + chr4.4:18880267-18880286 MS.gene35192:CDS 55.0%
ACCCCTGCTAACTGGAAGCC+AGG + chr4.4:18880328-18880347 MS.gene35192:CDS 60.0%
CCCCTGCTAACTGGAAGCCA+GGG + chr4.4:18880329-18880348 MS.gene35192:CDS 60.0%
CCCCTGGCTTCCAGTTAGCA+GGG - chr4.4:18880333-18880352 None:intergenic 60.0%
CCCTGCTAACTGGAAGCCAG+GGG + chr4.4:18880330-18880349 MS.gene35192:CDS 60.0%
CCCTGGCTTCCAGTTAGCAG+GGG - chr4.4:18880332-18880351 None:intergenic 60.0%
TCCCCTGGCTTCCAGTTAGC+AGG - chr4.4:18880334-18880353 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 18879644 18880471 18879644 ID=MS.gene35192
chr4.4 mRNA 18879644 18880471 18879644 ID=MS.gene35192.t1;Parent=MS.gene35192
chr4.4 exon 18879644 18879910 18879644 ID=MS.gene35192.t1.exon1;Parent=MS.gene35192.t1
chr4.4 CDS 18879644 18879910 18879644 ID=cds.MS.gene35192.t1;Parent=MS.gene35192.t1
chr4.4 exon 18879997 18880140 18879997 ID=MS.gene35192.t1.exon2;Parent=MS.gene35192.t1
chr4.4 CDS 18879997 18880140 18879997 ID=cds.MS.gene35192.t1;Parent=MS.gene35192.t1
chr4.4 exon 18880226 18880471 18880226 ID=MS.gene35192.t1.exon3;Parent=MS.gene35192.t1
chr4.4 CDS 18880226 18880471 18880226 ID=cds.MS.gene35192.t1;Parent=MS.gene35192.t1
Gene Sequence

>MS.gene35192

ATGCCAGGCCTTACTATAGGTGACACAATTCCTGACCTTGAAGTTGATACTACACAAGGCAAGATCAAACTCCATCACTTCTGTTCTGATACATGGACCATTCTCTTCTCTCATCCAGGTGATTTTACCCCAGTTTGTACCACTGAGCTTGGTAAGATGGCTCAATATGCTTCTGAGTTTAACAAACGAGGAGTTATGCTGTTAGGTATGTCTTGTGATGACCTTGAATCTCACAATGAGTGGATCAAAGACATTGAAGCACATACCGTAAGTTTTCCTATTTTCCACATGCATGCACACCATAATTTTGTATGCATGTTTCTAAATAAACTTATTTGCAATTGTAAATGCAGCCAGGTGCTAAGGTGAACTATCCAATAATTACTGATCCCAAAAGAGAAATCATCAAGCAACTCAACATGGTTGATCCTGATGAGAAAGATTCCAATGGGAATTTACCATCAAGGGCTCTTCATATTGTGGGACCAGATAAGAAGGTACATATATATCTTTTGACTAAATTATTTTTATAAAAATTTGCAGTCTTCATTCTTCCCTAAATGTTTGTTTAATTTGTTGCAGATTAAGTTGAGTTTTCTGTACCCTGCAACAACTGGGAGGAACATGGATGAAGTGCTGAGGGTGGTAGAGTCACTACAGAAAGCTTCGAAGTACAAAATTGCAACCCCTGCTAACTGGAAGCCAGGGGAACCTGTTGTCATTTCTCCTGATGTTACCAATGAACAAGCTAAGGATATGTTCCCTCAAGGTTTTAAGACTGCAGATCTTCCATCCAAAAAGGAGTATCTTAGGTTCACCAATGTTTGA
Protein sequence

>MS.gene35192.t1

MPGLTIGDTIPDLEVDTTQGKIKLHHFCSDTWTILFSHPGDFTPVCTTELGKMAQYASEFNKRGVMLLGMSCDDLESHNEWIKDIEAHTPGAKVNYPIITDPKREIIKQLNMVDPDEKDSNGNLPSRALHIVGPDKKIKLSFLYPATTGRNMDEVLRVVESLQKASKYKIATPANWKPGEPVVISPDVTNEQAKDMFPQGFKTADLPSKKEYLRFTNV