AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene91078

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene91078.t1 MTR_8g099190 95.385 195 9 0 1 195 1 195 6.09e-134 374
MS.gene91078.t1 MTR_8g099190 95.385 195 9 0 1 195 1 195 2.25e-133 373
MS.gene91078.t1 MTR_8g099190 95.385 195 9 0 1 195 1 195 4.15e-133 373
MS.gene91078.t1 MTR_8g099190 88.205 195 8 1 1 195 1 180 3.04e-118 335
MS.gene91078.t1 MTR_5g009720 77.720 193 33 1 1 193 1 183 6.52e-104 298
MS.gene91078.t1 MTR_4g073800 65.990 197 55 2 1 195 1 187 2.60e-86 255
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene91078.t1 AT4G11150 70.833 192 46 1 1 192 1 182 3.08e-93 271
MS.gene91078.t1 AT1G64200 70.312 192 53 1 1 192 1 188 2.20e-92 268
MS.gene91078.t1 AT1G64200 70.312 192 53 1 1 192 1 188 1.11e-91 268
MS.gene91078.t1 AT1G64200 70.312 192 53 1 1 192 1 188 1.24e-91 268
MS.gene91078.t1 AT3G08560 59.898 197 67 2 1 195 1 187 4.55e-74 223

Find 28 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTAAAAGATCTCATTGTTC+AGG 0.350211 4.2:+4928483 MS.gene91078:CDS
TTCGTGAGTGTTGTGATGCT+TGG 0.393565 4.2:-4929069 None:intergenic
CAATGCAGCTGAATGCTTCT+CGG 0.400725 4.2:+4928326 MS.gene91078:CDS
GGCGGATAAATCTCACCATC+TGG 0.473875 4.2:-4927352 None:intergenic
TCGTGAGTGTTGTGATGCTT+GGG 0.478089 4.2:-4929068 None:intergenic
GCTCACATTCAAAAGTTCCT+TGG 0.486133 4.2:-4928404 None:intergenic
GTGTTGTGATGCTTGGGTGC+AGG 0.495348 4.2:-4929062 None:intergenic
AATGAAAGAAGTTGCAGCCA+AGG 0.517165 4.2:+4928387 MS.gene91078:CDS
CAATATCGAGAAGCTTCAGT+TGG 0.524663 4.2:+4927548 MS.gene91078:CDS
ACAACACTCACGAACCCTAC+TGG 0.526388 4.2:+4929078 MS.gene91078:CDS
CTTCTGTCTTGTTGAGATGT+CGG 0.530658 4.2:+4928925 MS.gene91078:CDS
TTGTGGTCAACAATGATCTC+TGG 0.546406 4.2:-4929026 None:intergenic
TGTGCTGGATGCAGCTGCAC+AGG 0.546828 4.2:+4928974 MS.gene91078:CDS
GAACATGAACTTTACCAGTA+GGG 0.549069 4.2:-4929092 None:intergenic
TATCTTCAACACGGTGATGA+CGG 0.556951 4.2:-4928426 None:intergenic
GATCTCTCTCTCTGCTGAAG+AGG 0.568633 4.2:+4927400 MS.gene91078:CDS
TCGGAAACATGACGTGCACT+TGG 0.572529 4.2:+4928944 MS.gene91078:CDS
TTGTGATGCTTGGGTGCAGG+TGG 0.576383 4.2:-4929059 None:intergenic
CGACATCTCAACAAGACAGA+AGG 0.583156 4.2:-4928924 None:intergenic
GCACTTGGTAGAACATGTGC+TGG 0.602448 4.2:+4928959 MS.gene91078:CDS
CTCTAAGCAAATCCACCAGA+TGG 0.604393 4.2:+4927337 MS.gene91078:CDS
