AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene34483

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34483.t1 MTR_1g100643 98.864 176 2 0 1 176 1 176 4.09e-121 339
MS.gene34483.t1 MTR_1g100643 98.864 176 2 0 1 176 54 229 3.50e-120 339
MS.gene34483.t1 MTR_6g017105 45.087 173 94 1 1 172 55 227 9.92e-49 157
MS.gene34483.t1 MTR_1g033360 44.172 163 87 1 1 163 56 214 2.63e-44 146
MS.gene34483.t1 MTR_1g033390 40.994 161 92 1 1 161 50 207 9.72e-42 139
MS.gene34483.t1 MTR_5g053250 43.030 165 92 2 1 164 1 164 2.56e-41 137
MS.gene34483.t1 MTR_5g053250 43.030 165 92 2 1 164 61 224 7.99e-41 138
MS.gene34483.t1 MTR_5g053250 41.566 166 92 3 3 164 87 251 7.97e-36 125
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34483.t1 AT4G25570 72.727 165 45 0 1 165 54 218 2.75e-84 248
MS.gene34483.t1 AT4G25570 72.727 165 45 0 1 165 95 259 3.26e-84 249
MS.gene34483.t1 AT5G38630 45.665 173 91 2 1 172 55 225 2.73e-49 159
MS.gene34483.t1 AT1G26100 41.212 165 93 3 1 163 48 210 1.52e-36 127
MS.gene34483.t1 AT1G14730 37.267 161 97 1 1 161 61 217 4.37e-33 117

Find 52 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCCTGTTCTTATGCTTAT+TGG 0.086164 1.2:+75431960 None:intergenic
CTTATTGGATTAATAATAAT+TGG 0.145209 1.2:+75431975 MS.gene34483:CDS
ATTGGGGTTATTTCCCTTTA+TGG 0.155866 1.2:+75432279 MS.gene34483:CDS
GCAATAGTACTTGGAATAAT+TGG 0.165049 1.2:+75432183 MS.gene34483:CDS
TTATACCTGCAGTGGATATT+TGG 0.202191 1.2:+75432950 MS.gene34483:intron
GCTATAATCACAATCTTATT+TGG 0.204077 1.2:+75433169 MS.gene34483:CDS
GTTCCATGGCACGTGTTATT+TGG 0.218813 1.2:+75433025 MS.gene34483:CDS
TGGGCTGTTTGTGTATATTT+TGG 0.232991 1.2:+75433045 MS.gene34483:CDS
TATTTCCCTTTATGGCATTC+AGG 0.276914 1.2:+75432287 MS.gene34483:CDS
TACATTCATGGCTTGGAATT+GGG 0.284081 1.2:+75432262 MS.gene34483:CDS
GCTCTCGCCACTTCTTCTCT+TGG 0.292806 1.2:+75433067 MS.gene34483:CDS
CTCTCGCCACTTCTTCTCTT+GGG 0.293658 1.2:+75433068 MS.gene34483:CDS
TATACCTGCAGTGGATATTT+GGG 0.299078 1.2:+75432951 MS.gene34483:intron
TTACATTCATGGCTTGGAAT+TGG 0.315480 1.2:+75432261 MS.gene34483:CDS
TTCCATGGCACGTGTTATTT+GGG 0.316139 1.2:+75433026 MS.gene34483:CDS
ATCTGTACAGCTTACATTCA+TGG 0.324873 1.2:+75432250 MS.gene34483:CDS
CTCACATTCCTGGAGAGTTC+AGG 0.345122 1.2:+75433103 MS.gene34483:CDS
TCTCGAGAAGCTCACATTCC+TGG 0.351307 1.2:+75433093 MS.gene34483:CDS
