AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073908

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073908.t1 MTR_3g083080 55.135 185 83 0 2 186 23 207 4.32e-67 204
MS.gene073908.t1 MTR_3g083030 53.191 188 83 3 2 186 46 231 8.54e-62 191
MS.gene073908.t1 MTR_3g083050 55.621 169 72 2 19 186 42 208 1.21e-59 185
MS.gene073908.t1 MTR_3g082420 35.385 195 110 6 2 184 31 221 4.74e-28 105
MS.gene073908.t1 MTR_3g080680 36.316 190 102 8 9 184 14 198 4.72e-27 101
MS.gene073908.t1 MTR_3g082340 37.195 164 90 5 30 184 63 222 9.78e-26 99.0
MS.gene073908.t1 MTR_3g086030 48.515 101 50 1 9 109 5 103 2.37e-24 93.6
MS.gene073908.t1 MTR_3g083150 38.220 191 101 5 10 184 22 211 1.75e-23 92.8
MS.gene073908.t1 MTR_8g461300 36.269 193 94 12 10 184 17 198 9.29e-20 82.8
MS.gene073908.t1 MTR_3g083100 43.200 125 55 4 76 184 49 173 5.49e-16 72.4
MS.gene073908.t1 MTR_4g055800 33.566 143 75 5 34 168 143 273 2.90e-15 72.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 47 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCACTTTGTGTATAGGAATA+AGG 0.280516 1.3:-26942146 MS.gene073908:CDS
CCGCATAAACGCGCAATTGC+TGG 0.285411 1.3:+26941931 None:intergenic
GGCGTGTCCGGTTCCGATTT+TGG 0.286988 1.3:+26942256 None:intergenic
TCCCCTCTGCAAGCTTGCTT+TGG 0.301525 1.3:-26941860 MS.gene073908:CDS
TGCGAACACATAAACATATA+AGG 0.360061 1.3:+26942166 None:intergenic
GAAATACAATGCCGAGAATC+AGG 0.370063 1.3:-26941836 MS.gene073908:intron
TGTGTTCGCACTTTGTGTAT+AGG 0.382348 1.3:-26942153 MS.gene073908:CDS
ATCGATTCCCACGGCGTGTC+CGG 0.398303 1.3:+26942244 None:intergenic
CATGAGCTAGGTAGGCTTCA+TGG 0.407712 1.3:+26941551 None:intergenic
AGATGCTTACAGTTAGGTTA+CGG 0.415653 1.3:+26942065 None:intergenic
ACCGACGATGGAGCCAAAAT+CGG 0.429034 1.3:-26942269 MS.gene073908:CDS
GATGCTTACAGTTAGGTTAC+GGG 0.439754 1.3:+26942066 None:intergenic
TATTGAACCTACCTGATTCT+CGG 0.452481 1.3:+26941825 None:intergenic
AATACACAATACTACTTCCA+TGG 0.471254 1.3:+26941685 None:intergenic
TGCAGAGGGGAGTGAGTTCA+AGG 0.476525 1.3:+26941872 None:intergenic
TGGCTCCATCGTCGGTGGTA+AGG 0.478145 1.3:+26942276 None:intergenic
AGATCATCGTCCATGCGATC+AGG 0.496351 1.3:+26941898 None:intergenic
AGCAGGGCAGTTGGAAGGAT+GGG 0.501180 1.3:+26941635 None:intergenic
TCAGCCTGAAAAGTTATAGC+AGG 0.514365 1.3:+26941618 None:intergenic
CCAGCAATTGCGCGTTTATG+CGG 0.515594 1.3:-26941931 MS.gene073908:CDS
CTCCAAAGCAAGCTTGCAGA+GGG 0.518878 1.3:+26941858 None:intergenic
AGACTCGACTACAGGCGGTT+CGG 0.519469 1.3:+26941578 None:intergenic
GATGGAGCCAAAATCGGAAC+CGG 0.533510 1.3:-26942263 MS.gene073908:CDS
TAGCAGGGCAGTTGGAAGGA+TGG 0.540470 1.3:+26941634 None:intergenic
