AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040684

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040684.t1 MTR_4g119990 62.409 274 74 6 1 249 54 323 3.06e-107 315
MS.gene040684.t1 MTR_6g043890 59.363 251 73 5 1 229 54 297 1.06e-92 276
MS.gene040684.t1 MTR_1g035440 50.265 189 51 2 2 147 55 243 1.86e-39 137
MS.gene040684.t1 MTR_1g035460 29.044 272 139 9 15 246 38 295 2.32e-24 100
MS.gene040684.t1 MTR_1g108780 26.275 255 156 8 13 242 47 294 1.96e-21 92.8
MS.gene040684.t1 MTR_7g050710 27.778 234 145 6 12 223 62 293 7.65e-20 87.0
MS.gene040684.t1 MTR_5g044670 27.444 266 168 10 5 252 59 317 2.05e-19 86.3
MS.gene040684.t1 MTR_7g050580 28.507 221 143 5 12 223 62 276 3.98e-19 85.1
MS.gene040684.t1 MTR_3g098790 28.033 239 157 7 12 237 62 298 5.19e-19 85.1
MS.gene040684.t1 MTR_3g061310 29.339 242 153 8 5 237 53 285 1.12e-18 83.6
MS.gene040684.t1 MTR_3g061350 29.098 244 150 9 5 237 53 284 1.60e-18 82.8
MS.gene040684.t1 MTR_8g103940 26.357 258 159 9 13 246 89 339 7.55e-18 82.8
MS.gene040684.t1 MTR_7g050720 27.626 257 154 8 12 237 59 314 1.13e-17 81.3
MS.gene040684.t1 MTR_3g061320 28.980 245 144 9 5 237 53 279 1.36e-17 80.5
MS.gene040684.t1 MTR_3g061370 28.279 244 152 9 5 237 50 281 5.68e-17 78.6
MS.gene040684.t1 MTR_7g050590 27.350 234 146 6 12 223 35 266 8.36e-17 78.6
MS.gene040684.t1 MTR_3g061340 28.326 233 143 10 5 230 53 268 1.33e-16 77.4
MS.gene040684.t1 MTR_1g035640 28.689 244 155 10 2 236 45 278 3.41e-16 77.8
MS.gene040684.t1 MTR_7g050560 27.442 215 147 5 15 223 65 276 4.97e-16 76.6
MS.gene040684.t1 MTR_3g061330 28.351 194 123 6 5 192 53 236 1.40e-15 74.3
MS.gene040684.t1 MTR_1g021360 27.826 230 146 7 11 223 230 456 2.22e-14 72.4
MS.gene040684.t1 MTR_6g061070 25.979 281 164 11 5 249 61 333 3.31e-13 68.9
MS.gene040684.t1 MTR_5g070440 27.273 231 122 9 16 237 74 267 8.96e-13 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTATCTTTGTCAACAAAA+AGG 0.196489 1.2:-34077164 None:intergenic
GAAGAGAATAATTTGAAATT+TGG 0.198679 1.2:+34077249 MS.gene040684:CDS
CTCTATCAATGTATGACTTT+TGG 0.220204 1.2:-34076783 None:intergenic
TATAATTTACCTTCAAAATA+AGG 0.255936 1.2:-34077360 None:intergenic
CTTCGTCATCACGGGGTAAA+AGG 0.257683 1.2:+34076471 MS.gene040684:CDS
AAGTAGTTGTGATGATATTA+AGG 0.299219 1.2:+34076687 MS.gene040684:CDS
TTCTTACAAACTTTCATAGA+TGG 0.310675 1.2:-34076509 None:intergenic
GTCTTTAATGTGATTGTATT+CGG 0.330391 1.2:+34076359 MS.gene040684:CDS
ATTTCAAATTATTCTCTTCA+CGG 0.368199 1.2:-34077245 None:intergenic
GAGAAAATAACAACTTGAAA+TGG 0.395512 1.2:-34077315 None:intergenic
TTTCTCTTTGGAAAAGGACT+TGG 0.399841 1.2:+34077332 MS.gene040684:CDS
TGTGTCTTAACAAATTCATT+TGG 0.404885 1.2:-34077108 None:intergenic
CTTCCCTAGTTTCTATTGAC+GGG 0.432866 1.2:-34076406 None:intergenic