ATTGCCAAGTGAAATCTATA+TGG 0.363154 1.2:-75433251 None:intergenic
AGTTTACCTGAATGCCATAA+AGG 0.371648 1.2:-75432293 None:intergenic
TTCTTTACTTCCTTCTTCAA+TGG 0.389112 1.2:-75432132 None:intergenic
AGTTCAGGGGTGGCAAAATA+CGG 0.413559 1.2:+75433118 MS.gene34483:CDS
CACGCAATTGCAATAGTACT+TGG 0.418703 1.2:+75432174 MS.gene34483:CDS
TACAGCTTACATTCATGGCT+TGG 0.439824 1.2:+75432255 MS.gene34483:CDS
CAAATCTCTTCCATTGAAGA+AGG 0.443963 1.2:+75432122 MS.gene34483:CDS
GTTTACCTGAATGCCATAAA+GGG 0.448606 1.2:-75432292 None:intergenic
TGCCATATCTCAAGCTCCTC+CGG 0.452404 1.2:+75433210 MS.gene34483:CDS
GTTCAGGGGTGGCAAAATAC+GGG 0.462319 1.2:+75433119 MS.gene34483:CDS
GCAGTGGATATTTGGGTTTG+TGG 0.467870 1.2:+75432958 MS.gene34483:intron
AGCCGGAGGAGCTTGAGATA+TGG 0.468673 1.2:-75433212 None:intergenic
TCACATTCCTGGAGAGTTCA+GGG 0.480817 1.2:+75433104 MS.gene34483:CDS
ACATTCATGGCTTGGAATTG+GGG 0.481568 1.2:+75432263 MS.gene34483:CDS
TTGCCACCCCTGAACTCTCC+AGG 0.490584 1.2:-75433111 None:intergenic
CTTAACTCTGAACTCCCACC+AGG 0.491252 1.2:-75432992 None:intergenic
TTGCAATTGCGTGGAGTACA+AGG 0.507108 1.2:-75432164 None:intergenic
TTCAAGAATCACAATGAAAG+CGG 0.519058 1.2:+75432219 MS.gene34483:CDS
ATTGGATTAATAATAATTGG+AGG 0.527553 1.2:+75431978 MS.gene34483:CDS
TTGCCAAGTGAAATCTATAT+GGG 0.539206 1.2:-75433250 None:intergenic
TGAATGTAAGCTGTACAGAT+TGG 0.540351 1.2:-75432247 None:intergenic
TTAATAATAATTGGAGGTGA+AGG 0.541966 1.2:+75431984 MS.gene34483:CDS
AGCCCAAATAACACGTGCCA+TGG 0.544405 1.2:-75433028 None:intergenic
GAGAAACCCAAGAGAAGAAG+TGG 0.557201 1.2:-75433074 None:intergenic
TCAAGAATCACAATGAAAGC+GGG 0.565504 1.2:+75432220 MS.gene34483:CDS
GGTGCGTAGTCATCAGCAGC+CGG 0.592924 1.2:-75433229 None:intergenic
CAAGTACTATTGCAATTGCG+TGG 0.601621 1.2:-75432173 None:intergenic
TTCAGGGGTGGCAAAATACG+GGG 0.636117 1.2:+75433120 MS.gene34483:CDS
GCGTAGTCATCAGCAGCCGG+AGG 0.648131 1.2:-75433226 None:intergenic
TAAGACGTGAGTCAGTTCCA+TGG 0.663765 1.2:+75433011 MS.gene34483:CDS
TATGGCAGATAATACAACAA+AGG 0.664713 1.2:-75433194 None:intergenic
CACATTCCTGGAGAGTTCAG+GGG 0.667949 1.2:+75433105 MS.gene34483:CDS
ATTCCTGGAGAGTTCAGGGG+TGG 0.681886 1.2:+75433108 MS.gene34483:CDS
TTAACTCTGAACTCCCACCA+GGG 0.730733 1.2:-75432991 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATAAAATACATATGTT+AGG - chr1.2:75432930-75432949 None:intergenic 10.0%
