AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene59370

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene59370.t1 MTR_5g020230 90.377 239 12 5 1 232 1 235 1.42e-147 410
MS.gene59370.t1 MTR_8g077510 55.556 243 82 8 1 232 1 228 4.16e-59 186
MS.gene59370.t1 MTR_1g016170 38.889 90 52 2 89 177 155 242 3.17e-14 70.9
MS.gene59370.t1 MTR_7g112330 56.250 48 19 1 119 166 18 63 3.56e-13 64.7
MS.gene59370.t1 MTR_2g094600 40.000 60 36 0 96 155 189 248 1.07e-12 66.6
MS.gene59370.t1 MTR_4g121110 67.568 37 12 0 123 159 30 66 1.37e-12 63.5
MS.gene59370.t1 MTR_4g126350 69.048 42 12 1 111 152 175 215 1.77e-12 65.9
MS.gene59370.t1 MTR_4g058910 32.143 84 52 1 72 155 268 346 1.79e-11 63.2
MS.gene59370.t1 MTR_1g116010 62.857 35 13 0 121 155 162 196 2.43e-11 62.0
MS.gene59370.t1 MTR_1g094930 62.162 37 14 0 119 155 143 179 4.52e-11 61.2
MS.gene59370.t1 MTR_5g021340 38.571 70 41 1 88 155 263 332 7.46e-11 61.6
MS.gene59370.t1 MTR_1g094930 62.162 37 14 0 119 155 238 274 8.30e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene59370.t1 AT3G50870 41.281 281 104 10 5 232 9 281 1.61e-48 161
MS.gene59370.t1 AT4G36620 43.891 221 83 10 27 232 3 197 6.99e-39 134
MS.gene59370.t1 AT2G18380 41.304 230 93 8 19 230 2 207 1.64e-36 128
MS.gene59370.t1 AT5G56860 49.462 93 33 3 64 156 185 263 5.65e-17 79.3
MS.gene59370.t1 AT5G49300 53.731 67 27 2 98 162 11 75 4.41e-15 70.1
MS.gene59370.t1 AT4G26150 63.830 47 16 1 107 153 184 229 1.14e-13 69.7
MS.gene59370.t1 AT1G08010 45.070 71 33 2 105 170 203 272 1.36e-12 66.2
MS.gene59370.t1 AT1G08010 45.070 71 33 2 105 170 203 272 1.36e-12 66.2
MS.gene59370.t1 AT1G08010 45.070 71 33 2 105 170 203 272 1.36e-12 66.2
MS.gene59370.t1 AT3G54810 37.234 94 54 1 106 194 212 305 4.25e-12 65.1
MS.gene59370.t1 AT3G54810 37.234 94 54 1 106 194 212 305 4.25e-12 65.1
MS.gene59370.t1 AT5G26930 67.568 37 12 0 123 159 26 62 4.32e-12 61.6
MS.gene59370.t1 AT3G06740 71.429 35 10 0 125 159 43 77 7.06e-12 61.6
MS.gene59370.t1 AT3G20750 70.588 34 10 0 127 160 163 196 1.63e-11 62.0
MS.gene59370.t1 AT2G45050 36.585 82 45 2 74 155 137 211 6.99e-11 60.8
MS.gene59370.t1 AT4G34680 50.980 51 23 1 107 155 162 212 7.93e-11 60.8
MS.gene59370.t1 AT4G34680 50.980 51 23 1 107 155 162 212 7.93e-11 60.8