TGGTCAACAATGATCTCTGG+TGG 0.640783 4.2:-4929023 None:intergenic
AGATCAGACAAGAATATGAG+CGG 0.642819 4.2:+4927589 MS.gene91078:CDS
GGATAAATCTCACCATCTGG+TGG 0.662922 4.2:-4927349 None:intergenic
AGCAGAGAGAGAGATCTCGC+CGG 0.677723 4.2:-4927393 None:intergenic
CATGTAAAATATCTTCAACA+CGG 0.686965 4.2:-4928435 None:intergenic
CAGGTGGAAGATAGACATTG+TGG 0.702848 4.2:-4929043 None:intergenic
TCTTCTCCGAAAATGAACGA+TGG 0.714255 4.2:+4927308 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAAAAAAAAAAAAAAAAC+AGG - chr4.2:4927512-4927531 None:intergenic 10.0%
!! ATCTACAAATAATATAAAAT+TGG - chr4.2:4928635-4928654 None:intergenic 10.0%
!! TTTGAAAAAAATTAAGTAAT+TGG - chr4.2:4928058-4928077 None:intergenic 10.0%
!!! TTTTTTCAAAAAAAAAAATC+CGG + chr4.2:4928068-4928087 MS.gene91078:intron 10.0%
!! ATTTCAGATATTGAATATAT+TGG + chr4.2:4927789-4927808 MS.gene91078:intron 15.0%
!! TCAAATGATAATTATATTAC+TGG + chr4.2:4928781-4928800 MS.gene91078:intron 15.0%
!! CTAGTATATTCATGAAAAAT+TGG + chr4.2:4928717-4928736 MS.gene91078:intron 20.0%
!! TTGATATATTCTAATTTCTG+TGG + chr4.2:4928277-4928296 MS.gene91078:intron 20.0%
! AAAGAGAATGATTAGAGAAA+TGG - chr4.2:4927431-4927450 None:intergenic 25.0%
! AAGTAATTGGATGTAATCAA+AGG - chr4.2:4928045-4928064 None:intergenic 25.0%
! AATTGGTTGAAATTGAATTC+TGG + chr4.2:4927734-4927753 MS.gene91078:intron 25.0%
! CAAAAAACACAATGAAGATA+CGG - chr4.2:4927968-4927987 None:intergenic 25.0%
! CATGTAAAATATCTTCAACA+CGG - chr4.2:4928438-4928457 None:intergenic 25.0%
! CTACAAATGATAAAGATACT+TGG - chr4.2:4928562-4928581 None:intergenic 25.0%
! GATAATTATATTACTGGCAT+AGG + chr4.2:4928787-4928806 MS.gene91078:intron 25.0%
! TAATTGAAGTTACAAGTATG+TGG + chr4.2:4928841-4928860 MS.gene91078:intron 25.0%
! TACATGTCAGATTAAACTTA+AGG + chr4.2:4928133-4928152 MS.gene91078:intron 25.0%
! TATAACATTGAGATTGTGAT+CGG - chr4.2:4927769-4927788 None:intergenic 25.0%
! TATTTCCAAAATATGATGTG+TGG + chr4.2:4928161-4928180 MS.gene91078:intron 25.0%
!! AGATTCTTGTTTACACTTAT+CGG + chr4.2:4928580-4928599 MS.gene91078:intron 25.0%
!! CATGCTAACTTCAATTATTT+TGG - chr4.2:4928819-4928838 None:intergenic 25.0%
!! GTTGAAGATATTTTACATGT+GGG + chr4.2:4928439-4928458 MS.gene91078:CDS 25.0%
!! TGTTGAAGATATTTTACATG+TGG + chr4.2:4928438-4928457 MS.gene91078:CDS 25.0%
!! TTTGAAACAATCAATGAGAA+TGG - chr4.2:4928766-4928785 None:intergenic 25.0%
!! TTTTCTTTCGAATTTCAACT+TGG - chr4.2:4927623-4927642 None:intergenic 25.0%
