AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene039227

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039227.t1 MTR_2g071700 87.870 338 41 0 1 338 1 338 0.0 588
MS.gene039227.t1 MTR_2g070780 69.822 338 98 2 1 338 1 334 6.62e-168 471
MS.gene039227.t1 MTR_6g034190 52.601 346 145 5 1 340 1 333 5.89e-112 335
MS.gene039227.t1 MTR_2g072240 49.387 326 152 3 14 337 6 320 1.48e-103 311
MS.gene039227.t1 MTR_2g070660 70.408 196 28 1 1 196 1 166 2.12e-94 278
MS.gene039227.t1 MTR_2g070820 68.333 60 19 0 279 338 1 60 7.03e-21 87.4
MS.gene039227.t1 MTR_2g070810 64.583 48 16 1 1 48 49 95 4.06e-11 59.3
MS.gene039227.t1 MTR_1g014450 24.219 256 145 8 16 264 14 227 5.90e-11 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene039227.t1 AT1G80960 27.508 309 180 9 12 314 44 314 2.90e-18 85.5
MS.gene039227.t1 AT1G80960 27.508 309 180 9 12 314 44 314 4.01e-18 85.5
MS.gene039227.t1 AT1G80960 27.508 309 180 9 12 314 44 314 5.17e-18 85.1
MS.gene039227.t1 AT1G80960 27.508 309 180 9 12 314 44 314 5.17e-18 85.1
MS.gene039227.t1 AT1G80960 27.508 309 180 9 12 314 44 314 5.17e-18 85.1
MS.gene039227.t1 AT1G80960 27.451 306 178 9 15 314 8 275 6.90e-18 84.7
MS.gene039227.t1 AT1G67390 27.431 288 169 8 18 301 41 292 1.63e-15 77.8
MS.gene039227.t1 AT2G42730 28.458 253 137 8 18 264 5 219 8.46e-13 69.3
MS.gene039227.t1 AT2G26860 27.636 275 129 9 18 264 2 234 7.61e-11 63.2
MS.gene039227.t1 AT2G26860 27.636 275 129 9 18 264 2 234 7.61e-11 63.2

Find 53 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATGAATGTGCTCAGGATTT+TGG 0.185156 2.3:-24743417 MS.gene039227:CDS
TTTAAAATCTGCTGGGAATC+AGG 0.256489 2.3:+24743599 None:intergenic
CAACTCAAGAACCTTAAAAT+TGG 0.260477 2.3:+24743652 None:intergenic
TTAAGGAAAATACTGGAAAA+AGG 0.272692 2.3:-24743788 MS.gene039227:CDS
CCAAGCGATGGGAGTCATTA+TGG 0.279125 2.3:-24744322 MS.gene039227:CDS
GCACGAAGAACTTGAAGTTT+TGG 0.293746 2.3:+24743320 None:intergenic
AAGACTTCAACATTTGTCTT+TGG 0.296399 2.3:+24744273 None:intergenic
CGAAAATTTAGAACATTAGA+TGG 0.304117 2.3:+24743126 None:intergenic
GACTTGGATGCAATGCTTGC+TGG 0.308592 2.3:-24743707 MS.gene039227:CDS
ATCTTCATGACTACAAATAA+TGG 0.327696 2.3:+24743358 None:intergenic
TATTTGTAGTCATGAAGATT+TGG 0.359911 2.3:-24743354 MS.gene039227:CDS
TCAAAATATTCCTCGTTTGT+AGG 0.376000 2.3:+24743932 None:intergenic
CGGATATTGTGGGATGGTTA+AGG 0.379412 2.3:-24743805 MS.gene039227:CDS
TTTGTCTTTGGTCAAAACTA+AGG 0.395796 2.3:+24744285 None:intergenic
CATTTATTTACTTCCATACA+TGG 0.408214 2.3:-24744369 MS.gene039227:CDS
GAATCCTGTGATTATCTTAA+CGG 0.412542 2.3:-24743740 MS.gene039227:CDS
TCATGAAGATTTGGTCTTTG+AGG 0.413287 2.3:-24743345 MS.gene039227:CDS
