AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene072030

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene072030.t1 MTR_2g006900 86.408 103 11 1 63 162 1 103 4.74e-47 149
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene072030.t1 AT3G20750 58.974 39 16 0 101 139 159 197 1.44e-11 60.5

Find 48 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTGCTGCTGTCTCAATTT+TGG 0.174192 2.4:+75891851 MS.gene072030:CDS
CTTCTTCTTCAACTTCCTAA+TGG 0.279260 2.4:+75892501 MS.gene072030:CDS
ACGTCCTCCTCCTCAAAATA+TGG 0.327173 2.4:-75890952 None:intergenic
CGCCCAATGGCATTTCTTGA+TGG 0.332196 2.4:-75891920 None:intergenic
GGTTGGACATTGTTTGCAAT+TGG 0.397971 2.4:-75891813 None:intergenic
CGAGATGTCCCTGCTGCCTC+AGG 0.421876 2.4:+75892443 MS.gene072030:CDS
GCAATTGGAGCAGTAGCAAT+TGG 0.422553 2.4:-75891834 None:intergenic
GGATCTCCTCCCATGATTCC+AGG 0.423283 2.4:-75892479 None:intergenic
TGTCCCACCACCTGGAATCA+TGG 0.424311 2.4:+75892469 MS.gene072030:CDS
AAAATTGAGACAGCAGCAAT+TGG 0.438976 2.4:-75891849 None:intergenic
AACACTCCTATGTGGCGCTC+TGG 0.449276 2.4:+75892029 MS.gene072030:CDS
TCAAGAAATGCCATTGGGCG+TGG 0.452536 2.4:+75891923 MS.gene072030:CDS
TCAGGTTCTGTCCCACCACC+TGG 0.454678 2.4:+75892461 MS.gene072030:CDS
CCTCCCATGATTCCAGGTGG+TGG 0.456756 2.4:-75892473 None:intergenic
CTCGTCCGCGGCGGATGTAA+CGG 0.459014 2.4:-75891953 None:intergenic
TTTCTTGATGGGCACGGACA+TGG 0.477728 2.4:-75891908 None:intergenic
CATTTACTACAAGAAACATA+TGG 0.481434 2.4:+75892415 MS.gene072030:CDS
GGGACAGAACCTGAGGCAGC+AGG 0.482176 2.4:-75892452 None:intergenic
AAATTTACCTTTGGAACCAT+AGG 0.484328 2.4:-75892053 None:intergenic
TATGTGGCGCTCTGGACCTA+TGG 0.489769 2.4:+75892037 MS.gene072030:CDS
GAATTCAGACACTGAAAGTC+AGG 0.494441 2.4:+75890975 MS.gene072030:CDS
GTCCCACCACCTGGAATCAT+GGG 0.504732 2.4:+75892470 MS.gene072030:CDS
CAGAAGGTGGTCGGATCAGA+TGG 0.507419 2.4:-75891981 None:intergenic
TTGGAGCAGTAGCAATTGGT+TGG 0.512553 2.4:-75891830 None:intergenic
CTCCCATGATTCCAGGTGGT+GGG 0.519420 2.4:-75892472 None:intergenic
GCCCAATGGCATTTCTTGAT+GGG 0.521674 2.4:-75891919 None:intergenic
CGGCGCCGTCCCACGCCCAA+TGG 0.523396 2.4:-75891933 None:intergenic
GCCCATCAAGAAATGCCATT+GGG 0.529843 2.4:+75891918 MS.gene072030:CDS
TGCCCATCAAGAAATGCCAT+TGG 0.544247 2.4:+75891917 MS.gene072030:CDS
CTCTGGACCTATGGTTCCAA+AGG 0.548264 2.4:+75892046 MS.gene072030:CDS
CATTAGGAAGTTGAAGAAGA+AGG 0.548858 2.4:-75892500 None:intergenic
AAATGCCATTGGGCGTGGGA+CGG 0.561985 2.4:+75891928 MS.gene072030:CDS
ATGGCATTTCTTGATGGGCA+CGG 0.572953 2.4:-75891914 None:intergenic
GCAATGAAAATTTGTGCAGA+AGG 0.580559 2.4:-75891997 None:intergenic
