AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71285


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71285.t1 MTR_3g083080 45.113 133 64 4 18 150 72 195 5.10e-26 98.6
MS.gene71285.t1 MTR_3g080680 46.809 141 56 6 16 140 44 181 1.69e-23 92.0
MS.gene71285.t1 MTR_3g082420 37.143 175 74 7 2 140 30 204 2.92e-22 89.4
MS.gene71285.t1 MTR_3g082340 39.597 149 75 5 7 140 57 205 3.80e-22 89.0
MS.gene71285.t1 MTR_3g083030 45.528 123 59 4 18 140 97 211 1.67e-20 84.7
MS.gene71285.t1 MTR_3g083050 45.528 123 59 4 18 140 74 188 2.13e-20 84.0
MS.gene71285.t1 MTR_4g055800 36.364 154 64 4 11 139 127 271 2.32e-17 77.4
MS.gene71285.t1 MTR_3g083150 39.815 108 55 5 38 139 91 194 1.75e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCGGTTGTGATCCCAATTC+AGG 0.283996 3.4:+78142590 None:intergenic
TCTCTCCGACCTTGCTTTGA+AGG 0.298998 3.4:-78142267 MS.gene71285:CDS
CAAAATGTCGAAACCTGAAT+TGG 0.303444 3.4:-78142603 None:intergenic
AAGCATGACCAAATGCTTTA+CGG 0.311912 3.4:+78140899 None:intergenic
GTCAGCAATTAGTTCTTCTA+TGG 0.315331 3.4:+78142511 None:intergenic
AGTTGTTGTAGCATGGATAT+TGG 0.329322 3.4:+78142010 None:intergenic
CCCATTGCTAATAGGAATAT+AGG 0.355889 3.4:-78140928 MS.gene71285:CDS
AGAGGCAACCCATTGCTAAT+AGG 0.387747 3.4:-78140936 MS.gene71285:CDS
GGAATAAACCGTAAAGCATT+TGG 0.390050 3.4:-78140907 MS.gene71285:CDS
CCATGCTACAACAACTTTCC+AGG 0.393947 3.4:-78142003 MS.gene71285:CDS
TCCTATATTCCTATTAGCAA+TGG 0.443608 3.4:+78140927 None:intergenic
CCTATATTCCTATTAGCAAT+GGG 0.448136 3.4:+78140928 None:intergenic
ACTGCTATTGGCTGTGGTGG+TGG 0.463061 3.4:-78142080 MS.gene71285:CDS
TCCGAATCGTGTTTCGATTG+CGG 0.463704 3.4:+78142572 None:intergenic
AAGATCTTCGGTTAAGTCAA+TGG 0.464314 3.4:+78142307 None:intergenic
GGATTACAATCAAAATAATC+AGG 0.466466 3.4:-78142246 MS.gene71285:intron
TGCATATCAAGAATGTCTAC+AGG 0.476197 3.4:-78140877 MS.gene71285:CDS
CCACATAACTCTAGAACTGC+TGG 0.481125 3.4:+78142341 None:intergenic
AAAATGTCGAAACCTGAATT+GGG 0.487541 3.4:-78142602 MS.gene71285:CDS
GTCAAGTGTACCACTGCTAT+TGG 0.493427 3.4:-78142092 MS.gene71285:CDS
ACCGCAATCGAAACACGATT+CGG 0.495086 3.4:-78142573 MS.gene71285:CDS
CGACGACGATGACGAGTTTG+CGG 0.511755 3.4:-78142546 MS.gene71285:CDS
TCGGAGAGAGCAACGAGAGT+AGG 0.517372 3.4:+78142281 None:intergenic
