AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene70427

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene70427.t1 MTR_3g083050 79.524 210 16 3 1 185 1 208 2.32e-105 301
MS.gene70427.t1 MTR_3g083030 67.532 231 29 3 1 185 1 231 1.24e-100 290
MS.gene70427.t1 MTR_3g083080 49.528 212 75 3 1 185 1 207 7.12e-63 193
MS.gene70427.t1 MTR_3g086030 56.977 86 37 0 49 134 18 103 9.69e-27 99.8
MS.gene70427.t1 MTR_3g082340 37.821 156 85 3 1 148 1 152 2.00e-25 98.2
MS.gene70427.t1 MTR_3g082420 42.017 119 63 2 30 148 39 151 8.55e-25 96.7
MS.gene70427.t1 MTR_3g083150 33.180 217 107 5 1 184 1 212 9.69e-21 85.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 42 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTCTTTCATCGCAGCTTTC+TGG 0.028678 3.1:+66141528 None:intergenic
TTGCAGAATGTCGACAAATT+TGG 0.208783 3.1:-66141583 None:intergenic
GCGCTTTATTTACAAGAATA+AGG 0.246265 3.1:-66141361 MS.gene70427:CDS
CGCGCGCATATAAACATAAA+AGG 0.298624 3.1:+66141381 None:intergenic
CAGCCCTGTTATATCTTTCC+AGG 0.337582 3.1:-66140870 MS.gene70427:CDS
TCATCGCAGCTTTCTGGAGC+TGG 0.351234 3.1:+66141534 None:intergenic
AAAGAGGGAAGCGGGTGAAA+TGG 0.363098 3.1:-66141512 MS.gene70427:CDS
CAATTACAATGCTGAAAATC+AGG 0.386367 3.1:-66141081 MS.gene70427:CDS
TCCAGGCCGAAGTCAGGAAT+TGG 0.401904 3.1:-66140853 MS.gene70427:CDS
TCGGCCTGGAAAGATATAAC+AGG 0.404862 3.1:+66140866 None:intergenic
ATGGCACATGACTTGATGAT+AGG 0.460123 3.1:+66140818 None:intergenic
AGGCGACGATCATCGGTCAT+AGG 0.464071 3.1:+66141137 None:intergenic
AAGAGGGAAGCGGGTGAAAT+GGG 0.477294 3.1:-66141511 MS.gene70427:CDS
TATCTTTCCAGGCCGAAGTC+AGG 0.478343 3.1:-66140859 MS.gene70427:CDS
AAAGATATAACAGGGCTGTT+GGG 0.481315 3.1:+66140875 None:intergenic
TCCAATTCCTGACTTCGGCC+TGG 0.483561 3.1:+66140852 None:intergenic
GAAAGATATAACAGGGCTGT+TGG 0.497566 3.1:+66140874 None:intergenic
CGCAGCTTTCTGGAGCTGGT+CGG 0.524358 3.1:+66141538 None:intergenic
GAGACGAAGGCGACGATCAT+CGG 0.531298 3.1:+66141130 None:intergenic
TACAATGCTGAAAATCAGGC+AGG 0.532697 3.1:-66141077 MS.gene70427:intron
TCAGGAAAATGTGGCGGTGT+CGG 0.534211 3.1:-66141167 MS.gene70427:CDS
GTCTAACGCAAGCTTGCAGA+CGG 0.539023 3.1:+66141103 None:intergenic
GACGATCATCGGTCATAGGA+AGG 0.543064 3.1:+66141141 None:intergenic
CCAGAAAGCTGCGATGAAAG+AGG 0.543643 3.1:-66141528 MS.gene70427:CDS
CTGCGATGAAAGAGGGAAGC+GGG 0.550268 3.1:-66141520 MS.gene70427:CDS
CGATCATCGGTCATAGGAAG+GGG 0.552083 3.1:+66141143 None:intergenic
ACGATCATCGGTCATAGGAA+GGG 0.583505 3.1:+66141142 None:intergenic
TGGTCGGTTGACACTGAACA+AGG 0.584593 3.1:+66141554 None:intergenic
CAGAAAGCTGCGATGAAAGA+GGG 0.588588 3.1:-66141527 MS.gene70427:CDS