!! CTTATTGGATTAATAATAAT+TGG + chr1.2:75431975-75431994 MS.gene34483:CDS 15.0%
!! TATTAGATAAACAGAAAATT+AGG + chr1.2:75432774-75432793 MS.gene34483:intron 15.0%
!!! AATCAAATTTTATCATTCTA+TGG - chr1.2:75432497-75432516 None:intergenic 15.0%
!! AAACTATATCTTATACTATC+AGG + chr1.2:75432650-75432669 MS.gene34483:intron 20.0%
!! AATTTGATTACAATGAGTAT+AGG + chr1.2:75432508-75432527 MS.gene34483:intron 20.0%
!! ACAAATTAATAGAGAACTAA+AGG - chr1.2:75432726-75432745 None:intergenic 20.0%
!! ATTGGATTAATAATAATTGG+AGG + chr1.2:75431978-75431997 MS.gene34483:CDS 20.0%
!! TCCAATTATTAAGTTATGTA+CGG + chr1.2:75432694-75432713 MS.gene34483:intron 20.0%
!! TTAGTTAAGATCTGTTAATA+TGG - chr1.2:75432558-75432577 None:intergenic 20.0%
! ATAAACAGAAAATTAGGAGA+AGG + chr1.2:75432780-75432799 MS.gene34483:intron 25.0%
! ATAGGATACACTTTATATAG+TGG + chr1.2:75432526-75432545 MS.gene34483:intron 25.0%
! CCAATTATTAAGTTATGTAC+GGG + chr1.2:75432695-75432714 MS.gene34483:intron 25.0%
! CTTAATTGAAAATCCAAACT+TGG + chr1.2:75432839-75432858 MS.gene34483:intron 25.0%
! GCTATAATCACAATCTTATT+TGG + chr1.2:75433169-75433188 MS.gene34483:CDS 25.0%
! GTCAAATCAAATGATTCATT+TGG - chr1.2:75432870-75432889 None:intergenic 25.0%
! TAAGATCTGTTAATATGGTT+AGG - chr1.2:75432553-75432572 None:intergenic 25.0%
! TTAATAATAATTGGAGGTGA+AGG + chr1.2:75431984-75432003 MS.gene34483:CDS 25.0%
!! TATTTTATGAATCAGCTTGT+AGG - chr1.2:75432079-75432098 None:intergenic 25.0%
!!! TAGTTTGAGTTTGTTATAAG+TGG - chr1.2:75432636-75432655 None:intergenic 25.0%
!!! TTATTTTTTTATACCTGCAG+TGG + chr1.2:75432942-75432961 MS.gene34483:intron 25.0%
AGTATTGTCTAATTGAAAGC+AGG + chr1.2:75432329-75432348 MS.gene34483:intron 30.0%
CCCGTACATAACTTAATAAT+TGG - chr1.2:75432698-75432717 None:intergenic 30.0%
GAAAGCAGGATATGATTATA+TGG + chr1.2:75432343-75432362 MS.gene34483:intron 30.0%
GATAGTTACAACTTACAAGT+TGG - chr1.2:75432598-75432617 None:intergenic 30.0%
GCAATAGTACTTGGAATAAT+TGG + chr1.2:75432183-75432202 MS.gene34483:CDS 30.0%
TATGGCAGATAATACAACAA+AGG - chr1.2:75433197-75433216 None:intergenic 30.0%
TTCAAGAATCACAATGAAAG+CGG + chr1.2:75432219-75432238 MS.gene34483:CDS 30.0%
TTCTTTACTTCCTTCTTCAA+TGG - chr1.2:75432135-75432154 None:intergenic 30.0%
!! ACTTACAAGTTGGTTAGTAT+TGG - chr1.2:75432588-75432607 None:intergenic 30.0%