Find 48 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCAATCATGATTCTGAAAA+TGG 0.202815 5.4:+12358975 MS.gene59370:CDS
GGAGTGAAACAATAGGTTTC+AGG 0.229794 5.4:-12358352 None:intergenic
GTTGGAGTTGTTGTTATTAT+TGG 0.243633 5.4:-12358566 None:intergenic
GAAGAAGAAGATGAAGAATT+AGG 0.286532 5.4:-12358373 None:intergenic
ATGGCATTCCATTTCTCTCT+TGG 0.336081 5.4:+12358994 MS.gene59370:CDS
GAGAGAAACACTGCATCTTC+TGG 0.356763 5.4:-12358917 None:intergenic
AACGCCATCTATCGGCATAA+TGG 0.385803 5.4:+12358833 MS.gene59370:CDS
CGGAACTCGTTAGTCATTGC+TGG 0.406108 5.4:-12358939 None:intergenic
TGTTCATGTGGTATGTTTCA+TGG 0.414708 5.4:+12358283 MS.gene59370:CDS
CCACCTCCACACCGCTTTGG+AGG 0.424846 5.4:+12358629 MS.gene59370:CDS
TAGGTTTCAGGTTCATCATA+AGG 0.424993 5.4:-12358340 None:intergenic
ATGCCGATAGATGGCGTTGC+CGG 0.430815 5.4:-12358828 None:intergenic
TAGAGTCTCCAAGAGAGAAA+TGG 0.442835 5.4:-12359002 None:intergenic
AGAATTAGGAGTGAAACAAT+AGG 0.458450 5.4:-12358359 None:intergenic
AGAAGAGCAACTGCTGCAGC+CGG 0.462808 5.4:+12358801 MS.gene59370:CDS
ACACCACCTCCACACCGCTT+TGG 0.463073 5.4:+12358626 MS.gene59370:CDS
GATTCCATTATGCCGATAGA+TGG 0.464364 5.4:-12358837 None:intergenic
CCTCCAAAGCGGTGTGGAGG+TGG 0.470303 5.4:-12358629 None:intergenic
TGAGTACTGTTGTACTGTTT+AGG 0.483115 5.4:-12358514 None:intergenic
CACTGCATCTTCTGGTTCTG+TGG 0.485352 5.4:-12358909 None:intergenic
AGCAAGAAGAGAATCATTGT+TGG 0.486549 5.4:-12358584 None:intergenic
GATTGGTTTCATCAATGAAA+CGG 0.487226 5.4:-12358959 None:intergenic
AACTGCTGCAGCCGGCACAC+CGG 0.491074 5.4:+12358809 MS.gene59370:CDS
AGATGGCGTTGCCGGTGTGC+CGG 0.497703 5.4:-12358820 None:intergenic
ATCTCAAGGGCAACACGTGA+TGG 0.509206 5.4:+12358255 MS.gene59370:CDS
TCCACACCGCTTTGGAGGAA+CGG 0.515774 5.4:+12358634 MS.gene59370:CDS
GTTGATTGTACTCTTTCACT+TGG 0.527724 5.4:+12358397 MS.gene59370:CDS
ATGATGCATCGTTCATCTCA+AGG 0.533388 5.4:+12358241 MS.gene59370:CDS
CAGAACGACGTTCATGATGT+CGG 0.540322 5.4:-12358462 None:intergenic
ACACCGGCAACGCCATCTAT+CGG 0.547655 5.4:+12358825 MS.gene59370:CDS
TCTCAAGGGCAACACGTGAT+GGG 0.577571 5.4:+12358256 MS.gene59370:CDS
CAGTCACTATGCAATGCATG+TGG 0.582954 5.4:+12358756 MS.gene59370:intron
ACCACCATCACAACAACTCA+TGG 0.584082 5.4:+12358877 MS.gene59370:CDS
CAGTACTCAGTCTCAAACAA+AGG 0.584934 5.4:+12358528 MS.gene59370:CDS
TCTTCAGTGAAACGAGTGGA+TGG 0.587900 5.4:-12358424 None:intergenic