GTCGGTTGACACTGAACAAG+GGG 0.589765 3.1:+66141556 None:intergenic
TAAGGAGATTGAAGTAGCCA+TGG 0.591215 3.1:-66141322 MS.gene70427:CDS
AGGCCGAAGTCAGGAATTGG+AGG 0.613344 3.1:-66140850 MS.gene70427:CDS
TGCAGACGGGAGTGAGACGA+AGG 0.616805 3.1:+66141117 None:intergenic
ACTCCTCCAATTCCTGACTT+CGG 0.621511 3.1:+66140847 None:intergenic
TCTAACGCAAGCTTGCAGAC+GGG 0.623247 3.1:+66141104 None:intergenic
GCACTCATCATACTCAGCCA+TGG 0.631008 3.1:+66141305 None:intergenic
CGGCCTGGAAAGATATAACA+GGG 0.637548 3.1:+66140867 None:intergenic
GCTGCGATGAAAGAGGGAAG+CGG 0.653611 3.1:-66141521 MS.gene70427:CDS
GGTCGGTTGACACTGAACAA+GGG 0.674801 3.1:+66141555 None:intergenic
GCACATGACTTGATGATAGG+TGG 0.677186 3.1:+66140821 None:intergenic
AAAATCTCAGGAAAATGTGG+CGG 0.681893 3.1:-66141173 MS.gene70427:CDS
TCGGTTGACACTGAACAAGG+GGG 0.768468 3.1:+66141557 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTATTTTTATTTTTTA+GGG - chr3.1:66141395-66141414 MS.gene70427:CDS 0.0%
!!! TATTTTTATTTTTATTTTTT+AGG - chr3.1:66141394-66141413 MS.gene70427:CDS 0.0%
!!! TTAATTTTAATGATTCATTC+TGG - chr3.1:66141142-66141161 MS.gene70427:CDS 15.0%
!! GAAATCGAAAAAATATGAAT+GGG - chr3.1:66140915-66140934 MS.gene70427:intron 20.0%
!!! CATTCATATTTTTTCGATTT+CGG + chr3.1:66140916-66140935 None:intergenic 20.0%
! CGAAATCGAAAAAATATGAA+TGG - chr3.1:66140914-66140933 MS.gene70427:intron 25.0%
!!! TATTTTTTCGATTTCGGTTT+TGG + chr3.1:66140910-66140929 None:intergenic 25.0%
AATTTCTTCTTGTGCTTGAA+AGG + chr3.1:66141486-66141505 None:intergenic 30.0%
ACGTCAACAAAAACGAAATT+TGG + chr3.1:66141422-66141441 None:intergenic 30.0%
CAATTACAATGCTGAAAATC+AGG - chr3.1:66141300-66141319 MS.gene70427:CDS 30.0%
TAGTTGAGTTACTTACACTT+AGG + chr3.1:66141110-66141129 None:intergenic 30.0%
! CTCCTTATCTTTTTGAATCT+GGG + chr3.1:66141046-66141065 None:intergenic 30.0%
! TCTCCTTATCTTTTTGAATC+TGG + chr3.1:66141047-66141066 None:intergenic 30.0%
!! GCGCTTTATTTACAAGAATA+AGG - chr3.1:66141020-66141039 MS.gene70427:intron 30.0%
!! TTTTCCTGAGATTTTTGGAA+CGG + chr3.1:66141203-66141222 None:intergenic 30.0%
AAAATCTCAGGAAAATGTGG+CGG - chr3.1:66141208-66141227 MS.gene70427:intron 35.0%
AAAGATATAACAGGGCTGTT+GGG + chr3.1:66141509-66141528 None:intergenic 35.0%
CCAAAAATCTCAGGAAAATG+TGG - chr3.1:66141205-66141224 MS.gene70427:intron 35.0%
GTAATGTAATAGAAACCACC+AGG + chr3.1:66141464-66141483 None:intergenic 35.0%
! CCACATTTTCCTGAGATTTT+TGG + chr3.1:66141208-66141227 None:intergenic 35.0%
!!! TTCGATTTCGGTTTTGGTTT+TGG + chr3.1:66140904-66140923 None:intergenic 35.0%
!!! TTCGGTTTTGGTTTTGGTTT+TGG + chr3.1:66140898-66140917 None:intergenic 35.0%