CAAGAAATGCCATTGGGCGT+GGG 0.595904 2.4:+75891924 MS.gene072030:CDS
GGACAGAACCTGAGGCAGCA+GGG 0.617193 2.4:-75892451 None:intergenic
AAATTTGTGCAGAAGGTGGT+CGG 0.623430 2.4:-75891990 None:intergenic
ATGAAAATTTGTGCAGAAGG+TGG 0.644289 2.4:-75891994 None:intergenic
AGACAAGAAACACTCCTATG+TGG 0.647405 2.4:+75892021 MS.gene072030:CDS
ATAGGTCCAGAGCGCCACAT+AGG 0.654562 2.4:-75892035 None:intergenic
CAGACTTTGTGCAATGCGTG+TGG 0.657380 2.4:+75892392 MS.gene072030:intron
AGGTGGTGGGACAGAACCTG+AGG 0.657762 2.4:-75892459 None:intergenic
CAGATGGACGAGCTCGTCCG+CGG 0.664959 2.4:-75891965 None:intergenic
AAAGAATCAGTACAATACAT+CGG 0.676733 2.4:-75891885 None:intergenic
ATGGACGAGCTCGTCCGCGG+CGG 0.680751 2.4:-75891962 None:intergenic
CCACCACCTGGAATCATGGG+AGG 0.682520 2.4:+75892473 MS.gene072030:CDS
TCTCCTCCCATGATTCCAGG+TGG 0.693154 2.4:-75892476 None:intergenic
CGGCGCCGTTACATCCGCCG+CGG 0.715105 2.4:+75891948 MS.gene072030:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAATTGAAGAAAAATAA+AGG - chr2.4:75891502-75891521 None:intergenic 10.0%
!! TAAGACAAATTAATTTAATT+AGG + chr2.4:75891239-75891258 MS.gene072030:intron 10.0%
!!! GTCTAATATAATTTTTTTTA+AGG - chr2.4:75891192-75891211 None:intergenic 10.0%
!! AAAAATACATCAAATATAAG+TGG - chr2.4:75891345-75891364 None:intergenic 15.0%
!! ATATAAAAAGTAAGGAATTA+AGG + chr2.4:75892150-75892169 MS.gene072030:intron 15.0%
!! GATCTTATATATAAAAAGTA+AGG + chr2.4:75892142-75892161 MS.gene072030:intron 15.0%
!!! TTTTTTAACTAATAATCAGT+TGG - chr2.4:75892085-75892104 None:intergenic 15.0%
!! AGAAAAAAAAACTTACTTCA+GGG - chr2.4:75891035-75891054 None:intergenic 20.0%
! AAAGAATCAGTACAATACAT+CGG - chr2.4:75891888-75891907 None:intergenic 25.0%
! AACATAGAAGACTATTGTTA+TGG - chr2.4:75892363-75892382 None:intergenic 25.0%
! CATTTACTACAAGAAACATA+TGG + chr2.4:75892415-75892434 MS.gene072030:CDS 25.0%
! GAGAAAAAAAAACTTACTTC+AGG - chr2.4:75891036-75891055 None:intergenic 25.0%
! TCTCAAAAATTCAACTAAGT+TGG - chr2.4:75892224-75892243 None:intergenic 25.0%
!!! AAAAATTCAACTAAGTTGGT+GGG - chr2.4:75892220-75892239 None:intergenic 25.0%
AAACGTCAGAGACTTAATTA+CGG + chr2.4:75891643-75891662 MS.gene072030:intron 30.0%
AATTAGACGTTTCTTGACTT+TGG + chr2.4:75891557-75891576 MS.gene072030:intron 30.0%
AGTCTAATGCACCAAATAAA+TGG + chr2.4:75891597-75891616 MS.gene072030:intron 30.0%
CAAATTTCCCACCATTTATT+TGG - chr2.4:75891611-75891630 None:intergenic 30.0%
CATGTCGAGAGATAAATTTA+TGG - chr2.4:75891464-75891483 None:intergenic 30.0%
CTAAGAGATGAAAATTGACA+TGG + chr2.4:75891142-75891161 MS.gene072030:intron 30.0%
