AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene047782

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene047782.t1 MTR_5g020230 90.377 239 12 5 1 232 1 235 1.16e-147 411
MS.gene047782.t1 MTR_8g077510 55.144 243 83 8 1 232 1 228 4.25e-59 186
MS.gene047782.t1 MTR_1g016170 38.889 90 52 2 89 177 155 242 2.98e-14 70.9
MS.gene047782.t1 MTR_7g112330 56.250 48 19 1 119 166 18 63 3.75e-13 64.7
MS.gene047782.t1 MTR_2g094600 40.000 60 36 0 96 155 189 248 1.04e-12 66.6
MS.gene047782.t1 MTR_4g121110 67.568 37 12 0 123 159 30 66 1.38e-12 63.5
MS.gene047782.t1 MTR_4g126350 69.048 42 12 1 111 152 175 215 1.67e-12 66.2
MS.gene047782.t1 MTR_4g058910 32.143 84 52 1 72 155 268 346 1.76e-11 63.5
MS.gene047782.t1 MTR_1g116010 62.857 35 13 0 121 155 162 196 2.52e-11 62.0
MS.gene047782.t1 MTR_1g094930 62.162 37 14 0 119 155 143 179 4.61e-11 61.2
MS.gene047782.t1 MTR_5g021340 38.571 70 41 1 88 155 263 332 7.60e-11 61.6
MS.gene047782.t1 MTR_1g094930 62.162 37 14 0 119 155 238 274 8.62e-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.gene047782.t1 AT3G50870 41.281 281 104 10 5 232 9 281 1.09e-48 162
MS.gene047782.t1 AT4G36620 43.439 221 84 10 27 232 3 197 1.62e-38 133
MS.gene047782.t1 AT2G18380 40.870 230 94 8 19 230 2 207 3.58e-36 127
MS.gene047782.t1 AT5G56860 49.462 93 33 3 64 156 185 263 5.76e-17 79.3
MS.gene047782.t1 AT5G49300 53.731 67 27 2 98 162 11 75 4.32e-15 70.1
MS.gene047782.t1 AT4G26150 63.830 47 16 1 107 153 184 229 1.11e-13 69.7
MS.gene047782.t1 AT1G08010 45.070 71 33 2 105 170 203 272 1.32e-12 66.2
MS.gene047782.t1 AT1G08010 45.070 71 33 2 105 170 203 272 1.32e-12 66.2
MS.gene047782.t1 AT1G08010 45.070 71 33 2 105 170 203 272 1.32e-12 66.2
MS.gene047782.t1 AT3G54810 37.234 94 54 1 106 194 212 305 4.25e-12 65.1
MS.gene047782.t1 AT3G54810 37.234 94 54 1 106 194 212 305 4.25e-12 65.1
MS.gene047782.t1 AT5G26930 67.568 37 12 0 123 159 26 62 4.32e-12 61.6
MS.gene047782.t1 AT3G06740 71.429 35 10 0 125 159 43 77 7.98e-12 61.6
MS.gene047782.t1 AT3G20750 70.588 34 10 0 127 160 163 196 1.72e-11 62.0
MS.gene047782.t1 AT2G45050 36.585 82 45 2 74 155 137 211 6.92e-11 60.8
MS.gene047782.t1 AT4G34680 50.980 51 23 1 107 155 162 212 8.24e-11 60.8
MS.gene047782.t1 AT4G34680 50.980 51 23 1 107 155 162 212 8.24e-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 5.1:+11724687 MS.gene047782:CDS
GGAGTGAAACAATAGGTTTC+AGG 0.229794 5.1:-11724064 None:intergenic
GTTGGAGTTGTTGTTATTAT+TGG 0.243633 5.1:-11724278 None:intergenic
GCAGAAGAAGATGAAGAATT+AGG 0.274996 5.1:-11724085 None:intergenic
ATGGCATTCCATTTCTCTCT+TGG 0.336081 5.1:+11724706 MS.gene047782:CDS
GAGAGAAACACTGCATCTTC+TGG 0.356763 5.1:-11724629 None:intergenic
AACGCCATCTATCGGCATAA+TGG 0.385803 5.1:+11724545 MS.gene047782:CDS
CGGAACTCGTTAGTCATTGC+TGG 0.406108 5.1:-11724651 None:intergenic
TGTTCATGTGGTATGTTTCA+TGG 0.414708 5.1:+11723995 MS.gene047782:CDS