AATATTATCCCCTTCATGCA+AGG - chr1.2:75432758-75432777 None:intergenic 35.0%
AGTTTACCTGAATGCCATAA+AGG - chr1.2:75432296-75432315 None:intergenic 35.0%
ATACTATCAGGACTTGATCT+AGG + chr1.2:75432662-75432681 MS.gene34483:intron 35.0%
ATATTATCCCCTTCATGCAA+GGG - chr1.2:75432757-75432776 None:intergenic 35.0%
ATCTGTACAGCTTACATTCA+TGG + chr1.2:75432250-75432269 MS.gene34483:CDS 35.0%
CAAATCTCTTCCATTGAAGA+AGG + chr1.2:75432122-75432141 MS.gene34483:CDS 35.0%
GTTTACCTGAATGCCATAAA+GGG - chr1.2:75432295-75432314 None:intergenic 35.0%
TATACCTGCAGTGGATATTT+GGG + chr1.2:75432951-75432970 MS.gene34483:intron 35.0%
TATTTCCCTTTATGGCATTC+AGG + chr1.2:75432287-75432306 MS.gene34483:CDS 35.0%
TCAAGAATCACAATGAAAGC+GGG + chr1.2:75432220-75432239 MS.gene34483:CDS 35.0%
TCATTTGGATAAGCCAAGTT+TGG - chr1.2:75432855-75432874 None:intergenic 35.0%
TGAATGTAAGCTGTACAGAT+TGG - chr1.2:75432250-75432269 None:intergenic 35.0%
TTATACCTGCAGTGGATATT+TGG + chr1.2:75432950-75432969 MS.gene34483:intron 35.0%
TTGTAGGTCAACAAAAATCC+AGG - chr1.2:75432063-75432082 None:intergenic 35.0%
! ATTGGGGTTATTTCCCTTTA+TGG + chr1.2:75432279-75432298 MS.gene34483:CDS 35.0%
! TACATTCATGGCTTGGAATT+GGG + chr1.2:75432262-75432281 MS.gene34483:CDS 35.0%
! TGGGCTGTTTGTGTATATTT+TGG + chr1.2:75433045-75433064 MS.gene34483:CDS 35.0%
! TTACATTCATGGCTTGGAAT+TGG + chr1.2:75432261-75432280 MS.gene34483:CDS 35.0%
! TTTGTGGTATTTTTCTACCC+TGG + chr1.2:75432974-75432993 MS.gene34483:CDS 35.0%
AGTTTGCACTTTGCACCATT+GGG - chr1.2:75432819-75432838 None:intergenic 40.0%
CAAGTACTATTGCAATTGCG+TGG - chr1.2:75432176-75432195 None:intergenic 40.0%
CACGCAATTGCAATAGTACT+TGG + chr1.2:75432174-75432193 MS.gene34483:CDS 40.0%
TACAGCTTACATTCATGGCT+TGG + chr1.2:75432255-75432274 MS.gene34483:CDS 40.0%
TTAACACCATGTCACTGTGA+CGG + chr1.2:75432420-75432439 MS.gene34483:intron 40.0%
TTTACGAGTCATTGCTATCC+TGG + chr1.2:75432042-75432061 MS.gene34483:intron 40.0%
! ACATTCATGGCTTGGAATTG+GGG + chr1.2:75432263-75432282 MS.gene34483:CDS 40.0%
! TGGTATTTTTCTACCCTGGT+GGG + chr1.2:75432978-75432997 MS.gene34483:CDS 40.0%
!! ACAGTAAACAGAAGCGCTAA+TGG - chr1.2:75432379-75432398 None:intergenic 40.0%
!! TTCCATGGCACGTGTTATTT+GGG + chr1.2:75433026-75433045 MS.gene34483:CDS 40.0%
AGTTCAGGGGTGGCAAAATA+CGG + chr1.2:75433118-75433137 MS.gene34483:CDS 45.0%