!!! TTTTTTTTGTTTCTTCGTGT+AGG + chr4.2:4927521-4927540 MS.gene91078:intron 25.0%
ATGAAAAATTGGAGTGATCA+GGG + chr4.2:4928728-4928747 MS.gene91078:intron 30.0%
ATTACTTTGACATTTGTCTG+TGG + chr4.2:4927711-4927730 MS.gene91078:intron 30.0%
TCAATGAGAATGGTTCATTA+AGG - chr4.2:4928756-4928775 None:intergenic 30.0%
TCTAAAAGATCTCATTGTTC+AGG + chr4.2:4928483-4928502 MS.gene91078:CDS 30.0%
TGCAAGATCAAACGATAATT+AGG - chr4.2:4928534-4928553 None:intergenic 30.0%
! AAGTTCCACACATCATATTT+TGG - chr4.2:4928169-4928188 None:intergenic 30.0%
! GAACAATGAGATCTTTTAGA+AGG - chr4.2:4928483-4928502 None:intergenic 30.0%
AAGTTACAAGTATGTGGACT+AGG + chr4.2:4928847-4928866 MS.gene91078:intron 35.0%
AATGACCAGAAATCAAGCTT+TGG - chr4.2:4927882-4927901 None:intergenic 35.0%
AGATCAGACAAGAATATGAG+CGG + chr4.2:4927589-4927608 MS.gene91078:CDS 35.0%
ATGGAAGACGTGTTATATGT+CGG + chr4.2:4928008-4928027 MS.gene91078:intron 35.0%
ATTTGCCAAAGCTTGATTTC+TGG + chr4.2:4927874-4927893 MS.gene91078:intron 35.0%
CATGAAAAATTGGAGTGATC+AGG + chr4.2:4928727-4928746 MS.gene91078:intron 35.0%
GCATTGAAATTTGATCCTCT+CGG + chr4.2:4927474-4927493 MS.gene91078:intron 35.0%
TGAAAAATTGGAGTGATCAG+GGG + chr4.2:4928729-4928748 MS.gene91078:intron 35.0%
TGGATCATTATCGTGATGTT+CGG + chr4.2:4927908-4927927 MS.gene91078:intron 35.0%
TTGACATTTGTCTGTGGAAT+TGG + chr4.2:4927717-4927736 MS.gene91078:intron 35.0%
AATGAAAGAAGTTGCAGCCA+AGG + chr4.2:4928387-4928406 MS.gene91078:CDS 40.0%
ACTCACTGCCACAAACAATT+GGG - chr4.2:4928303-4928322 None:intergenic 40.0%
CAAGAAGCTGAAGAAAAAGC+CGG + chr4.2:4927374-4927393 MS.gene91078:CDS 40.0%
CAATATCGAGAAGCTTCAGT+TGG + chr4.2:4927548-4927567 MS.gene91078:CDS 40.0%
GCTCACATTCAAAAGTTCCT+TGG - chr4.2:4928407-4928426 None:intergenic 40.0%
GGATGTAATCAAAGGCAAGT+TGG - chr4.2:4928037-4928056 None:intergenic 40.0%
TACTCACTGCCACAAACAAT+TGG - chr4.2:4928304-4928323 None:intergenic 40.0%
TATCTTCAACACGGTGATGA+CGG - chr4.2:4928429-4928448 None:intergenic 40.0%
TGTAGAACTGACACTTCTGA+TGG + chr4.2:4927989-4928008 MS.gene91078:intron 40.0%
TTGTGGTCAACAATGATCTC+TGG - chr4.2:4929029-4929048 None:intergenic 40.0%
! CTTCTGTCTTGTTGAGATGT+CGG + chr4.2:4928925-4928944 MS.gene91078:CDS 40.0%
! CTTTTTCTTCAGCTTCTTGG+CGG - chr4.2:4927373-4927392 None:intergenic 40.0%
! TTGTGTCACTATCACATGCA+AGG - chr4.2:4927836-4927855 None:intergenic 40.0%