ATGAGTTGTTGTGATGGTGG+TGG 0.588375 5.4:-12358875 None:intergenic
TGATGCATCGTTCATCTCAA+GGG 0.590177 5.4:+12358242 MS.gene59370:CDS
GTTCCTCCAAAGCGGTGTGG+AGG 0.595180 5.4:-12358632 None:intergenic
GAACGGTCCACGAGGCCCAA+AGG 0.609147 5.4:+12358651 MS.gene59370:CDS
ACCGTTCCTCCAAAGCGGTG+TGG 0.617219 5.4:-12358635 None:intergenic
TTCATCTTCAGTGAAACGAG+TGG 0.627984 5.4:-12358428 None:intergenic
ATGTGGGATCAGATTCAAGA+AGG 0.634149 5.4:+12358773 MS.gene59370:CDS
ACCATGAGTTGTTGTGATGG+TGG 0.656581 5.4:-12358878 None:intergenic
AGTCACTATGCAATGCATGT+GGG 0.668102 5.4:+12358757 MS.gene59370:intron
CGTACCATGAGTTGTTGTGA+TGG 0.677789 5.4:-12358881 None:intergenic
CGTGGACCGTTCCTCCAAAG+CGG 0.688334 5.4:-12358640 None:intergenic
CTTTGGAGGAACGGTCCACG+AGG 0.702547 5.4:+12358643 MS.gene59370:CDS
GTGATGGGACACTGTTCATG+TGG 0.723745 5.4:+12358271 MS.gene59370:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAATGTTATATTTCATGT+TGG - chr5.4:12358721-12358740 None:intergenic 15.0%
!!! ATATAACATTTTATGTTGAA+TGG + chr5.4:12358728-12358747 MS.gene59370:intron 15.0%
!! TTATATTTCATGTTGGTATT+TGG - chr5.4:12358714-12358733 None:intergenic 20.0%
!!! ATGTAGAGTATTTTTACCTT+TGG - chr5.4:12358670-12358689 None:intergenic 25.0%
!!! TGTAGAGTATTTTTACCTTT+GGG - chr5.4:12358669-12358688 None:intergenic 25.0%
AGAATTAGGAGTGAAACAAT+AGG - chr5.4:12358362-12358381 None:intergenic 30.0%
GAAGAAGAAGATGAAGAATT+AGG - chr5.4:12358376-12358395 None:intergenic 30.0%
TTCTGTCAAAAACTTCTGTT+GGG + chr5.4:12358480-12358499 MS.gene59370:CDS 30.0%
! ACCAATCATGATTCTGAAAA+TGG + chr5.4:12358975-12358994 MS.gene59370:CDS 30.0%
! GTTGGAGTTGTTGTTATTAT+TGG - chr5.4:12358569-12358588 None:intergenic 30.0%
!! GATTGGTTTCATCAATGAAA+CGG - chr5.4:12358962-12358981 None:intergenic 30.0%
AGCAAGAAGAGAATCATTGT+TGG - chr5.4:12358587-12358606 None:intergenic 35.0%
GTTCTGTCAAAAACTTCTGT+TGG + chr5.4:12358479-12358498 MS.gene59370:CDS 35.0%
GTTGATTGTACTCTTTCACT+TGG + chr5.4:12358397-12358416 MS.gene59370:CDS 35.0%
TGTTCATGTGGTATGTTTCA+TGG + chr5.4:12358283-12358302 MS.gene59370:CDS 35.0%
! TGAGTACTGTTGTACTGTTT+AGG - chr5.4:12358517-12358536 None:intergenic 35.0%
!! GCCATTTTCAGAATCATGAT+TGG - chr5.4:12358979-12358998 None:intergenic 35.0%
!! TAGGTTTCAGGTTCATCATA+AGG - chr5.4:12358343-12358362 None:intergenic 35.0%