!!! TTTCCTGAGATTTTTGGAAC+GGG + chr3.1:66141202-66141221 None:intergenic 35.0%
ATAGAAACCACCAGGTCTAT+AGG + chr3.1:66141456-66141475 None:intergenic 40.0%
CGCGCGCATATAAACATAAA+AGG + chr3.1:66141003-66141022 None:intergenic 40.0%
GAAAGATATAACAGGGCTGT+TGG + chr3.1:66141510-66141529 None:intergenic 40.0%
GGCCCAGATTCAAAAAGATA+AGG - chr3.1:66141041-66141060 MS.gene70427:intron 40.0%
TAAGGAGATTGAAGTAGCCA+TGG - chr3.1:66141059-66141078 MS.gene70427:intron 40.0%
TACAATGCTGAAAATCAGGC+AGG - chr3.1:66141304-66141323 MS.gene70427:CDS 40.0%
! ATGGCACATGACTTGATGAT+AGG + chr3.1:66141566-66141585 None:intergenic 40.0%
!!! TTCCTGAGATTTTTGGAACG+GGG + chr3.1:66141201-66141220 None:intergenic 40.0%
AAGACAACCTATAGACCTGG+TGG - chr3.1:66141446-66141465 MS.gene70427:CDS 45.0%
ACGATCATCGGTCATAGGAA+GGG + chr3.1:66141242-66141261 None:intergenic 45.0%
ACTCCTCCAATTCCTGACTT+CGG + chr3.1:66141537-66141556 None:intergenic 45.0%
ATCCCCGTTCCAAAAATCTC+AGG - chr3.1:66141196-66141215 MS.gene70427:CDS 45.0%
CAGAAAGCTGCGATGAAAGA+GGG - chr3.1:66140854-66140873 MS.gene70427:CDS 45.0%
CAGCCCTGTTATATCTTTCC+AGG - chr3.1:66141511-66141530 MS.gene70427:CDS 45.0%
CGGCCTGGAAAGATATAACA+GGG + chr3.1:66141517-66141536 None:intergenic 45.0%
GTCAAGACAACCTATAGACC+TGG - chr3.1:66141443-66141462 MS.gene70427:CDS 45.0%
TCGGCCTGGAAAGATATAAC+AGG + chr3.1:66141518-66141537 None:intergenic 45.0%
TGGACAACACAACACAACAC+AGG - chr3.1:66141162-66141181 MS.gene70427:CDS 45.0%
! GCACATGACTTGATGATAGG+TGG + chr3.1:66141563-66141582 None:intergenic 45.0%
AAAGAGGGAAGCGGGTGAAA+TGG - chr3.1:66140869-66140888 MS.gene70427:CDS 50.0%
AAGAGGGAAGCGGGTGAAAT+GGG - chr3.1:66140870-66140889 MS.gene70427:CDS 50.0%
CCAGAAAGCTGCGATGAAAG+AGG - chr3.1:66140853-66140872 MS.gene70427:CDS 50.0%
CCTCTTTCATCGCAGCTTTC+TGG + chr3.1:66140856-66140875 None:intergenic 50.0%
CGATCATCGGTCATAGGAAG+GGG + chr3.1:66141241-66141260 None:intergenic 50.0%
GACGATCATCGGTCATAGGA+AGG + chr3.1:66141243-66141262 None:intergenic 50.0%
GCACTCATCATACTCAGCCA+TGG + chr3.1:66141079-66141098 None:intergenic 50.0%
GGTCGGTTGACACTGAACAA+GGG + chr3.1:66140829-66140848 None:intergenic 50.0%
GTCGGTTGACACTGAACAAG+GGG + chr3.1:66140828-66140847 None:intergenic 50.0%
GTCTAACGCAAGCTTGCAGA+CGG + chr3.1:66141281-66141300 None:intergenic 50.0%
TATCTTTCCAGGCCGAAGTC+AGG - chr3.1:66141522-66141541 MS.gene70427:CDS 50.0%
TCAGGAAAATGTGGCGGTGT+CGG - chr3.1:66141214-66141233 MS.gene70427:intron 50.0%
TCGGTTGACACTGAACAAGG+GGG + chr3.1:66140827-66140846 None:intergenic 50.0%
TCTAACGCAAGCTTGCAGAC+GGG + chr3.1:66141280-66141299 None:intergenic 50.0%