TGAATTTGTTAAGACACATA+TGG 0.433535 1.2:+34077113 MS.gene040684:CDS
TGAGAATCCTTCGTCATCAC+GGG 0.459175 1.2:+34076463 MS.gene040684:CDS
TCTTCCCTAGTTTCTATTGA+CGG 0.476450 1.2:-34076407 None:intergenic
AATACCCGTCAATAGAAACT+AGG 0.499623 1.2:+34076402 MS.gene040684:CDS
TTGAGAATCCTTCGTCATCA+CGG 0.526374 1.2:+34076462 MS.gene040684:CDS
ATACATTGATAGAGATCGCT+TGG 0.539899 1.2:+34076792 MS.gene040684:CDS
AATCTGCACTAACTTGTGGT+TGG 0.573287 1.2:+34077214 MS.gene040684:CDS
ATACCCGTCAATAGAAACTA+GGG 0.574891 1.2:+34076403 MS.gene040684:CDS
TAAGACACATATGGACATGA+TGG 0.584937 1.2:+34077122 MS.gene040684:CDS
AAACAATCTGCACTAACTTG+TGG 0.589005 1.2:+34077210 MS.gene040684:CDS
ACACATATGGACATGATGGA+AGG 0.627742 1.2:+34077126 MS.gene040684:CDS
AGGGAAGAATCTGAAGAGAG+TGG 0.632551 1.2:+34076422 MS.gene040684:CDS
GAGAATCCTTCGTCATCACG+GGG 0.717191 1.2:+34076464 MS.gene040684:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AACAATTTATGAAAATTTTA+TGG + chr1.2:34077436-34077455 MS.gene040684:intron 10.0%
!! TATAATTTACCTTCAAAATA+AGG - chr1.2:34077363-34077382 None:intergenic 15.0%
!!! TTTTTGCTACTAATTTTTTT+TGG + chr1.2:34076641-34076660 MS.gene040684:intron 15.0%
!! AACTATATGTGTGTATTTAT+AGG + chr1.2:34077080-34077099 MS.gene040684:intron 20.0%
!! ATTTATCTTTGTCAACAAAA+AGG - chr1.2:34077167-34077186 None:intergenic 20.0%
!! ATTTCAAATTATTCTCTTCA+CGG - chr1.2:34077248-34077267 None:intergenic 20.0%
!! CAATATAATAATTCATGTGT+TGG + chr1.2:34077481-34077500 MS.gene040684:intron 20.0%
!! GGAAATTCATTTAATATGAT+GGG + chr1.2:34077400-34077419 MS.gene040684:intron 20.0%
!! TTTATCTTTGTCAACAAAAA+GGG - chr1.2:34077166-34077185 None:intergenic 20.0%
!!! CTTTAAAAATACCTACATAA+TGG + chr1.2:34076967-34076986 MS.gene040684:intron 20.0%
!!! GAAGAGAATAATTTGAAATT+TGG + chr1.2:34077249-34077268 MS.gene040684:CDS 20.0%
!!! TGAATTCTTATTTTTTTAGC+AGG + chr1.2:34076664-34076683 MS.gene040684:intron 20.0%
!!! TTTGAATGAATCACAATTTT+TGG + chr1.2:34076313-34076332 MS.gene040684:CDS 20.0%
!!! TTTTTGTTGACAAAGATAAA+TGG + chr1.2:34077166-34077185 MS.gene040684:CDS 20.0%
! AAGTAGTTGTGATGATATTA+AGG + chr1.2:34076687-34076706 MS.gene040684:CDS 25.0%
! CATATTAAATGAATTTCCGA+TGG - chr1.2:34077398-34077417 None:intergenic 25.0%
! CCAAATTAGTATACCATAAT+TGG + chr1.2:34076917-34076936 MS.gene040684:intron 25.0%
! CCAATTATGGTATACTAATT+TGG - chr1.2:34076920-34076939 None:intergenic 25.0%
! CGGAAATTCATTTAATATGA+TGG + chr1.2:34077399-34077418 MS.gene040684:intron 25.0%
! GAGAAAATAACAACTTGAAA+TGG - chr1.2:34077318-34077337 None:intergenic 25.0%
! GTCTTTAATGTGATTGTATT+CGG + chr1.2:34076359-34076378 MS.gene040684:CDS 25.0%
! TATATTTGATTAGTGTCCAT+CGG + chr1.2:34077379-34077398 MS.gene040684:intron 25.0%