AGTCACTATGCAATGCATGT+GGG + chr5.4:12358757-12358776 MS.gene59370:intron 40.0%
ATGATGCATCGTTCATCTCA+AGG + chr5.4:12358241-12358260 MS.gene59370:CDS 40.0%
ATGGCATTCCATTTCTCTCT+TGG + chr5.4:12358994-12359013 MS.gene59370:CDS 40.0%
ATGTGGGATCAGATTCAAGA+AGG + chr5.4:12358773-12358792 MS.gene59370:CDS 40.0%
CAGTACTCAGTCTCAAACAA+AGG + chr5.4:12358528-12358547 MS.gene59370:CDS 40.0%
GATTCCATTATGCCGATAGA+TGG - chr5.4:12358840-12358859 None:intergenic 40.0%
GGAGTGAAACAATAGGTTTC+AGG - chr5.4:12358355-12358374 None:intergenic 40.0%
TAGAGTCTCCAAGAGAGAAA+TGG - chr5.4:12359005-12359024 None:intergenic 40.0%
TGATGCATCGTTCATCTCAA+GGG + chr5.4:12358242-12358261 MS.gene59370:CDS 40.0%
TTCATCTTCAGTGAAACGAG+TGG - chr5.4:12358431-12358450 None:intergenic 40.0%
AACGCCATCTATCGGCATAA+TGG + chr5.4:12358833-12358852 MS.gene59370:CDS 45.0%
ACCACCATCACAACAACTCA+TGG + chr5.4:12358877-12358896 MS.gene59370:CDS 45.0%
ACCATGAGTTGTTGTGATGG+TGG - chr5.4:12358881-12358900 None:intergenic 45.0%
CAGAACGACGTTCATGATGT+CGG - chr5.4:12358465-12358484 None:intergenic 45.0%
CAGTCACTATGCAATGCATG+TGG + chr5.4:12358756-12358775 MS.gene59370:intron 45.0%
CGTACCATGAGTTGTTGTGA+TGG - chr5.4:12358884-12358903 None:intergenic 45.0%
GAGAGAAACACTGCATCTTC+TGG - chr5.4:12358920-12358939 None:intergenic 45.0%
TCTTCAGTGAAACGAGTGGA+TGG - chr5.4:12358427-12358446 None:intergenic 45.0%
! ATTTTTACCTTTGGGCCTCG+TGG - chr5.4:12358661-12358680 None:intergenic 45.0%
!! ATGAGTTGTTGTGATGGTGG+TGG - chr5.4:12358878-12358897 None:intergenic 45.0%
ATCTCAAGGGCAACACGTGA+TGG + chr5.4:12358255-12358274 MS.gene59370:CDS 50.0%
CGGAACTCGTTAGTCATTGC+TGG - chr5.4:12358942-12358961 None:intergenic 50.0%
TCTCAAGGGCAACACGTGAT+GGG + chr5.4:12358256-12358275 MS.gene59370:CDS 50.0%
! GTGATGGGACACTGTTCATG+TGG + chr5.4:12358271-12358290 MS.gene59370:CDS 50.0%
!! CACTGCATCTTCTGGTTCTG+TGG - chr5.4:12358912-12358931 None:intergenic 50.0%
ACACCGGCAACGCCATCTAT+CGG + chr5.4:12358825-12358844 MS.gene59370:CDS 55.0%
AGAAGAGCAACTGCTGCAGC+CGG + chr5.4:12358801-12358820 MS.gene59370:CDS 55.0%
ATGCCGATAGATGGCGTTGC+CGG - chr5.4:12358831-12358850 None:intergenic 55.0%
!! TCCACACCGCTTTGGAGGAA+CGG + chr5.4:12358634-12358653 MS.gene59370:CDS 55.0%
ACACCACCTCCACACCGCTT+TGG + chr5.4:12358626-12358645 MS.gene59370:CDS 60.0%