AGATCTTCGGTTAAGTCAAT+GGG 0.517721 3.4:+78142308 None:intergenic
CGAGTTTGCGGAAGAGAAAG+AGG 0.530206 3.4:-78142534 MS.gene71285:CDS
GAGAGTAGGACGAAGATCTT+CGG 0.531389 3.4:+78142295 None:intergenic
TGTACCACTGCTATTGGCTG+TGG 0.535578 3.4:-78142086 MS.gene71285:CDS
GATTGTAATCCTTCAAAGCA+AGG 0.537388 3.4:+78142258 None:intergenic
CATCATCCCATACTTCGGCC+TGG 0.538029 3.4:+78141985 None:intergenic
ACCACTGCTATTGGCTGTGG+TGG 0.563850 3.4:-78142083 MS.gene71285:CDS
CCTGGAAAGTTGTTGTAGCA+TGG 0.566074 3.4:+78142003 None:intergenic
GTTGTAGCATGGATATTGGA+AGG 0.573026 3.4:+78142014 None:intergenic
CCAGCAGTTCTAGAGTTATG+TGG 0.599177 3.4:-78142341 MS.gene71285:CDS
TAGCAGTGGTACACTTGACA+AGG 0.661404 3.4:+78142096 None:intergenic
GGATGATAGATAGCATCGAA+CGG 0.667704 3.4:+78142362 None:intergenic
ACCACCACAGCCAATAGCAG+TGG 0.671651 3.4:+78142082 None:intergenic
GTAATCCTTCAAAGCAAGGT+CGG 0.676410 3.4:+78142262 None:intergenic
GCATATCAAGAATGTCTACA+GGG 0.693559 3.4:-78140876 MS.gene71285:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAATTTAAAACTTTTTAAC+CGG + chr3.4:78142258-78142277 None:intergenic 10.0%
!! AATTGTTCTTCTTAATTATT+AGG - chr3.4:78141331-78141350 MS.gene71285:intron 15.0%
!! ATTGTTCTTCTTAATTATTA+GGG - chr3.4:78141332-78141351 MS.gene71285:intron 15.0%
!!! TTTTCTTGGAAATTTATAAA+TGG - chr3.4:78141600-78141619 MS.gene71285:intron 15.0%
!! AAAGTCAAATACAAAATCAA+TGG + chr3.4:78141641-78141660 None:intergenic 20.0%
!! AAGAAAAGATTAAACATGTA+AGG + chr3.4:78141587-78141606 None:intergenic 20.0%
!! ATCTTAATAATATACAACCA+TGG + chr3.4:78141809-78141828 None:intergenic 20.0%
!! ATTAAATATCGTAACTTCAA+TGG + chr3.4:78141682-78141701 None:intergenic 20.0%
!!! TAGAGTGTATTAGATTTTAA+TGG + chr3.4:78141543-78141562 None:intergenic 20.0%
!!! TTACATGTTTAATCTTTTCT+TGG - chr3.4:78141586-78141605 MS.gene71285:intron 20.0%
! CCATATAGATAATCAGAATT+CGG - chr3.4:78142386-78142405 MS.gene71285:intron 25.0%
! GAAGTTACGATATTTAATTG+TGG - chr3.4:78141684-78141703 MS.gene71285:intron 25.0%
! GGATGAAATTATTATTACCA+AGG + chr3.4:78141566-78141585 None:intergenic 25.0%
! GGATTACAATCAAAATAATC+AGG - chr3.4:78141226-78141245 MS.gene71285:intron 25.0%
! TCTAATTGTTCAATCATTTC+TGG - chr3.4:78141981-78142000 MS.gene71285:intron 25.0%
! TTACTTTAACACTGAATACA+TGG - chr3.4:78142284-78142303 MS.gene71285:CDS 25.0%