CAAACCCAAATATCCACTGC+AGG - chr1.2:75432958-75432977 None:intergenic 45.0%
GAGAAACCCAAGAGAAGAAG+TGG - chr1.2:75433077-75433096 None:intergenic 45.0%
GAGTTTGCACTTTGCACCAT+TGG - chr1.2:75432820-75432839 None:intergenic 45.0%
TAAGACGTGAGTCAGTTCCA+TGG + chr1.2:75433011-75433030 MS.gene34483:CDS 45.0%
TACTCTCTCCCTTGCATGAA+GGG + chr1.2:75432746-75432765 MS.gene34483:intron 45.0%
TCACATTCCTGGAGAGTTCA+GGG + chr1.2:75433104-75433123 MS.gene34483:CDS 45.0%
TTAACTCTGAACTCCCACCA+GGG - chr1.2:75432994-75433013 None:intergenic 45.0%
TTACTCTCTCCCTTGCATGA+AGG + chr1.2:75432745-75432764 MS.gene34483:intron 45.0%
TTGCAATTGCGTGGAGTACA+AGG - chr1.2:75432167-75432186 None:intergenic 45.0%
! GCAGTGGATATTTGGGTTTG+TGG + chr1.2:75432958-75432977 MS.gene34483:intron 45.0%
! GGAACTGACTCATAACCCAA+TGG + chr1.2:75432801-75432820 MS.gene34483:intron 45.0%
! GTGGTATTTTTCTACCCTGG+TGG + chr1.2:75432977-75432996 MS.gene34483:CDS 45.0%
! GTTCCATGGCACGTGTTATT+TGG + chr1.2:75433025-75433044 MS.gene34483:CDS 45.0%
AATCCACCGTCACAGTGACA+TGG - chr1.2:75432429-75432448 None:intergenic 50.0%
ACTCTCTCCCTTGCATGAAG+GGG + chr1.2:75432747-75432766 MS.gene34483:intron 50.0%
AGCCCAAATAACACGTGCCA+TGG - chr1.2:75433031-75433050 None:intergenic 50.0%
CACATTCCTGGAGAGTTCAG+GGG + chr1.2:75433105-75433124 MS.gene34483:CDS 50.0%
CTCACATTCCTGGAGAGTTC+AGG + chr1.2:75433103-75433122 MS.gene34483:CDS 50.0%
CTCTCGCCACTTCTTCTCTT+GGG + chr1.2:75433068-75433087 MS.gene34483:CDS 50.0%
CTTAACTCTGAACTCCCACC+AGG - chr1.2:75432995-75433014 None:intergenic 50.0%
GCTAGCTGCTATAGTCTGCA+AGG + chr1.2:75432457-75432476 MS.gene34483:intron 50.0%
GTTCAGGGGTGGCAAAATAC+GGG + chr1.2:75433119-75433138 MS.gene34483:CDS 50.0%
TCTCGAGAAGCTCACATTCC+TGG + chr1.2:75433093-75433112 MS.gene34483:CDS 50.0%
TGCCATATCTCAAGCTCCTC+CGG + chr1.2:75433210-75433229 MS.gene34483:CDS 50.0%
TTCAGGGGTGGCAAAATACG+GGG + chr1.2:75433120-75433139 MS.gene34483:CDS 50.0%
ACACCATGTCACTGTGACGG+TGG + chr1.2:75432423-75432442 MS.gene34483:intron 55.0%
AGCCGGAGGAGCTTGAGATA+TGG - chr1.2:75433215-75433234 None:intergenic 55.0%
ATTCCTGGAGAGTTCAGGGG+TGG + chr1.2:75433108-75433127 MS.gene34483:CDS 55.0%
GCTCTCGCCACTTCTTCTCT+TGG + chr1.2:75433067-75433086 MS.gene34483:CDS 55.0%
GGTGCGTAGTCATCAGCAGC+CGG - chr1.2:75433232-75433251 None:intergenic 60.0%
TTGCCACCCCTGAACTCTCC+AGG - chr1.2:75433114-75433133 None:intergenic 60.0%