TAATGCACCAAATAAATGGT+GGG + chr2.4:75891601-75891620 MS.gene072030:intron 30.0%
TTATGTCAAATAGTCTAGTG+TGG + chr2.4:75892106-75892125 MS.gene072030:intron 30.0%
! AATAAATGGTGGGAAATTTG+AGG + chr2.4:75891611-75891630 MS.gene072030:intron 30.0%
! CAAAAATTCAACTAAGTTGG+TGG - chr2.4:75892221-75892240 None:intergenic 30.0%
! CTTAAACATGCCATATTTTG+AGG + chr2.4:75890942-75890961 MS.gene072030:CDS 30.0%
!! AAATTTACCTTTGGAACCAT+AGG - chr2.4:75892056-75892075 None:intergenic 30.0%
!! TGGTGTTGTAAATTTACCTT+TGG - chr2.4:75892065-75892084 None:intergenic 30.0%
!! TTTATTTGGTGCATTAGACT+TGG - chr2.4:75891597-75891616 None:intergenic 30.0%
!!! ACTCAAAAGTTTTGATTAGC+GGG - chr2.4:75891399-75891418 None:intergenic 30.0%
!!! GACTCAAAAGTTTTGATTAG+CGG - chr2.4:75891400-75891419 None:intergenic 30.0%
!!! GTTAGTTTTGAGTGTATTTG+AGG - chr2.4:75891778-75891797 None:intergenic 30.0%
AAAATTGAGACAGCAGCAAT+TGG - chr2.4:75891852-75891871 None:intergenic 35.0%
ATGAAAATTTGTGCAGAAGG+TGG - chr2.4:75891997-75892016 None:intergenic 35.0%
CAAAACTAACGTTTGTGAAC+AGG + chr2.4:75891788-75891807 MS.gene072030:intron 35.0%
CTAATGCACCAAATAAATGG+TGG + chr2.4:75891600-75891619 MS.gene072030:intron 35.0%
GCAATGAAAATTTGTGCAGA+AGG - chr2.4:75892000-75892019 None:intergenic 35.0%
GTAATTAAGTCTCTGACGTT+TGG - chr2.4:75891644-75891663 None:intergenic 35.0%
TATCTCTCGACATGTGATTT+GGG + chr2.4:75891470-75891489 MS.gene072030:intron 35.0%
TTATCTCTCGACATGTGATT+TGG + chr2.4:75891469-75891488 MS.gene072030:intron 35.0%
! AATTGCTGCTGTCTCAATTT+TGG + chr2.4:75891851-75891870 MS.gene072030:CDS 35.0%
!! AAACATGCCATATTTTGAGG+AGG + chr2.4:75890945-75890964 MS.gene072030:CDS 35.0%
!! GCATGAACATTTTGGTATGT+TGG - chr2.4:75892191-75892210 None:intergenic 35.0%
!!! CTCAAAAGTTTTGATTAGCG+GGG - chr2.4:75891398-75891417 None:intergenic 35.0%
AAATTTGTGCAGAAGGTGGT+CGG - chr2.4:75891993-75892012 None:intergenic 40.0%
AGACAAGAAACACTCCTATG+TGG + chr2.4:75892021-75892040 MS.gene072030:CDS 40.0%
ATCTCTCGACATGTGATTTG+GGG + chr2.4:75891471-75891490 MS.gene072030:intron 40.0%
GAATTCAGACACTGAAAGTC+AGG + chr2.4:75890975-75890994 MS.gene072030:CDS 40.0%
GGTTGGACATTGTTTGCAAT+TGG - chr2.4:75891816-75891835 None:intergenic 40.0%
TTAAGTCTCTGACGTTTGGT+AGG - chr2.4:75891640-75891659 None:intergenic 40.0%
! GGCTAACTGCATGAACATTT+TGG - chr2.4:75892199-75892218 None:intergenic 40.0%
ACGTCCTCCTCCTCAAAATA+TGG - chr2.4:75890955-75890974 None:intergenic 45.0%
GCAATTGGAGCAGTAGCAAT+TGG - chr2.4:75891837-75891856 None:intergenic 45.0%
GCCCAATGGCATTTCTTGAT+GGG - chr2.4:75891922-75891941 None:intergenic 45.0%
GCCCATCAAGAAATGCCATT+GGG + chr2.4:75891918-75891937 MS.gene072030:CDS 45.0%