!! AAAATTTGATGATTTGGCAT+TGG - chr3.4:78141738-78141757 MS.gene71285:intron 25.0%
!! ACCTTGAAAATTTGATGATT+TGG - chr3.4:78141732-78141751 MS.gene71285:intron 25.0%
!! ACTGTGTTTTTCACTTTATT+TGG - chr3.4:78142065-78142084 MS.gene71285:CDS 25.0%
!!! CTGTGTTTTTCACTTTATTT+GGG - chr3.4:78142066-78142085 MS.gene71285:CDS 25.0%
!!! GTATAGATCGTATTTTTGTA+TGG + chr3.4:78141859-78141878 None:intergenic 25.0%
!!! TGTGTTTTTCACTTTATTTG+GGG - chr3.4:78142067-78142086 MS.gene71285:CDS 25.0%
AAATCTAATACACTCTACCT+TGG - chr3.4:78141546-78141565 MS.gene71285:intron 30.0%
AGACATATCGTATATTACAG+AGG - chr3.4:78142518-78142537 MS.gene71285:CDS 30.0%
ATAGATAGTTTCGTACACTT+AGG + chr3.4:78141007-78141026 None:intergenic 30.0%
CCGAATTCTGATTATCTATA+TGG + chr3.4:78142389-78142408 None:intergenic 30.0%
CCTATATTCCTATTAGCAAT+GGG + chr3.4:78142547-78142566 None:intergenic 30.0%
GAATACATGGCAAATCAAAT+CGG - chr3.4:78142297-78142316 MS.gene71285:CDS 30.0%
TCCTATATTCCTATTAGCAA+TGG + chr3.4:78142548-78142567 None:intergenic 30.0%
TCCTTGCTTGTAATAAAAAC+AGG + chr3.4:78142180-78142199 None:intergenic 30.0%
TGATAACTGAACTTGTATCA+GGG - chr3.4:78142462-78142481 MS.gene71285:intron 30.0%
! AATCAAGTTCTAGCAATGAT+AGG + chr3.4:78142139-78142158 None:intergenic 30.0%
! ATTTTCTTTAGCAGTTGTGA+TGG + chr3.4:78142345-78142364 None:intergenic 30.0%
! GCCAAATCATCAAATTTTCA+AGG + chr3.4:78141736-78141755 None:intergenic 30.0%
! TCAAACTAGACTTTGTTTGT+TGG - chr3.4:78142012-78142031 MS.gene71285:CDS 30.0%
! TTGATAACTGAACTTGTATC+AGG - chr3.4:78142461-78142480 MS.gene71285:intron 30.0%
!!! ACCTGTTTTTATTACAAGCA+AGG - chr3.4:78142176-78142195 MS.gene71285:intron 30.0%
AAGATCTTCGGTTAAGTCAA+TGG + chr3.4:78141168-78141187 None:intergenic 35.0%
AAGCATGACCAAATGCTTTA+CGG + chr3.4:78142576-78142595 None:intergenic 35.0%
AGATCTTCGGTTAAGTCAAT+GGG + chr3.4:78141167-78141186 None:intergenic 35.0%
AGTTGTTGTAGCATGGATAT+TGG + chr3.4:78141465-78141484 None:intergenic 35.0%
ATATGAAGAGTAGAGAGACA+CGG + chr3.4:78141905-78141924 None:intergenic 35.0%
ATCATCATCATCCCATACTT+CGG + chr3.4:78141495-78141514 None:intergenic 35.0%
CCCATTGCTAATAGGAATAT+AGG - chr3.4:78142544-78142563 MS.gene71285:CDS 35.0%
CGGTAAATATGCAAATCATC+AGG - chr3.4:78142406-78142425 MS.gene71285:intron 35.0%
CTAGCAATGATAGGTAATAG+TGG + chr3.4:78142130-78142149 None:intergenic 35.0%