CCACCTCCACACCGCTTTGG+AGG 0.424846 5.1:+11724341 MS.gene047782:CDS
TAGGTTTCAGGTTCATCATA+AGG 0.424993 5.1:-11724052 None:intergenic
ATGCCGATAGATGGCGTTGC+CGG 0.430815 5.1:-11724540 None:intergenic
TAGAGTCTCCAAGAGAGAAA+TGG 0.442835 5.1:-11724714 None:intergenic
AGAATTAGGAGTGAAACAAT+AGG 0.458450 5.1:-11724071 None:intergenic
AGAAGAGCAACTGCTGCAGC+CGG 0.462808 5.1:+11724513 MS.gene047782:CDS
ACACCACCTCCACACCGCTT+TGG 0.463073 5.1:+11724338 MS.gene047782:CDS
GATTCCATTATGCCGATAGA+TGG 0.464364 5.1:-11724549 None:intergenic
CCTCCAAAGCGGTGTGGAGG+TGG 0.470303 5.1:-11724341 None:intergenic
TGAGTACTGTTGTACTGTTT+AGG 0.483115 5.1:-11724226 None:intergenic
CACTGCATCTTCTGGTTCTG+TGG 0.485352 5.1:-11724621 None:intergenic
AGCAAGAAGAGAATCATTGT+TGG 0.486549 5.1:-11724296 None:intergenic
GATTGGTTTCATCAATGAAA+CGG 0.487226 5.1:-11724671 None:intergenic
AACTGCTGCAGCCGGCACAC+CGG 0.491074 5.1:+11724521 MS.gene047782:CDS
AGATGGCGTTGCCGGTGTGC+CGG 0.497703 5.1:-11724532 None:intergenic
ATCTCAAGGGCAACACGTGA+TGG 0.509206 5.1:+11723967 MS.gene047782:CDS
TCCACACCGCTTTGGAGGAA+CGG 0.515774 5.1:+11724346 MS.gene047782:CDS
ATGATGCATCGTTCATCTCA+AGG 0.533388 5.1:+11723953 MS.gene047782:CDS
CAGAACGACGTTCATGATGT+CGG 0.540322 5.1:-11724174 None:intergenic
ACACCGGCAACGCCATCTAT+CGG 0.547655 5.1:+11724537 MS.gene047782:CDS
GTTGATTGTACTCTTTCACT+TGG 0.548015 5.1:+11724109 MS.gene047782:CDS
TCTCAAGGGCAACACGTGAT+GGG 0.577571 5.1:+11723968 MS.gene047782:CDS
CAGTCACTATGCAATGCATG+TGG 0.582954 5.1:+11724468 MS.gene047782:intron
ACCACCATCACAACAACTCA+TGG 0.584082 5.1:+11724589 MS.gene047782:CDS
CAGTACTCAGTCTCAAACAA+AGG 0.584934 5.1:+11724240 MS.gene047782:CDS
TCTTCAGTGAAACGAGTGGA+TGG 0.587900 5.1:-11724136 None:intergenic
ATGAGTTGTTGTGATGGTGG+TGG 0.588375 5.1:-11724587 None:intergenic
TGATGCATCGTTCATCTCAA+GGG 0.590177 5.1:+11723954 MS.gene047782:CDS
GTTCCTCCAAAGCGGTGTGG+AGG 0.595180 5.1:-11724344 None:intergenic
GAACGGTCCACGAGGCCCAA+AGG 0.609147 5.1:+11724363 MS.gene047782:CDS
ACCGTTCCTCCAAAGCGGTG+TGG 0.617219 5.1:-11724347 None:intergenic
TTCATCTTCAGTGAAACGAG+TGG 0.627984 5.1:-11724140 None:intergenic
ATGTGGGATCAGATTCAAGA+AGG 0.634149 5.1:+11724485 MS.gene047782:CDS
ACCATGAGTTGTTGTGATGG+TGG 0.656581 5.1:-11724590 None:intergenic
AGTCACTATGCAATGCATGT+GGG 0.668102 5.1:+11724469 MS.gene047782:intron
CGTACCATGAGTTGTTGTGA+TGG 0.677789 5.1:-11724593 None:intergenic
CGTGGACCGTTCCTCCAAAG+CGG 0.688334 5.1:-11724352 None:intergenic
CTTTGGAGGAACGGTCCACG+AGG 0.702547 5.1:+11724355 MS.gene047782:CDS
GTGATGGGACACTGTTCATG+TGG 0.723745 5.1:+11723983 MS.gene047782:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAATGTTATATTTCATGT+TGG - chr5.1:11724433-11724452 None:intergenic 15.0%
!!! ATATAACATTTTATGTTGAA+TGG + chr5.1:11724440-11724459 MS.gene047782:intron 15.0%
!! TTATATTTCATGTTGGTATT+TGG - chr5.1:11724426-11724445 None:intergenic 20.0%