!! CAGGAGTATTCTGAAAAAGC+AGG + chr4.2:4928993-4929012 MS.gene91078:CDS 40.0%
!! GATTTCTGGTCATTGTCTAG+TGG + chr4.2:4927888-4927907 MS.gene91078:intron 40.0%
AGGAGAATTACATTGCCGAG+AGG - chr4.2:4927492-4927511 None:intergenic 45.0%
CAATGCAGCTGAATGCTTCT+CGG + chr4.2:4928326-4928345 MS.gene91078:CDS 45.0%
CAGGTGGAAGATAGACATTG+TGG - chr4.2:4929046-4929065 None:intergenic 45.0%
CGACATCTCAACAAGACAGA+AGG - chr4.2:4928927-4928946 None:intergenic 45.0%
CTCTAAGCAAATCCACCAGA+TGG + chr4.2:4927337-4927356 MS.gene91078:CDS 45.0%
GGATAAATCTCACCATCTGG+TGG - chr4.2:4927352-4927371 None:intergenic 45.0%
TGGTCAACAATGATCTCTGG+TGG - chr4.2:4929026-4929045 None:intergenic 45.0%
TTCTGTGGCCCAATTGTTTG+TGG + chr4.2:4928292-4928311 MS.gene91078:intron 45.0%
! TCGTGAGTGTTGTGATGCTT+GGG - chr4.2:4929071-4929090 None:intergenic 45.0%
! TTCGTGAGTGTTGTGATGCT+TGG - chr4.2:4929072-4929091 None:intergenic 45.0%
!! CGGCTTTTTCTTCAGCTTCT+TGG - chr4.2:4927376-4927395 None:intergenic 45.0%
GATCTCTCTCTCTGCTGAAG+AGG + chr4.2:4927400-4927419 MS.gene91078:CDS 50.0%
GCACTTGGTAGAACATGTGC+TGG + chr4.2:4928959-4928978 MS.gene91078:CDS 50.0%
GGCGGATAAATCTCACCATC+TGG - chr4.2:4927355-4927374 None:intergenic 50.0%
TCGGAAACATGACGTGCACT+TGG + chr4.2:4928944-4928963 MS.gene91078:CDS 50.0%
!! ATGAAGCACCGAGAGAGACA+CGG - chr4.2:4928114-4928133 None:intergenic 50.0%
AGCAGAGAGAGAGATCTCGC+CGG - chr4.2:4927396-4927415 None:intergenic 55.0%
CACCAGACACACGTTGACAC+CGG - chr4.2:4928090-4928109 None:intergenic 55.0%
GTGTTGTGATGCTTGGGTGC+AGG - chr4.2:4929065-4929084 None:intergenic 55.0%
TCTGGTGTCCGTGTCTCTCT+CGG + chr4.2:4928103-4928122 MS.gene91078:intron 55.0%
TTGTGATGCTTGGGTGCAGG+TGG - chr4.2:4929062-4929081 None:intergenic 55.0%
! ATCCGGTGTCAACGTGTGTC+TGG + chr4.2:4928085-4928104 MS.gene91078:intron 55.0%
TGTGCTGGATGCAGCTGCAC+AGG + chr4.2:4928974-4928993 MS.gene91078:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 4927320 4929099 4927320 ID=MS.gene91078
chr4.2 mRNA 4927320 4929099 4927320 ID=MS.gene91078.t1;Parent=MS.gene91078
chr4.2 exon 4927320 4927421 4927320 ID=MS.gene91078.t1.exon1;Parent=MS.gene91078.t1
chr4.2 CDS 4927320 4927421 4927320 ID=cds.MS.gene91078.t1;Parent=MS.gene91078.t1
chr4.2 exon 4927543 4927643 4927543 ID=MS.gene91078.t1.exon2;Parent=MS.gene91078.t1
chr4.2 CDS 4927543 4927643 4927543 ID=cds.MS.gene91078.t1;Parent=MS.gene91078.t1