GCGTAGTCATCAGCAGCCGG+AGG - chr1.2:75433229-75433248 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 75431972 75433258 75431972 ID=MS.gene34483
chr1.2 mRNA 75431972 75433258 75431972 ID=MS.gene34483.t1;Parent=MS.gene34483
chr1.2 exon 75431972 75432005 75431972 ID=MS.gene34483.t1.exon1;Parent=MS.gene34483.t1
chr1.2 CDS 75431972 75432005 75431972 ID=cds.MS.gene34483.t1;Parent=MS.gene34483.t1
chr1.2 exon 75432109 75432308 75432109 ID=MS.gene34483.t1.exon2;Parent=MS.gene34483.t1
chr1.2 CDS 75432109 75432308 75432109 ID=cds.MS.gene34483.t1;Parent=MS.gene34483.t1
chr1.2 exon 75432962 75433258 75432962 ID=MS.gene34483.t1.exon3;Parent=MS.gene34483.t1
chr1.2 CDS 75432962 75433258 75432962 ID=cds.MS.gene34483.t1;Parent=MS.gene34483.t1
Gene Sequence

>MS.gene34483

ATGCTTATTGGATTAATAATAATTGGAGGTGAAGGTAAGCAAAATAAGTTCACACTTCACATGTTACTTCTTTACGAGTCATTGCTATCCTGGATTTTTGTTGACCTACAAGCTGATTCATAAAATAAAAATTGCAGCTATTATAAGTTACAAATCTCTTCCATTGAAGAAGGAAGTAAAGAAATTGATACACCTTGTACTCCACGCAATTGCAATAGTACTTGGAATAATTGGAATTTGTGCTGCGTTCAAGAATCACAATGAAAGCGGGATTGCCAATCTGTACAGCTTACATTCATGGCTTGGAATTGGGGTTATTTCCCTTTATGGCATTCAGGTAAACTATTTGATAGTACTAGTATTGTCTAATTGAAAGCAGGATATGATTATATGGTCTCTTATTGCCATTAGCGCTTCTGTTTACTGTGAATGCATCAGTGTTGTCAAATTAACACCATGTCACTGTGACGGTGGATTCTATGTCAGCTAGCTGCTATAGTCTGCAAGGAGAAAATTTGAAATCCATAGAATGATAAAATTTGATTACAATGAGTATAGGATACACTTTATATAGTGGTCCTAACCATATTAACAGATCTTAACTAATTTGCAACCAATACTAACCAACTTGTAAGTTGTAACTATCTTTAACAAACTCTAACCACTTATAACAAACTCAAACTATATCTTATACTATCAGGACTTGATCTAGGTAGTTATGATCCAATTATTAAGTTATGTACGGGTTCTTCCTTTAGTTCTCTATTAATTTGTTACTCTCTCCCTTGCATGAAGGGGATAATATTAGATAAACAGAAAATTAGGAGAAGGAACTGACTCATAACCCAATGGTGCAAAGTGCAAACTCTTAATTGAAAATCCAAACTTGGCTTATCCAAATGAATCATTTGATTTGACATCATGCTATATTAGAACACAATTATCTTTCAATTTTCCTAACATATGTATTTTATTTTTTTATACCTGCAGTGGATATTTGGGTTTGTGGTATTTTTCTACCCTGGTGGGAGTTCAGAGTTAAGACGTGAGTCAGTTCCATGGCACGTGTTATTTGGGCTGTTTGTGTATATTTTGGCTCTCGCCACTTCTTCTCTTGGGTTTCTCGAGAAGCTCACATTCCTGGAGAGTTCAGGGGTGGCAAAATACGGGGCTGAAGCTTTACTTGTCAACTTCAATGCTATAATCACAATCTTATTTGGTACCTTTGTTGTATTATCTGCCATATCTCAAGCTCCTCCGGCTGCTGATGACTACGCACCCATATAG
Protein sequence

>MS.gene34483.t1

MLIGLIIIGGEAIISYKSLPLKKEVKKLIHLVLHAIAIVLGIIGICAAFKNHNESGIANLYSLHSWLGIGVISLYGIQWIFGFVVFFYPGGSSELRRESVPWHVLFGLFVYILALATSSLGFLEKLTFLESSGVAKYGAEALLVNFNAIITILFGTFVVLSAISQAPPAADDYAPI