!!! ATGTAGAGTATTTTTACCTT+TGG - chr5.1:11724382-11724401 None:intergenic 25.0%
!!! TGTAGAGTATTTTTACCTTT+GGG - chr5.1:11724381-11724400 None:intergenic 25.0%
AGAATTAGGAGTGAAACAAT+AGG - chr5.1:11724074-11724093 None:intergenic 30.0%
TTCTGTCAAAAACTTCTGTT+GGG + chr5.1:11724192-11724211 MS.gene047782:CDS 30.0%
! ACCAATCATGATTCTGAAAA+TGG + chr5.1:11724687-11724706 MS.gene047782:CDS 30.0%
! GTTGGAGTTGTTGTTATTAT+TGG - chr5.1:11724281-11724300 None:intergenic 30.0%
!! GATTGGTTTCATCAATGAAA+CGG - chr5.1:11724674-11724693 None:intergenic 30.0%
AGCAAGAAGAGAATCATTGT+TGG - chr5.1:11724299-11724318 None:intergenic 35.0%
GCAGAAGAAGATGAAGAATT+AGG - chr5.1:11724088-11724107 None:intergenic 35.0%
GTTCTGTCAAAAACTTCTGT+TGG + chr5.1:11724191-11724210 MS.gene047782:CDS 35.0%
GTTGATTGTACTCTTTCACT+TGG + chr5.1:11724109-11724128 MS.gene047782:CDS 35.0%
TGTTCATGTGGTATGTTTCA+TGG + chr5.1:11723995-11724014 MS.gene047782:CDS 35.0%
! TGAGTACTGTTGTACTGTTT+AGG - chr5.1:11724229-11724248 None:intergenic 35.0%
!! GCCATTTTCAGAATCATGAT+TGG - chr5.1:11724691-11724710 None:intergenic 35.0%
!! TAGGTTTCAGGTTCATCATA+AGG - chr5.1:11724055-11724074 None:intergenic 35.0%
AGTCACTATGCAATGCATGT+GGG + chr5.1:11724469-11724488 MS.gene047782:intron 40.0%
ATGATGCATCGTTCATCTCA+AGG + chr5.1:11723953-11723972 MS.gene047782:CDS 40.0%
ATGGCATTCCATTTCTCTCT+TGG + chr5.1:11724706-11724725 MS.gene047782:CDS 40.0%
ATGTGGGATCAGATTCAAGA+AGG + chr5.1:11724485-11724504 MS.gene047782:CDS 40.0%
CAGTACTCAGTCTCAAACAA+AGG + chr5.1:11724240-11724259 MS.gene047782:CDS 40.0%
GATTCCATTATGCCGATAGA+TGG - chr5.1:11724552-11724571 None:intergenic 40.0%
GGAGTGAAACAATAGGTTTC+AGG - chr5.1:11724067-11724086 None:intergenic 40.0%
TAGAGTCTCCAAGAGAGAAA+TGG - chr5.1:11724717-11724736 None:intergenic 40.0%
TGATGCATCGTTCATCTCAA+GGG + chr5.1:11723954-11723973 MS.gene047782:CDS 40.0%
TTCATCTTCAGTGAAACGAG+TGG - chr5.1:11724143-11724162 None:intergenic 40.0%
AACGCCATCTATCGGCATAA+TGG + chr5.1:11724545-11724564 MS.gene047782:CDS 45.0%
ACCACCATCACAACAACTCA+TGG + chr5.1:11724589-11724608 MS.gene047782:CDS 45.0%
ACCATGAGTTGTTGTGATGG+TGG - chr5.1:11724593-11724612 None:intergenic 45.0%
CAGAACGACGTTCATGATGT+CGG - chr5.1:11724177-11724196 None:intergenic 45.0%
CAGTCACTATGCAATGCATG+TGG + chr5.1:11724468-11724487 MS.gene047782:intron 45.0%
CGTACCATGAGTTGTTGTGA+TGG - chr5.1:11724596-11724615 None:intergenic 45.0%
GAGAGAAACACTGCATCTTC+TGG - chr5.1:11724632-11724651 None:intergenic 45.0%
TCTTCAGTGAAACGAGTGGA+TGG - chr5.1:11724139-11724158 None:intergenic 45.0%
! ATTTTTACCTTTGGGCCTCG+TGG - chr5.1:11724373-11724392 None:intergenic 45.0%
!! ATGAGTTGTTGTGATGGTGG+TGG - chr5.1:11724590-11724609 None:intergenic 45.0%
ATCTCAAGGGCAACACGTGA+TGG + chr5.1:11723967-11723986 MS.gene047782:CDS 50.0%
CGGAACTCGTTAGTCATTGC+TGG - chr5.1:11724654-11724673 None:intergenic 50.0%
TCTCAAGGGCAACACGTGAT+GGG + chr5.1:11723968-11723987 MS.gene047782:CDS 50.0%