TCAAATATTGACAATCATAT+TGG 0.420752 2.3:-24743878 MS.gene039227:CDS
GTTCTCACAACTTCCATGTA+TGG 0.439142 2.3:+24744356 None:intergenic
TCGAATGGTACAACTCTTCA+AGG 0.460907 2.3:+24743853 None:intergenic
GGGATGGTTAAGGAAAATAC+TGG 0.478734 2.3:-24743795 MS.gene039227:CDS
TTAAAATCTGCTGGGAATCA+GGG 0.490298 2.3:+24743600 None:intergenic
GATAGAACCTAAAAGTTCAT+CGG 0.492455 2.3:+24744391 None:intergenic
ATAGAACCTAAAAGTTCATC+GGG 0.493156 2.3:+24744392 None:intergenic
CTTTGGTCAAAACTAAGGTC+AGG 0.496709 2.3:+24744290 None:intergenic
TTTGTAATATGAATGTGCTC+AGG 0.508079 2.3:-24743424 MS.gene039227:CDS
AATCACAATTCTCGACGGTA+AGG 0.523805 2.3:+24743498 None:intergenic
CAAGTGTGCTTTCCAAGCGA+TGG 0.528071 2.3:-24744334 MS.gene039227:CDS
AACCTCAAAAGGTAAATCAA+TGG 0.528655 2.3:+24743679 None:intergenic
CCATAATGACTCCCATCGCT+TGG 0.530097 2.3:+24744322 None:intergenic
AAATTGGAGAAAACCTCAAA+AGG 0.535849 2.3:+24743668 None:intergenic
TTGTGCAAGTGCGGATATTG+TGG 0.536933 2.3:-24743816 MS.gene039227:CDS
TCCTCCGTTAAGATAATCAC+AGG 0.561644 2.3:+24743736 None:intergenic
TGTGCAAGTGCGGATATTGT+GGG 0.576522 2.3:-24743815 MS.gene039227:CDS
AAGTGTGCTTTCCAAGCGAT+GGG 0.578750 2.3:-24744333 MS.gene039227:CDS
GCCTCAGAGTTGTGCAAGTG+CGG 0.587060 2.3:-24743825 MS.gene039227:CDS
TAACGGAGGAGTATTAGACT+TGG 0.595966 2.3:-24743723 MS.gene039227:CDS
AATCTGCTGGGAATCAGGGG+AGG 0.596089 2.3:+24743604 None:intergenic
TAAAATCTGCTGGGAATCAG+GGG 0.602098 2.3:+24743601 None:intergenic
ATCTGCTGGGAATCAGGGGA+GGG 0.602271 2.3:+24743605 None:intergenic
AATATTTGATGTAATCATCA+TGG 0.606995 2.3:+24743892 None:intergenic
ATTGTAAGACGGTCATCAAG+TGG 0.611036 2.3:+24744224 None:intergenic
TACAATGGCTATGCAACGCA+AGG 0.612851 2.3:-24744207 MS.gene039227:intron
GTTGCATAGCCATTGTAAGA+CGG 0.627198 2.3:+24744213 None:intergenic
TAACACGAAGGAATGAGTGA+AGG 0.630821 2.3:-24744473 None:intergenic
CGAATGGTACAACTCTTCAA+GGG 0.641099 2.3:+24743854 None:intergenic
ACTCTGAGGCAAGTGTCGAA+TGG 0.644749 2.3:+24743838 None:intergenic
ACTTGATGACCGTCTTACAA+TGG 0.648825 2.3:-24744222 MS.gene039227:CDS
TAAGAAATCACAATTCTCGA+CGG 0.656792 2.3:+24743493 None:intergenic
TCCTGTGATTATCTTAACGG+AGG 0.660021 2.3:-24743737 MS.gene039227:CDS
TCCGCACTTGCACAACTCTG+AGG 0.670878 2.3:+24743824 None:intergenic
CAAGTGCGGATATTGTGGGA+TGG 0.701358 2.3:-24743811 MS.gene039227:CDS
ACAGGTAGCTCCTACAAACG+AGG 0.745117 2.3:-24743942 MS.gene039227:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAATAATTAGATTATTCAAA+TGG - chr2.3:24743494-24743513 MS.gene039227:CDS 15.0%
!!! ATTTTAATATATTTCAGACT+TGG + chr2.3:24744159-24744178 None:intergenic 15.0%