TGCCCATCAAGAAATGCCAT+TGG + chr2.4:75891917-75891936 MS.gene072030:CDS 45.0%
TTGGAGCAGTAGCAATTGGT+TGG - chr2.4:75891833-75891852 None:intergenic 45.0%
! ATGGCATTTCTTGATGGGCA+CGG - chr2.4:75891917-75891936 None:intergenic 45.0%
!! CATGCCATATTTTGAGGAGG+AGG + chr2.4:75890948-75890967 MS.gene072030:CDS 45.0%
!! AATTAATTAAAAAAGAAATT+AGG + chr2.4:75892264-75892283 MS.gene072030:intron 5.0%
!!! TTTTTATTGAAATAATAAAA+TGG + chr2.4:75891747-75891766 MS.gene072030:intron 5.0%
CAAGAAATGCCATTGGGCGT+GGG + chr2.4:75891924-75891943 MS.gene072030:CDS 50.0%
CAGACTTTGTGCAATGCGTG+TGG + chr2.4:75892392-75892411 MS.gene072030:intron 50.0%
CGCCCAATGGCATTTCTTGA+TGG - chr2.4:75891923-75891942 None:intergenic 50.0%
CTCTGGACCTATGGTTCCAA+AGG + chr2.4:75892046-75892065 MS.gene072030:CDS 50.0%
TCAAGAAATGCCATTGGGCG+TGG + chr2.4:75891923-75891942 MS.gene072030:CDS 50.0%
! TTTCTTGATGGGCACGGACA+TGG - chr2.4:75891911-75891930 None:intergenic 50.0%
AAATGCCATTGGGCGTGGGA+CGG + chr2.4:75891928-75891947 MS.gene072030:CDS 55.0%
AACACTCCTATGTGGCGCTC+TGG + chr2.4:75892029-75892048 MS.gene072030:CDS 55.0%
CAGAAGGTGGTCGGATCAGA+TGG - chr2.4:75891984-75892003 None:intergenic 55.0%
CTCCCATGATTCCAGGTGGT+GGG - chr2.4:75892475-75892494 None:intergenic 55.0%
GGATCTCCTCCCATGATTCC+AGG - chr2.4:75892482-75892501 None:intergenic 55.0%
GTCCCACCACCTGGAATCAT+GGG + chr2.4:75892470-75892489 MS.gene072030:CDS 55.0%
TCTCCTCCCATGATTCCAGG+TGG - chr2.4:75892479-75892498 None:intergenic 55.0%
TGTCCCACCACCTGGAATCA+TGG + chr2.4:75892469-75892488 MS.gene072030:CDS 55.0%
! ATAGGTCCAGAGCGCCACAT+AGG - chr2.4:75892038-75892057 None:intergenic 55.0%
! TATGTGGCGCTCTGGACCTA+TGG + chr2.4:75892037-75892056 MS.gene072030:CDS 55.0%
CCACCACCTGGAATCATGGG+AGG + chr2.4:75892473-75892492 MS.gene072030:CDS 60.0%
CCTCCCATGATTCCAGGTGG+TGG - chr2.4:75892476-75892495 None:intergenic 60.0%
GGACAGAACCTGAGGCAGCA+GGG - chr2.4:75892454-75892473 None:intergenic 60.0%
TCAGGTTCTGTCCCACCACC+TGG + chr2.4:75892461-75892480 MS.gene072030:CDS 60.0%
!! AGGTGGTGGGACAGAACCTG+AGG - chr2.4:75892462-75892481 None:intergenic 60.0%
CAGATGGACGAGCTCGTCCG+CGG - chr2.4:75891968-75891987 None:intergenic 65.0%
CGAGATGTCCCTGCTGCCTC+AGG + chr2.4:75892443-75892462 MS.gene072030:CDS 65.0%
CTCGTCCGCGGCGGATGTAA+CGG - chr2.4:75891956-75891975 None:intergenic 65.0%
GGGACAGAACCTGAGGCAGC+AGG - chr2.4:75892455-75892474 None:intergenic 65.0%
ATGGACGAGCTCGTCCGCGG+CGG - chr2.4:75891965-75891984 None:intergenic 70.0%
CGGCGCCGTTACATCCGCCG+CGG + chr2.4:75891948-75891967 MS.gene072030:CDS 75.0%