! TGTGTCTTAACAAATTCATT+TGG - chr1.2:34077111-34077130 None:intergenic 25.0%
! TTCTTACAAACTTTCATAGA+TGG - chr1.2:34076512-34076531 None:intergenic 25.0%
!! TATGAAGTTATGTTTTGCAA+TGG + chr1.2:34076263-34076282 MS.gene040684:CDS 25.0%
!!! TCAAGTTGTTATTTTCTCTT+TGG + chr1.2:34077320-34077339 MS.gene040684:CDS 25.0%
!!! TGAATTTGTTAAGACACATA+TGG + chr1.2:34077113-34077132 MS.gene040684:CDS 25.0%
!!! TGTTATTTTCTCTTTGGAAA+AGG + chr1.2:34077326-34077345 MS.gene040684:CDS 25.0%
AATACAGCAAAGTCCAATTA+TGG - chr1.2:34076933-34076952 None:intergenic 30.0%
GAAAAAATTCGACTCTGATA+AGG + chr1.2:34076741-34076760 MS.gene040684:CDS 30.0%
! AAGTTATGTTTTGCAATGGT+TGG + chr1.2:34076267-34076286 MS.gene040684:CDS 30.0%
! CTCTATCAATGTATGACTTT+TGG - chr1.2:34076786-34076805 None:intergenic 30.0%
!! TGTGTTTTTGTGCTAAACAA+AGG + chr1.2:34077279-34077298 MS.gene040684:CDS 30.0%
!!! CGAATTTTTTCTTCACTTTC+TGG - chr1.2:34076732-34076751 None:intergenic 30.0%
!!! GGTGGAAAAGAAAGTTTTTT+GGG + chr1.2:34076226-34076245 MS.gene040684:CDS 30.0%
!!! TGGTGGAAAAGAAAGTTTTT+TGG + chr1.2:34076225-34076244 MS.gene040684:CDS 30.0%
!!! TTGGAAACTCCTTATTTTGA+AGG + chr1.2:34077351-34077370 MS.gene040684:CDS 30.0%
AAACAATCTGCACTAACTTG+TGG + chr1.2:34077210-34077229 MS.gene040684:CDS 35.0%
AATACCCGTCAATAGAAACT+AGG + chr1.2:34076402-34076421 MS.gene040684:CDS 35.0%
ATACATTGATAGAGATCGCT+TGG + chr1.2:34076792-34076811 MS.gene040684:CDS 35.0%
ATACCCGTCAATAGAAACTA+GGG + chr1.2:34076403-34076422 MS.gene040684:CDS 35.0%
CCAATCACAATCCATTATGT+AGG - chr1.2:34076981-34077000 None:intergenic 35.0%
TAAGACACATATGGACATGA+TGG + chr1.2:34077122-34077141 MS.gene040684:CDS 35.0%
TCTTCCCTAGTTTCTATTGA+CGG - chr1.2:34076410-34076429 None:intergenic 35.0%
! TTTCTCTTTGGAAAAGGACT+TGG + chr1.2:34077332-34077351 MS.gene040684:CDS 35.0%
!! CCTACATAATGGATTGTGAT+TGG + chr1.2:34076978-34076997 MS.gene040684:intron 35.0%
CTTCCCTAGTTTCTATTGAC+GGG - chr1.2:34076409-34076428 None:intergenic 40.0%
TCATGTGTTGGACTATTGCA+GGG + chr1.2:34077493-34077512 MS.gene040684:intron 40.0%
TTCATGTGTTGGACTATTGC+AGG + chr1.2:34077492-34077511 MS.gene040684:intron 40.0%
TTGAGAATCCTTCGTCATCA+CGG + chr1.2:34076462-34076481 MS.gene040684:CDS 40.0%
! AATCTGCACTAACTTGTGGT+TGG + chr1.2:34077214-34077233 MS.gene040684:CDS 40.0%
! ACACATATGGACATGATGGA+AGG + chr1.2:34077126-34077145 MS.gene040684:CDS 40.0%
AAGCGTGAGCATGTGAACAA+TGG + chr1.2:34076566-34076585 MS.gene040684:intron 45.0%
AGGGAAGAATCTGAAGAGAG+TGG + chr1.2:34076422-34076441 MS.gene040684:CDS 45.0%
GTGAGCATGTGAACAATGGT+TGG + chr1.2:34076570-34076589 MS.gene040684:intron 45.0%
TGAGAATCCTTCGTCATCAC+GGG + chr1.2:34076463-34076482 MS.gene040684:CDS 45.0%
CTTCGTCATCACGGGGTAAA+AGG + chr1.2:34076471-34076490 MS.gene040684:CDS 50.0%