ATGGCACAAGACTCGACTAC+AGG 0.541204 1.3:+26941570 None:intergenic
GATACGCAATGAAGAACTCA+TGG 0.541786 1.3:-26942224 MS.gene073908:CDS
AATCGGAACCGGACACGCCG+TGG 0.541893 1.3:-26942252 MS.gene073908:CDS
AAAAGTTATAGCAGGGCAGT+TGG 0.545343 1.3:+26941626 None:intergenic
TATTAATGCATGAGCTAGGT+AGG 0.547710 1.3:+26941543 None:intergenic
TAAACGCGCAATTGCTGGAG+GGG 0.549997 1.3:+26941936 None:intergenic
ATACACAATACTACTTCCAT+GGG 0.570581 1.3:+26941686 None:intergenic
CATAAACGCGCAATTGCTGG+AGG 0.575760 1.3:+26941934 None:intergenic
GGCATTCTTAAGTCAACCCA+TGG 0.579015 1.3:-26941702 MS.gene073908:CDS
GTTATAGCAGGGCAGTTGGA+AGG 0.582712 1.3:+26941630 None:intergenic
GCGCTTTCTATGCTCAGCCA+TGG 0.587248 1.3:+26942090 None:intergenic
GCAATTGCGCGTTTATGCGG+CGG 0.590566 1.3:-26941928 MS.gene073908:CDS
ATCGGAACCGGACACGCCGT+GGG 0.595257 1.3:-26942251 MS.gene073908:CDS
TGAAGAAATTCGAGTCGCCA+TGG 0.603715 1.3:-26942107 MS.gene073908:CDS
CGGTATCAGACCTGATCGCA+TGG 0.607640 1.3:-26941908 MS.gene073908:CDS
TCTCCAAAGCAAGCTTGCAG+AGG 0.618622 1.3:+26941857 None:intergenic
AGCTACCTTACCACCGACGA+TGG 0.624415 1.3:-26942281 MS.gene073908:CDS
TCATTGCGTATCGATTCCCA+CGG 0.632393 1.3:+26942235 None:intergenic
CAGCCTGAAAAGTTATAGCA+GGG 0.635889 1.3:+26941619 None:intergenic
ATAAACGCGCAATTGCTGGA+GGG 0.641638 1.3:+26941935 None:intergenic
GCACAAGACTCGACTACAGG+CGG 0.694421 1.3:+26941573 None:intergenic
TCCAAAGCAAGCTTGCAGAG+GGG 0.721977 1.3:+26941859 None:intergenic
AGAGGGGAGTGAGTTCAAGG+CGG 0.771754 1.3:+26941875 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTATTCTTGTTAATTATTA+GGG - chr1.3:26942099-26942118 MS.gene073908:CDS 15.0%
!! TAGTATTCTTGTTAATTATT+AGG - chr1.3:26942098-26942117 MS.gene073908:CDS 15.0%
! AATTAAGTGAAACGCAAAAT+TGG + chr1.3:26941827-26941846 None:intergenic 25.0%
! ATAAATAGATGCTTACAGTT+AGG + chr1.3:26941787-26941806 None:intergenic 25.0%
AATACACAATACTACTTCCA+TGG + chr1.3:26942161-26942180 None:intergenic 30.0%
ATACACAATACTACTTCCAT+GGG + chr1.3:26942160-26942179 None:intergenic 30.0%
TGCGAACACATAAACATATA+AGG + chr1.3:26941680-26941699 None:intergenic 30.0%
!! TAATCTCTTGATTTTGATCC+TGG - chr1.3:26941864-26941883 MS.gene073908:CDS 30.0%
AGATGCTTACAGTTAGGTTA+CGG + chr1.3:26941781-26941800 None:intergenic 35.0%
GCACTTTGTGTATAGGAATA+AGG - chr1.3:26941697-26941716 MS.gene073908:CDS 35.0%
TATTGAACCTACCTGATTCT+CGG + chr1.3:26942021-26942040 None:intergenic 35.0%
! GGTGCAAATTTTGTGTTTGA+TGG - chr1.3:26942120-26942139 MS.gene073908:CDS 35.0%
AAAAGTTATAGCAGGGCAGT+TGG + chr1.3:26942220-26942239 None:intergenic 40.0%
ATAGCATCAAATACCTGTCC+AGG + chr1.3:26941885-26941904 None:intergenic 40.0%