! CGGCGCCGTCCCACGCCCAA+TGG - chr2.4:75891936-75891955 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 75890931 75892520 75890931 ID=MS.gene072030
chr2.4 mRNA 75890931 75892520 75890931 ID=MS.gene072030.t1;Parent=MS.gene072030
chr2.4 exon 75890931 75891038 75890931 ID=MS.gene072030.t1.exon1;Parent=MS.gene072030.t1
chr2.4 CDS 75890931 75891038 75890931 ID=cds.MS.gene072030.t1;Parent=MS.gene072030.t1
chr2.4 exon 75891810 75892067 75891810 ID=MS.gene072030.t1.exon2;Parent=MS.gene072030.t1
chr2.4 CDS 75891810 75892067 75891810 ID=cds.MS.gene072030.t1;Parent=MS.gene072030.t1
chr2.4 exon 75892395 75892520 75892395 ID=MS.gene072030.t1.exon3;Parent=MS.gene072030.t1
chr2.4 CDS 75892395 75892520 75892395 ID=cds.MS.gene072030.t1;Parent=MS.gene072030.t1
Gene Sequence

>MS.gene072030

ATGGACTTTGACTTAAACATGCCATATTTTGAGGAGGAGGACGTGAATTCAGACACTGAAAGTCAGGTTTCATCACTCATTCAGAGCAATACTGAAAATATCCCTGAAGTAAGTTTTTTTTTCTCTTTCTATAATAATGAATGTCACATACATAATAGTAGTACATATAATGACTGTTAAAAAAAGTTAACATTGTCGATTTTTGTATCATCTAAGAGATGAAAATTGACATGGCTGTTAAAAAAACTAGAACTTTTTCCTTAAAAAAAATTATATTAGACTTAATTCATTTGTACAAAATCGACTTGTAAGACAAATTAATTTAATTAGGATATTTTGTTATTATGCAATTATTTTATACGTGAATCTAATTATGTGTTGTCACTTTTTTTTATATAAAATTATTATTTACCACTTATATTTGATGTATTTTTATAAATATTCATCATAGCATAGAAGTATGTCCCCGCTAATCAAAACTTTTGAGTCTAACTTATAAGATCTTGTGTGTCACTCTTCTATGAATTTTACCATAAATTTATCTCTCGACATGTGATTTGGGGATTTTCCTTTATTTTTCTTCAATTTTTTATGTGATGATGCAATTTAATCATCATGTGAGTAAAAATTAGACGTTTCTTGACTTTGGTATTTAGTCGCATACCAAGTCTAATGCACCAAATAAATGGTGGGAAATTTGAGGATGCCTACCAAACGTCAGAGACTTAATTACGGTAGAATAATTAACATACAAAAAGTGAACAACTAGTGTTATTATGTGATTTTAAATAATTAAATAAAATGATTGTGTATTTATTTTTATTGAAATAATAAAATGGCGACACCTCAAATACACTCAAAACTAACGTTTGTGAACAGGATCCAATTGCAAACAATGTCCAACCAATTGCTACTGCTCCAATTGCTGCTGTCTCAATTTTGGTTGATGCTCAACCGATGTATTGTACTGATTCTTTCCATGTCCGTGCCCATCAAGAAATGCCATTGGGCGTGGGACGGCGCCGTTACATCCGCCGCGGACGAGCTCGTCCATCTGATCCGACCACCTTCTGCACAAATTTTCATTGCAAGACAAGAAACACTCCTATGTGGCGCTCTGGACCTATGGTTCCAAAGGTAAATTTACAACACCAACTGATTATTAGTTAAAAAAATTATGTCAAATAGTCTAGTGTGGAGAATAACACATCGATCTTATATATAAAAAGTAAGGAATTAAGGATTGAAACTCACGCTCCAACATACCAAAATGTTCATGCAGTTAGCCCACCAACTTAGTTGAATTTTTGAGACATTATTTATACAATCTAATAATTAATTAAAAAAGAAATTAGGAAACACACTATTTATTAATAATAGTAATATTAATAACTATTTTACGATCGTCATTATTCTTATCTTTATGTTTCCATAACAATAGTCTTCTATGTTATATATGTGCAGACTTTGTGCAATGCGTGTGGCATTTACTACAAGAAACATATGGTTCGTCGAGATGTCCCTGCTGCCTCAGGTTCTGTCCCACCACCTGGAATCATGGGAGGAGATCCTTCTTCTTCAACTTCCTAA
Protein sequence

>MS.gene072030.t1

MDFDLNMPYFEEEDVNSDTESQVSSLIQSNTENIPEDPIANNVQPIATAPIAAVSILVDAQPMYCTDSFHVRAHQEMPLGVGRRRYIRRGRARPSDPTTFCTNFHCKTRNTPMWRSGPMVPKTLCNACGIYYKKHMVRRDVPAASGSVPPPGIMGGDPSSSTS