! GTGATGGGACACTGTTCATG+TGG + chr5.1:11723983-11724002 MS.gene047782:CDS 50.0%
!! CACTGCATCTTCTGGTTCTG+TGG - chr5.1:11724624-11724643 None:intergenic 50.0%
ACACCGGCAACGCCATCTAT+CGG + chr5.1:11724537-11724556 MS.gene047782:CDS 55.0%
AGAAGAGCAACTGCTGCAGC+CGG + chr5.1:11724513-11724532 MS.gene047782:CDS 55.0%
ATGCCGATAGATGGCGTTGC+CGG - chr5.1:11724543-11724562 None:intergenic 55.0%
!! TCCACACCGCTTTGGAGGAA+CGG + chr5.1:11724346-11724365 MS.gene047782:CDS 55.0%
ACACCACCTCCACACCGCTT+TGG + chr5.1:11724338-11724357 MS.gene047782:CDS 60.0%
ACCGTTCCTCCAAAGCGGTG+TGG - chr5.1:11724350-11724369 None:intergenic 60.0%
CGTGGACCGTTCCTCCAAAG+CGG - chr5.1:11724355-11724374 None:intergenic 60.0%
GTTCCTCCAAAGCGGTGTGG+AGG - chr5.1:11724347-11724366 None:intergenic 60.0%
! CTTTGGAGGAACGGTCCACG+AGG + chr5.1:11724355-11724374 MS.gene047782:CDS 60.0%
AACTGCTGCAGCCGGCACAC+CGG + chr5.1:11724521-11724540 MS.gene047782:CDS 65.0%
AGATGGCGTTGCCGGTGTGC+CGG - chr5.1:11724535-11724554 None:intergenic 65.0%
CCACCTCCACACCGCTTTGG+AGG + chr5.1:11724341-11724360 MS.gene047782:CDS 65.0%
CCTCCAAAGCGGTGTGGAGG+TGG - chr5.1:11724344-11724363 None:intergenic 65.0%
GAACGGTCCACGAGGCCCAA+AGG + chr5.1:11724363-11724382 MS.gene047782:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 11723953 11724737 11723953 ID=MS.gene047782
chr5.1 mRNA 11723953 11724737 11723953 ID=MS.gene047782.t1;Parent=MS.gene047782
chr5.1 exon 11723953 11724384 11723953 ID=MS.gene047782.t1.exon1;Parent=MS.gene047782.t1
chr5.1 CDS 11723953 11724384 11723953 ID=cds.MS.gene047782.t1;Parent=MS.gene047782.t1
chr5.1 exon 11724471 11724737 11724471 ID=MS.gene047782.t1.exon2;Parent=MS.gene047782.t1
chr5.1 CDS 11724471 11724737 11724471 ID=cds.MS.gene047782.t1;Parent=MS.gene047782.t1
Gene Sequence

>MS.gene047782

ATGATGCATCGTTCATCTCAAGGGCAACACGTGATGGGACACTGTTCATGTGGTATGTTTCATGGACAAAACAACTCATTCTCAATGTTATTCTCTACACCTTATGATGAACCTGAAACCTATTGTTTCACTCCTAATTCTTCATCTTCTTCTGCTGTTGATTGTACTCTTTCACTTGGAACACCATCCACTCGTTTCACTGAAGATGAAGAGAAAAGAAGCCGACATCATGAACGTCGTTCTGTCAAAAACTTCTGTTGGGATTTGTTAACACCTAAACAGTACAACAGTACTCAGTCTCAAACAAAGGCAACACGTGCAAATACCAATAATAACAACAACTCCAACAATGATTCTCTTCTTGCTCGTAGATGTGCAAACTGTGACACCACCTCCACACCGCTTTGGAGGAACGGTCCACGAGGCCCAAAGGTAAAAATACTCTACATATATATATAACTATATGCATTCCAAATACCAACATGAAATATAACATTTTATGTTGAATGGAATTACAGTCACTATGCAATGCATGTGGGATCAGATTCAAGAAGGAAGAGAGAAGAGCAACTGCTGCAGCCGGCACACCGGCAACGCCATCTATCGGCATAATGGAATCAGCTTCGATGTATAACCACCACCATCACAACAACTCATGGTACGTACAACCACAGAACCAGAAGATGCAGTGTTTCTCTCCAGCAATGACTAACGAGTTCCGTTTCATTGATGAAACCAATCATGATTCTGAAAATGGCATTCCATTTCTCTCTTGGAGACTCTAA
Protein sequence

>MS.gene047782.t1

MMHRSSQGQHVMGHCSCGMFHGQNNSFSMLFSTPYDEPETYCFTPNSSSSSAVDCTLSLGTPSTRFTEDEEKRSRHHERRSVKNFCWDLLTPKQYNSTQSQTKATRANTNNNNNSNNDSLLARRCANCDTTSTPLWRNGPRGPKSLCNACGIRFKKEERRATAAAGTPATPSIGIMESASMYNHHHHNNSWYVQPQNQKMQCFSPAMTNEFRFIDETNHDSENGIPFLSWRL