chr4.2 exon 4928318 4928504 4928318 ID=MS.gene91078.t1.exon3;Parent=MS.gene91078.t1
chr4.2 CDS 4928318 4928504 4928318 ID=cds.MS.gene91078.t1;Parent=MS.gene91078.t1
chr4.2 exon 4928903 4929099 4928903 ID=MS.gene91078.t1.exon4;Parent=MS.gene91078.t1
chr4.2 CDS 4928903 4929099 4928903 ID=cds.MS.gene91078.t1;Parent=MS.gene91078.t1
Gene Sequence

>MS.gene91078

ATGAACGATGGTGATGTCTCTAAGCAAATCCACCAGATGGTGAGATTTATCCGCCAAGAAGCTGAAGAAAAAGCCGGCGAGATCTCTCTCTCTGCTGAAGAGGTAACGCCATTTCTCTAATCATTCTCTTTTCTCGATCAAGCTTCATTGCATTGCATTGAAATTTGATCCTCTCGGCAATGTAATTCTCCTGTTTTTTTTTTTTTTTTGTTTCTTCGTGTAGGAATTCAATATCGAGAAGCTTCAGTTGGTTGAAGCTGAGAAGAAGAAGATCAGACAAGAATATGAGCGGAAAGAGCGCCAAGTTGAAATTCGAAAGAAAATGTAATTTTCTCTGAGCTTTTTTTACGCTGTTTTTTTCACTGATAATTTGAACTTTCAATTGTTTTTTATTACTTTGACATTTGTCTGTGGAATTGGTTGAAATTGAATTCTGGTGATCGTTTCCGATCACAATCTCAATGTTATAATTTCAGATATTGAATATATTGGCATATATCTTGTTTTTTTTATCCTTGCATGTGATAGTGACACAAAGCATGTTGATTATTATTATTTGCCAAAGCTTGATTTCTGGTCATTGTCTAGTGGATCATTATCGTGATGTTCGGTTAAATGTAGTTTGATGTTTAATTTAGCTTCACTCCGTATCTTCATTGTGTTTTTTGATGTAGAACTGACACTTCTGATGGAAGACGTGTTATATGTCGGACACCAACTTGCCTTTGATTACATCCAATTACTTAATTTTTTTCAAAAAAAAAAATCCGGTGTCAACGTGTGTCTGGTGTCCGTGTCTCTCTCGGTGCTTCATACATGTCAGATTAAACTTAAGGTTTTTTATTTCCAAAATATGATGTGTGGAACTTATTTTTTTATGTGAAACTTAATTTGTTACATGATGTGAATATTGTGCATTTCTGTATTGTTATTCTAAACTTATAAAAATAGTGCTAGTTGATATATTCTAATTTCTGTGGCCCAATTGTTTGTGGCAGTGAGTACTCAATGCAGCTGAATGCTTCTCGGATCAAAGTTCTTCAAGCTCAAGATGACATTGTTAATTCAATGAAAGAAGTTGCAGCCAAGGAACTTTTGAATGTGAGCCGTCATCACCGTGTTGAAGATATTTTACATGTGGGAAATCATGAGTACAGAAACCTTCTAAAAGATCTCATTGTTCAGGTCAGTTAACATTTAAATATTTTACACCTAATTATCGTTTGATCTTGCATTTTGCCAAGTATCTTTATCATTTGTAGATTCTTGTTTACACTTATCGGTAGTGTTGCTGTTACTTACTTACTGTGTTCCAATTTTATATTATTTGTAGATTTTCGTTTGATCTTGAACATTACACTTATTGTTCACACTTATTGAAGTTACAAGTTATATAACTAGTATATTCATGAAAAATTGGAGTGATCAGGGGACCTTAATGAACCATTCTCATTGATTGTTTCAAATGATAATTATATTACTGGCATAGGAAGCAACCAAAATAATTGAAGTTAGCATGTTTAATTGAAGTTACAAGTATGTGGACTAGGAGTATAATGTAATATAAGATTTGTACATTGCAGAGTTTGCTAAGACTGAGAGAACCTTCTGTCTTGTTGAGATGTCGGAAACATGACGTGCACTTGGTAGAACATGTGCTGGATGCAGCTGCACAGGAGTATTCTGAAAAAGCAGGTGTTCATCCACCAGAGATCATTGTTGACCACAATGTCTATCTTCCACCTGCACCCAAGCATCACAACACTCACGAACCCTACTG
Protein sequence

>MS.gene91078.t1

MNDGDVSKQIHQMVRFIRQEAEEKAGEISLSAEEEFNIEKLQLVEAEKKKIRQEYERKERQVEIRKKIEYSMQLNASRIKVLQAQDDIVNSMKEVAAKELLNVSRHHRVEDILHVGNHEYRNLLKDLIVQSLLRLREPSVLLRCRKHDVHLVEHVLDAAAQEYSEKAGVHPPEIIVDHNVYLPPAPKHHNTHEPY