GAGGTCTAAAAATTGTTCCA+TGG - chr3.4:78141789-78141808 MS.gene71285:intron 35.0%
GATTGTAATCCTTCAAAGCA+AGG + chr3.4:78141217-78141236 None:intergenic 35.0%
GCATATCAAGAATGTCTACA+GGG - chr3.4:78142596-78142615 MS.gene71285:CDS 35.0%
GTAATAGTGGCTTATCACAA+GGG + chr3.4:78142117-78142136 None:intergenic 35.0%
TGCATATCAAGAATGTCTAC+AGG - chr3.4:78142595-78142614 MS.gene71285:CDS 35.0%
! ACTCTTCATATTTGAAGCCT+AGG - chr3.4:78141914-78141933 MS.gene71285:intron 35.0%
! GGAATAAACCGTAAAGCATT+TGG - chr3.4:78142565-78142584 MS.gene71285:CDS 35.0%
! GTCAGCAATTAGTTCTTCTA+TGG + chr3.4:78140964-78140983 None:intergenic 35.0%
! TTTGTTTGTTGGCAACACTT+TGG - chr3.4:78142023-78142042 MS.gene71285:CDS 35.0%
!! ATGGCAAATCAAATCGGTTT+TGG - chr3.4:78142303-78142322 MS.gene71285:CDS 35.0%
AAAAGAATCATGCTGCAGTC+CGG - chr3.4:78142236-78142255 MS.gene71285:intron 40.0%
AGTGTGACACATTAGATTGG+AGG - chr3.4:78141770-78141789 MS.gene71285:intron 40.0%
CTAAAGAAAATGTTGCGCAG+GGG - chr3.4:78142354-78142373 MS.gene71285:CDS 40.0%
GCTAAAGAAAATGTTGCGCA+GGG - chr3.4:78142353-78142372 MS.gene71285:CDS 40.0%
GGTAATAGTGGCTTATCACA+AGG + chr3.4:78142118-78142137 None:intergenic 40.0%
GTAATCCTTCAAAGCAAGGT+CGG + chr3.4:78141213-78141232 None:intergenic 40.0%
GTTGTAGCATGGATATTGGA+AGG + chr3.4:78141461-78141480 None:intergenic 40.0%
TGCTAAAGAAAATGTTGCGC+AGG - chr3.4:78142352-78142371 MS.gene71285:CDS 40.0%
TTTGTTGGCAACACTTTGGA+TGG - chr3.4:78142027-78142046 MS.gene71285:CDS 40.0%
! CTGAACTTGTATCAGGGTTT+TGG - chr3.4:78142468-78142487 MS.gene71285:intron 40.0%
! GAGAGTGTGACACATTAGAT+TGG - chr3.4:78141767-78141786 MS.gene71285:intron 40.0%
! GGATGATAGATAGCATCGAA+CGG + chr3.4:78141113-78141132 None:intergenic 40.0%
AAAATGTTGCGCAGGGGATT+AGG - chr3.4:78142360-78142379 MS.gene71285:CDS 45.0%
AACTTTCCAGGCCGAAGTAT+GGG - chr3.4:78141481-78141500 MS.gene71285:intron 45.0%
ACCGCAATCGAAACACGATT+CGG - chr3.4:78140899-78140918 MS.gene71285:CDS 45.0%
AGAGGCAACCCATTGCTAAT+AGG - chr3.4:78142536-78142555 MS.gene71285:CDS 45.0%
CCATGCTACAACAACTTTCC+AGG - chr3.4:78141469-78141488 MS.gene71285:intron 45.0%
CCTGGAAAGTTGTTGTAGCA+TGG + chr3.4:78141472-78141491 None:intergenic 45.0%
GAAACAGAGAGATTCAGCCT+AGG + chr3.4:78141934-78141953 None:intergenic 45.0%