CAGCCTGAAAAGTTATAGCA+GGG + chr1.3:26942227-26942246 None:intergenic 40.0%
GAAATACAATGCCGAGAATC+AGG - chr1.3:26942007-26942026 MS.gene073908:intron 40.0%
GATACGCAATGAAGAACTCA+TGG - chr1.3:26941619-26941638 MS.gene073908:CDS 40.0%
GATGCTTACAGTTAGGTTAC+GGG + chr1.3:26941780-26941799 None:intergenic 40.0%
TCAGCCTGAAAAGTTATAGC+AGG + chr1.3:26942228-26942247 None:intergenic 40.0%
TGTGTTCGCACTTTGTGTAT+AGG - chr1.3:26941690-26941709 MS.gene073908:CDS 40.0%
!! TCTTGATTTTGATCCTGGAC+AGG - chr1.3:26941869-26941888 MS.gene073908:CDS 40.0%
ATAAACGCGCAATTGCTGGA+GGG + chr1.3:26941911-26941930 None:intergenic 45.0%
GGCATTCTTAAGTCAACCCA+TGG - chr1.3:26942141-26942160 MS.gene073908:CDS 45.0%
TACAATGCCGAGAATCAGGT+AGG - chr1.3:26942011-26942030 MS.gene073908:intron 45.0%
TGAAGAAATTCGAGTCGCCA+TGG - chr1.3:26941736-26941755 MS.gene073908:intron 45.0%
! AGGCTGAAGTCTTTTGCAGT+AGG - chr1.3:26942241-26942260 MS.gene073908:CDS 45.0%
! CTGCCCTGCTATAACTTTTC+AGG - chr1.3:26942221-26942240 MS.gene073908:CDS 45.0%
! GGCAGCATCTTTTGCTTGAA+AGG + chr1.3:26942190-26942209 None:intergenic 45.0%
!! TCATTGCGTATCGATTCCCA+CGG + chr1.3:26941611-26941630 None:intergenic 45.0%
ACCGACGATGGAGCCAAAAT+CGG - chr1.3:26941574-26941593 MS.gene073908:CDS 50.0%
AGATCATCGTCCATGCGATC+AGG + chr1.3:26941948-26941967 None:intergenic 50.0%
ATGGCACAAGACTCGACTAC+AGG + chr1.3:26942276-26942295 None:intergenic 50.0%
CATAAACGCGCAATTGCTGG+AGG + chr1.3:26941912-26941931 None:intergenic 50.0%
CCAGCAATTGCGCGTTTATG+CGG - chr1.3:26941912-26941931 MS.gene073908:CDS 50.0%
CTCCAAAGCAAGCTTGCAGA+GGG + chr1.3:26941988-26942007 None:intergenic 50.0%
GATGGAGCCAAAATCGGAAC+CGG - chr1.3:26941580-26941599 MS.gene073908:CDS 50.0%
GTTATAGCAGGGCAGTTGGA+AGG + chr1.3:26942216-26942235 None:intergenic 50.0%
TAAACGCGCAATTGCTGGAG+GGG + chr1.3:26941910-26941929 None:intergenic 50.0%
TCCAAAGCAAGCTTGCAGAG+GGG + chr1.3:26941987-26942006 None:intergenic 50.0%
TCTCCAAAGCAAGCTTGCAG+AGG + chr1.3:26941989-26942008 None:intergenic 50.0%
!!! TCCGATTTTGGCTCCATCGT+CGG + chr1.3:26941578-26941597 None:intergenic 50.0%
AGACTCGACTACAGGCGGTT+CGG + chr1.3:26942268-26942287 None:intergenic 55.0%
AGAGGGGAGTGAGTTCAAGG+CGG + chr1.3:26941971-26941990 None:intergenic 55.0%
AGCAGGGCAGTTGGAAGGAT+GGG + chr1.3:26942211-26942230 None:intergenic 55.0%
AGCTACCTTACCACCGACGA+TGG - chr1.3:26941562-26941581 MS.gene073908:CDS 55.0%
CCGCATAAACGCGCAATTGC+TGG + chr1.3:26941915-26941934 None:intergenic 55.0%
CGGTATCAGACCTGATCGCA+TGG - chr1.3:26941935-26941954 MS.gene073908:CDS 55.0%
GCAATTGCGCGTTTATGCGG+CGG - chr1.3:26941915-26941934 MS.gene073908:CDS 55.0%