TGGTCGGTTGACACTGAACA+AGG + chr3.1:66140830-66140849 None:intergenic 50.0%
AGGCCGAAGTCAGGAATTGG+AGG - chr3.1:66141531-66141550 MS.gene70427:CDS 55.0%
AGGCGACGATCATCGGTCAT+AGG + chr3.1:66141247-66141266 None:intergenic 55.0%
CTGCGATGAAAGAGGGAAGC+GGG - chr3.1:66140861-66140880 MS.gene70427:CDS 55.0%
GAGACGAAGGCGACGATCAT+CGG + chr3.1:66141254-66141273 None:intergenic 55.0%
GCTGCGATGAAAGAGGGAAG+CGG - chr3.1:66140860-66140879 MS.gene70427:CDS 55.0%
TCCAATTCCTGACTTCGGCC+TGG + chr3.1:66141532-66141551 None:intergenic 55.0%
TCCAGGCCGAAGTCAGGAAT+TGG - chr3.1:66141528-66141547 MS.gene70427:CDS 55.0%
!! TCATCGCAGCTTTCTGGAGC+TGG + chr3.1:66140850-66140869 None:intergenic 55.0%
TGCAGACGGGAGTGAGACGA+AGG + chr3.1:66141267-66141286 None:intergenic 60.0%
!! CGCAGCTTTCTGGAGCTGGT+CGG + chr3.1:66140846-66140865 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 66140805 66141598 66140805 ID=MS.gene70427
chr3.1 mRNA 66140805 66141598 66140805 ID=MS.gene70427.t1;Parent=MS.gene70427
chr3.1 exon 66141290 66141598 66141290 ID=MS.gene70427.t1.exon1;Parent=MS.gene70427.t1
chr3.1 CDS 66141290 66141598 66141290 ID=cds.MS.gene70427.t1;Parent=MS.gene70427.t1
chr3.1 exon 66141078 66141219 66141078 ID=MS.gene70427.t1.exon2;Parent=MS.gene70427.t1
chr3.1 CDS 66141078 66141219 66141078 ID=cds.MS.gene70427.t1;Parent=MS.gene70427.t1
chr3.1 exon 66140805 66140911 66140805 ID=MS.gene70427.t1.exon3;Parent=MS.gene70427.t1
chr3.1 CDS 66140805 66140911 66140805 ID=cds.MS.gene70427.t1;Parent=MS.gene70427.t1
Gene Sequence

>MS.gene70427

ATGTCGACAAATTTGGATACCCCCTTGTTCAGTGTCAACCGACCAGCTCCAGAAAGCTGCGATGAAAGAGGGAAGCGGGTGAAATGGGAACCAAAACCAAAACCAAAACCGAAATCGAAAAAATATGAATGGGAATCGAAACGCGTTGAAGATCTTGAGATGAGTGACTTCTCTATGTATGACGATGACATTGAGCCTTTTATGTTTATATGCGCGCGCTTTATTTACAAGAATAAGGCCCAGATTCAAAAAGATAAGGAGATTGAAGTAGCCATGGCTGAGTATGATGAGTGCTCTCGCAACCTAAGTGTAAGTAACTCAACTATCTATCTTAATTTTAATTTTAATGATTCATTCTGGACAACACAACACAACACAGGTGTTCGATGCTATCCCCGTTCCAAAAATCTCAGGAAAATGTGGCGGTGTCGGTCCCCTTCCTATGACCGATGATCGTCGCCTTCGTCTCACTCCCGTCTGCAAGCTTGCGTTAGACAATTACAATGCTGAAAATCAGGCAGGTTTCAATACTTATGATGATTATAGTATGTTTATGTTTATTTATTCATTCATTGATCATCTAATATACTATTTTTATTTTTATTTTTTAGGGTCCAAATTTCGTTTTTGTTGACGTTGTCAAGACAACCTATAGACCTGGTGGTTTCTATTACATTACCTTTCAAGCACAAGAAGAAATTCCCAACAGCCCTGTTATATCTTTCCAGGCCGAAGTCAGGAATTGGAGGAGTCAGCCACCTATCATCAAGTCATGTGCCATTAAAACTACTTAA
Protein sequence

>MS.gene70427.t1

MSTNLDTPLFSVNRPAPESCDERGKRVKWEPKPKPKPKSKKYEWESKRVEDLEMSDFSMYDDDIEPFMFICARFIYKNKAQIQKDKEIEVAMAEYDECSRNLSVFDAIPVPKISGKCGGVGPLPMTDDRRLRLTPVCKLALDNYNAENQAAQEEIPNSPVISFQAEVRNWRSQPPIIKSCAIKTT