GAGAGTAGGACGAAGATCTT+CGG + chr3.4:78141180-78141199 None:intergenic 45.0%
GTCAAGTGTACCACTGCTAT+TGG - chr3.4:78141380-78141399 MS.gene71285:intron 45.0%
TAGCAGTGGTACACTTGACA+AGG + chr3.4:78141379-78141398 None:intergenic 45.0%
TCCGAATCGTGTTTCGATTG+CGG + chr3.4:78140903-78140922 None:intergenic 45.0%
! AACAGGTTCTAGCATTGCTG+AGG + chr3.4:78142163-78142182 None:intergenic 45.0%
! TGATGATGATGATGCCGATG+AGG - chr3.4:78141505-78141524 MS.gene71285:intron 45.0%
!! CCACATAACTCTAGAACTGC+TGG + chr3.4:78141134-78141153 None:intergenic 45.0%
!! CCAGCAGTTCTAGAGTTATG+TGG - chr3.4:78141131-78141150 MS.gene71285:intron 45.0%
CAACTTTCCAGGCCGAAGTA+TGG - chr3.4:78141480-78141499 MS.gene71285:intron 50.0%
CGAGTTTGCGGAAGAGAAAG+AGG - chr3.4:78140938-78140957 MS.gene71285:intron 50.0%
GGCACACGATATGACCTCAT+CGG + chr3.4:78141522-78141541 None:intergenic 50.0%
TCTCTCCGACCTTGCTTTGA+AGG - chr3.4:78141205-78141224 MS.gene71285:intron 50.0%
TGCGGTTGTGATCCCAATTC+AGG + chr3.4:78140885-78140904 None:intergenic 50.0%
! TGTACCACTGCTATTGGCTG+TGG - chr3.4:78141386-78141405 MS.gene71285:intron 50.0%
ACCACCACAGCCAATAGCAG+TGG + chr3.4:78141393-78141412 None:intergenic 55.0%
ATGTTGCGCAGGGGATTAGG+TGG - chr3.4:78142363-78142382 MS.gene71285:CDS 55.0%
CATCATCCCATACTTCGGCC+TGG + chr3.4:78141490-78141509 None:intergenic 55.0%
CGACGACGATGACGAGTTTG+CGG - chr3.4:78140926-78140945 MS.gene71285:CDS 55.0%
TCGGAGAGAGCAACGAGAGT+AGG + chr3.4:78141194-78141213 None:intergenic 55.0%
! ACCACTGCTATTGGCTGTGG+TGG - chr3.4:78141389-78141408 MS.gene71285:intron 55.0%
! ACTGCTATTGGCTGTGGTGG+TGG - chr3.4:78141392-78141411 MS.gene71285:intron 55.0%
! ATAGCATCGAACGGCTGCGT+TGG + chr3.4:78141104-78141123 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 78140873 78142621 78140873 ID=MS.gene71285
chr3.4 mRNA 78140873 78142621 78140873 ID=MS.gene71285.t1;Parent=MS.gene71285
chr3.4 exon 78142484 78142621 78142484 ID=MS.gene71285.t1.exon1;Parent=MS.gene71285.t1
chr3.4 CDS 78142484 78142621 78142484 ID=cds.MS.gene71285.t1;Parent=MS.gene71285.t1
chr3.4 exon 78142247 78142384 78142247 ID=MS.gene71285.t1.exon2;Parent=MS.gene71285.t1
chr3.4 CDS 78142247 78142384 78142247 ID=cds.MS.gene71285.t1;Parent=MS.gene71285.t1
chr3.4 exon 78141998 78142141 78141998 ID=MS.gene71285.t1.exon3;Parent=MS.gene71285.t1