GCACAAGACTCGACTACAGG+CGG + chr1.3:26942273-26942292 None:intergenic 55.0%
GCGCTTTCTATGCTCAGCCA+TGG + chr1.3:26941756-26941775 None:intergenic 55.0%
TAGCAGGGCAGTTGGAAGGA+TGG + chr1.3:26942212-26942231 None:intergenic 55.0%
TGCAGAGGGGAGTGAGTTCA+AGG + chr1.3:26941974-26941993 None:intergenic 55.0%
! TCCCCTCTGCAAGCTTGCTT+TGG - chr1.3:26941983-26942002 MS.gene073908:intron 55.0%
!!! GATTTTGGCTCCATCGTCGG+TGG + chr1.3:26941575-26941594 None:intergenic 55.0%
TGGCTCCATCGTCGGTGGTA+AGG + chr1.3:26941570-26941589 None:intergenic 60.0%
! ATCGATTCCCACGGCGTGTC+CGG + chr1.3:26941602-26941621 None:intergenic 60.0%
! GGCGTGTCCGGTTCCGATTT+TGG + chr1.3:26941590-26941609 None:intergenic 60.0%
AATCGGAACCGGACACGCCG+TGG - chr1.3:26941591-26941610 MS.gene073908:CDS 65.0%
ATCGGAACCGGACACGCCGT+GGG - chr1.3:26941592-26941611 MS.gene073908:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 26941557 26942308 26941557 ID=MS.gene073908
chr1.3 mRNA 26941557 26942308 26941557 ID=MS.gene073908.t1;Parent=MS.gene073908
chr1.3 exon 26942075 26942308 26942075 ID=MS.gene073908.t1.exon1;Parent=MS.gene073908.t1
chr1.3 CDS 26942075 26942308 26942075 ID=cds.MS.gene073908.t1;Parent=MS.gene073908.t1
chr1.3 exon 26941837 26941974 26941837 ID=MS.gene073908.t1.exon2;Parent=MS.gene073908.t1
chr1.3 CDS 26941837 26941974 26941837 ID=cds.MS.gene073908.t1;Parent=MS.gene073908.t1
chr1.3 exon 26941557 26941745 26941557 ID=MS.gene073908.t1.exon3;Parent=MS.gene073908.t1
chr1.3 CDS 26941557 26941745 26941557 ID=cds.MS.gene073908.t1;Parent=MS.gene073908.t1
Gene Sequence

>MS.gene073908

ATGGAAGCTACCTTACCACCGACGATGGAGCCAAAATCGGAACCGGACACGCCGTGGGAATCGATACGCAATGAAGAACTCATGGAAAGTGACTTTTCTATCTACGACGATCTCGATTATCCTTATATGTTTATGTGTTCGCACTTTGTGTATAGGAATAAGGTTCAGATAAAAAAAGATGAAGAAATTCGAGTCGCCATGGCTGAGCATAGAAAGCGCTCCCGTAACCTAACTGTAAGCATCTATTTATCTATCTCATTTTGATTTCCAATTTTGCGTTTCACTTAATTTGTTATTAAAATAATCATAATCTCTTGATTTTGATCCTGGACAGGTATTTGATGCTATTTCCCCTCCAGCAATTGCGCGTTTATGCGGCGGTATCAGACCTGATCGCATGGACGATGATCTCCGCCTTGAACTCACTCCCCTCTGCAAGCTTGCTTTGGAGAAATACAATGCCGAGAATCAGGTAGGTTCAATACTTTTTAGAGTAAACTTATGAATATAGTTTATTTATTCATTCATTGATCAACTAATATAGTATTCTTGTTAATTATTAGGGTGCAAATTTTGTGTTTGATGGCATTCTTAAGTCAACCCATGGAAGTAGTATTGTGTATTACATGACCTTTCAAGCAAAAGATGCTGCCCATCCTTCCAACTGCCCTGCTATAACTTTTCAGGCTGAAGTCTTTTGCAGTAGGTCCGAACCGCCTGTAGTCGAGTCTTGTGCCATGAAGCCTACCTAG
Protein sequence

>MS.gene073908.t1

MEATLPPTMEPKSEPDTPWESIRNEELMESDFSIYDDLDYPYMFMCSHFVYRNKVQIKKDEEIRVAMAEHRKRSRNLTVFDAISPPAIARLCGGIRPDRMDDDLRLELTPLCKLALEKYNAENQGANFVFDGILKSTHGSSIVYYMTFQAKDAAHPSNCPAITFQAEVFCSRSEPPVVESCAMKPT