GAGAATCCTTCGTCATCACG+GGG + chr1.2:34076464-34076483 MS.gene040684:CDS 50.0%
GTGTTGGACTATTGCAGGGT+TGG + chr1.2:34077497-34077516 MS.gene040684:intron 50.0%
!! CTTTTACCCCGTGATGACGA+AGG - chr1.2:34076473-34076492 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 34076224 34077524 34076224 ID=MS.gene040684
chr1.2 mRNA 34076224 34077524 34076224 ID=MS.gene040684.t1;Parent=MS.gene040684
chr1.2 exon 34076224 34076569 34076224 ID=MS.gene040684.t1.exon1;Parent=MS.gene040684.t1
chr1.2 CDS 34076224 34076569 34076224 ID=cds.MS.gene040684.t1;Parent=MS.gene040684.t1
chr1.2 exon 34076683 34076813 34076683 ID=MS.gene040684.t1.exon2;Parent=MS.gene040684.t1
chr1.2 CDS 34076683 34076813 34076683 ID=cds.MS.gene040684.t1;Parent=MS.gene040684.t1
chr1.2 exon 34077102 34077372 34077102 ID=MS.gene040684.t1.exon3;Parent=MS.gene040684.t1
chr1.2 CDS 34077102 34077372 34077102 ID=cds.MS.gene040684.t1;Parent=MS.gene040684.t1
chr1.2 exon 34077514 34077524 34077514 ID=MS.gene040684.t1.exon4;Parent=MS.gene040684.t1
chr1.2 CDS 34077514 34077524 34077514 ID=cds.MS.gene040684.t1;Parent=MS.gene040684.t1
Gene Sequence

>MS.gene040684

ATGGTGGAAAAGAAAGTTTTTTGGGAGAAAACTAGTGATTATGAAGTTATGTTTTGCAATGGTTGGAAAGAACTTGCAAATTATTTGTCTTTGAATGAATCACAATTTTTGGTGTTTCAATATCAAGAAAATTCTGTCTTTAATGTGATTGTATTCGGTAGATGCAGATTAGAAATAAAATACCCGTCAATAGAAACTAGGGAAGAATCTGAAGAGAGTGGTAGTTCTTTGAAAATTATTGAGAATCCTTCGTCATCACGGGGTAAAAGGCTAAAATCTTCAGCACCATCTATGAAAGTTTGTAAGAAGATGAAAATCAACTCAAAAGAACAAAAAAATTCTAAGCGTGAGCATGTGAACAATGGTTGGTTTTGTTCTATCATCATGTTGTGTTTCTTTTTATCTATTCTTGACTTATTTTTGCTACTAATTTTTTTTGGTGAATTCTTATTTTTTTAGCAGGAAGTAGTTGTGATGATATTAAGGAGAGAAGTAGAATTTTGTTCCAGAAAGTGAAGAAAAAATTCGACTCTGATAAGGACTTTTTTGCATGTATGATCCAAAAGTCATACATTGATAGAGATCGCTTGGTAATAAACTATTTTATTTGATCACTTTAATTAGTATTAATTCAATAATATATGTGAATATTATCAAAGCAGTGTATGTAAATATTTTGTACATATCACTCAACCAAATTAGTATACCATAATTGGACTTTGCTGTATTTTATCTTAGAACATCTTTAAAAATACCTACATAATGGATTGTGATTGGTTGCATATGAACAATGCATGCTAACTAAATCACTCATTGATATGTCTAATGTATATTTGTGTACTTTTCTTTTTATGCAAACTATATGTGTGTATTTATAGGTCATACCAAATGAATTTGTTAAGACACATATGGACATGATGGAAGGAAGAGATGATGCTACCCTTTTTGTTGACAAAGATAAATGGAATGTGAAGCTCACTTTAAATAAACAATCTGCACTAACTTGTGGTTGGAGAGAATTCCGTGAAGAGAATAATTTGAAATTTGGTGATGTTTGTGTTTTTGTGCTAAACAAAGGCAAAGAAACTGTTCCATTTCAAGTTGTTATTTTCTCTTTGGAAAAGGACTTGGAAACTCCTTATTTTGAAGGTAAATTATATTTGATTAGTGTCCATCGGAAATTCATTTAATATGATGGGAAAATTGTGATCTAACAATTTATGAAAATTTTATGGTTTGTAAAATTATTTTTTTCATCAATATAATAATTCATGTGTTGGACTATTGCAGGGTTGGCTTGA
Protein sequence

>MS.gene040684.t1

MVEKKVFWEKTSDYEVMFCNGWKELANYLSLNESQFLVFQYQENSVFNVIVFGRCRLEIKYPSIETREESEESGSSLKIIENPSSSRGKRLKSSAPSMKVCKKMKINSKEQKNSKPGSSCDDIKERSRILFQKVKKKFDSDKDFFACMIQKSYIDRDRLVIPNEFVKTHMDMMEGRDDATLFVDKDKWNVKLTLNKQSALTCGWREFREENNLKFGDVCVFVLNKGKETVPFQVVIFSLEKDLETPYFEGLA