chr3.4 CDS 78141998 78142141 78141998 ID=cds.MS.gene71285.t1;Parent=MS.gene71285.t1
chr3.4 exon 78140873 78140956 78140873 ID=MS.gene71285.t1.exon4;Parent=MS.gene71285.t1
chr3.4 CDS 78140873 78140956 78140873 ID=cds.MS.gene71285.t1;Parent=MS.gene71285.t1
Gene Sequence

>MS.gene71285

ATGTCGAAACCTGAATTGGGATCACAACCGCAATCGAAACACGATTCGGAGTACGACGACGATGACGAGTTTGCGGAAGAGAAAGAGGCCATAGAAGAACTAATTGCTGACTATACAGAGAAGTCTCGCAACCTAAGTGTACGAAACTATCTATCTATCTATCTATTTCAATTTATTTTCAATTTTATCATGTATGTTTCACTCTAATAATTTTGATGATGATTCTGTCCAACGCAGCCGTTCGATGCTATCTATCATCCAGCAGTTCTAGAGTTATGTGGCTGTGTCGTACCCATTGACTTAACCGAAGATCTTCGTCCTACTCTCGTTGCTCTCTCCGACCTTGCTTTGAAGGATTACAATCAAAATAATCAGGTACGTTACAATCTACTGTATGAATGAATGTTATATGTTATATGTTGTTTATTCAATTATTCATCAACTAAACTGATAATAATAATTGTTCTTCTTAATTATTAGGGTACAACTTTTGTGTTTCATGACCTTGTCAAGTGTACCACTGCTATTGGCTGTGGTGGTGGTGATTTGTATTACATCACTTTTCAAGCTAAAGCAGAAGAAGATCCTTCCAATATCCATGCTACAACAACTTTCCAGGCCGAAGTATGGGATGATGATGATGATGCCGATGAGGTCATATCGTGTGCCATTAAAATCTAATACACTCTACCTTGGTAATAATAATTTCATCCTTACATGTTTAATCTTTTCTTGGAAATTTATAAATGGTCATAGTTTATAGTTCCATTGATTTTGTATTTGACTTTGTTACATATATTAGTATTCCATTGAAGTTACGATATTTAATTGTGGATTACTATAAGTGTTGATAAAATGTACCTTGAAAATTTGATGATTTGGCATTGGATGCTTGAGAGTGTGACACATTAGATTGGAGGTCTAAAAATTGTTCCATGGTTGTATATTATTAAGATTAAGATTAGATCTTATGCTGATTTCAACCATACAAAAATACGATCTATACGATCTAGCATCTGTTGCTTGACACCGTGTCTCTCTACTCTTCATATTTGAAGCCTAGGCTGAATCTCTCTGTTTCATGTCTGAATACGACATTAGTGCAACATCTAATTGTTCAATCATTTCTGGCTTTACTTTCAAACTAGACTTTGTTTGTTGGCAACACTTTGGATGGTGATAAATGTAAGAAACTGTGTTTTTCACTTTATTTGGGGCTTTCTTCATGTTGTTAGATTTTTCCCTTGTGATAAGCCACTATTACCTATCATTGCTAGAACTTGATTTCCTCAGCAATGCTAGAACCTGTTTTTATTACAAGCAAGGAAATAAATTTTTAGTTGCTTTGCTGTTTGTACTATGAAAAAGAATCATGCTGCAGTCCGGTTAAAAAGTTTTAAATTTATATTAGTTACTTTAACACTGAATACATGGCAAATCAAATCGGTTTTGGAGTCTGATTTTGTTAGCCATCACAACTGCTAAAGAAAATGTTGCGCAGGGGATTAGGTGGCCATATAGATAATCAGAATTCGGTAAATATGCAAATCATCAGGTTTATTCAGTATCAATATTAATATGCACATAGTTGATAACTGAACTTGTATCAGGGTTTTGGTGTCAAGTTGATGTACTCACAATAGTTAGACATATCGTATATTACAGAGGCAACCCATTGCTAATAGGAATATAGGAATAAACCGTAAAGCATTTGGTCATGCTTGCATATCAAGAATGTCTACAGGGTGA

Protein sequence

>MS.gene71285.t1

MSKPELGSQPQSKHDSEYDDDDEFAEEKEAIEELIADYTEKSRNLSPFDAIYHPAVLELCGCVVPIDLTEDLRPTLVALSDLALKDYNQNNQGTTFVFHDLVKCTTAIGCGGGDLYYITFQAKAEEDPSNIHATTTFQAERQPIANRNIGINRKAFGHACISRMSTG