ACCGTTCCTCCAAAGCGGTG+TGG - chr5.4:12358638-12358657 None:intergenic 60.0%
CGTGGACCGTTCCTCCAAAG+CGG - chr5.4:12358643-12358662 None:intergenic 60.0%
GTTCCTCCAAAGCGGTGTGG+AGG - chr5.4:12358635-12358654 None:intergenic 60.0%
! CTTTGGAGGAACGGTCCACG+AGG + chr5.4:12358643-12358662 MS.gene59370:CDS 60.0%
AACTGCTGCAGCCGGCACAC+CGG + chr5.4:12358809-12358828 MS.gene59370:CDS 65.0%
AGATGGCGTTGCCGGTGTGC+CGG - chr5.4:12358823-12358842 None:intergenic 65.0%
CCACCTCCACACCGCTTTGG+AGG + chr5.4:12358629-12358648 MS.gene59370:CDS 65.0%
CCTCCAAAGCGGTGTGGAGG+TGG - chr5.4:12358632-12358651 None:intergenic 65.0%
GAACGGTCCACGAGGCCCAA+AGG + chr5.4:12358651-12358670 MS.gene59370:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 12358241 12359025 12358241 ID=MS.gene59370
chr5.4 mRNA 12358241 12359025 12358241 ID=MS.gene59370.t1;Parent=MS.gene59370
chr5.4 exon 12358241 12358672 12358241 ID=MS.gene59370.t1.exon1;Parent=MS.gene59370.t1
chr5.4 CDS 12358241 12358672 12358241 ID=cds.MS.gene59370.t1;Parent=MS.gene59370.t1
chr5.4 exon 12358759 12359025 12358759 ID=MS.gene59370.t1.exon2;Parent=MS.gene59370.t1
chr5.4 CDS 12358759 12359025 12358759 ID=cds.MS.gene59370.t1;Parent=MS.gene59370.t1
Gene Sequence

>MS.gene59370

ATGATGCATCGTTCATCTCAAGGGCAACACGTGATGGGACACTGTTCATGTGGTATGTTTCATGGACAAAACAACTCATTCTCAATGTTATTCTCTACACCTTATGATGAACCTGAAACCTATTGTTTCACTCCTAATTCTTCATCTTCTTCTTCTGTTGATTGTACTCTTTCACTTGGAACACCATCCACTCGTTTCACTGAAGATGAAGAGAAAAGAAGCCGACATCATGAACGTCGTTCTGTCAAAAACTTCTGTTGGGATTTGTTAACACCTAAACAGTACAACAGTACTCAGTCTCAAACAAAGGCAACACGTGCAAATACCAATAATAACAACAACTCCAACAATGATTCTCTTCTTGCTCGTAGATGTGCAAACTGTGACACCACCTCCACACCGCTTTGGAGGAACGGTCCACGAGGCCCAAAGGTAAAAATACTCTACATATATATATAACTATATGCATTCCAAATACCAACATGAAATATAACATTTTATGTTGAATGGAATTACAGTCACTATGCAATGCATGTGGGATCAGATTCAAGAAGGAAGAGAGAAGAGCAACTGCTGCAGCCGGCACACCGGCAACGCCATCTATCGGCATAATGGAATCAGCTTCGATGTATAACCACCACCATCACAACAACTCATGGTACGTACAACCACAGAACCAGAAGATGCAGTGTTTCTCTCCAGCAATGACTAACGAGTTCCGTTTCATTGATGAAACCAATCATGATTCTGAAAATGGCATTCCATTTCTCTCTTGGAGACTCTAA
Protein sequence

>MS.gene59370.t1

MMHRSSQGQHVMGHCSCGMFHGQNNSFSMLFSTPYDEPETYCFTPNSSSSSSVDCTLSLGTPSTRFTEDEEKRSRHHERRSVKNFCWDLLTPKQYNSTQSQTKATRANTNNNNNSNNDSLLARRCANCDTTSTPLWRNGPRGPKSLCNACGIRFKKEERRATAAAGTPATPSIGIMESASMYNHHHHNNSWYVQPQNQKMQCFSPAMTNEFRFIDETNHDSENGIPFLSWRL