!! AATATTTGATGTAATCATCA+TGG + chr2.3:24743713-24743732 None:intergenic 20.0%
!! TCAAATATTGACAATCATAT+TGG - chr2.3:24743724-24743743 MS.gene039227:CDS 20.0%
!!! AGAGATGTTATAGAAATTTT+CGG - chr2.3:24744369-24744388 MS.gene039227:CDS 20.0%
! ATCTTCATGACTACAAATAA+TGG + chr2.3:24744247-24744266 None:intergenic 25.0%
! CATTCATTTCATTCAGAAAA+TGG + chr2.3:24743584-24743603 None:intergenic 25.0%
! CATTTATTTACTTCCATACA+TGG - chr2.3:24743233-24743252 MS.gene039227:CDS 25.0%
! TAAGGAAAATACTGGAAAAA+GGG - chr2.3:24743815-24743834 MS.gene039227:CDS 25.0%
! TATTTGTAGTCATGAAGATT+TGG - chr2.3:24744248-24744267 MS.gene039227:CDS 25.0%
! TTAAGGAAAATACTGGAAAA+AGG - chr2.3:24743814-24743833 MS.gene039227:CDS 25.0%
!! TACAACGATTTTCAAATTCT+TGG - chr2.3:24744306-24744325 MS.gene039227:CDS 25.0%
!!! AAGTGTTTTTAAAATCTGCT+GGG + chr2.3:24744013-24744032 None:intergenic 25.0%
!!! GGAGAAATTTTATTTCTTGA+TGG - chr2.3:24744327-24744346 MS.gene039227:CDS 25.0%
!!! TAAGTGTTTTTAAAATCTGC+TGG + chr2.3:24744014-24744033 None:intergenic 25.0%
AAATTGGAGAAAACCTCAAA+AGG + chr2.3:24743937-24743956 None:intergenic 30.0%
AACCTCAAAAGGTAAATCAA+TGG + chr2.3:24743926-24743945 None:intergenic 30.0%
AAGACTTCAACATTTGTCTT+TGG + chr2.3:24743332-24743351 None:intergenic 30.0%
AAGGAAAATACTGGAAAAAG+GGG - chr2.3:24743816-24743835 MS.gene039227:CDS 30.0%
AGAACAGAAAAAAGTGAAAG+TGG - chr2.3:24743152-24743171 MS.gene039227:intron 30.0%
ATAGAACCTAAAAGTTCATC+GGG + chr2.3:24743213-24743232 None:intergenic 30.0%
CAACTCAAGAACCTTAAAAT+TGG + chr2.3:24743953-24743972 None:intergenic 30.0%
GAATCCTGTGATTATCTTAA+CGG - chr2.3:24743862-24743881 MS.gene039227:CDS 30.0%
GATAGAACCTAAAAGTTCAT+CGG + chr2.3:24743214-24743233 None:intergenic 30.0%
TAAGAAATCACAATTCTCGA+CGG + chr2.3:24744112-24744131 None:intergenic 30.0%
TCAAAATATTCCTCGTTTGT+AGG + chr2.3:24743673-24743692 None:intergenic 30.0%
TTTGTAATATGAATGTGCTC+AGG - chr2.3:24744178-24744197 MS.gene039227:intron 30.0%
TTTGTCTTTGGTCAAAACTA+AGG + chr2.3:24743320-24743339 None:intergenic 30.0%
! GATGTTATAGAAATTTTCGG+TGG - chr2.3:24744372-24744391 MS.gene039227:CDS 30.0%
! TGAGGTTTTCTCCAATTTTA+AGG - chr2.3:24743939-24743958 MS.gene039227:CDS 30.0%
GAAAAAAGTGAAAGTGGTAG+AGG - chr2.3:24743158-24743177 MS.gene039227:intron 35.0%
TTAAAATCTGCTGGGAATCA+GGG + chr2.3:24744005-24744024 None:intergenic 35.0%
! ACGAAGAACTTGAAGTTTTG+GGG + chr2.3:24744283-24744302 None:intergenic 35.0%
! AGAAATTTTCGGTGGTATTC+TGG - chr2.3:24744380-24744399 MS.gene039227:CDS 35.0%
! ATTTTCATGAAGAGTCAACC+AGG - chr2.3:24743522-24743541 MS.gene039227:CDS 35.0%
! CACGAAGAACTTGAAGTTTT+GGG + chr2.3:24744284-24744303 None:intergenic 35.0%
! GCAACGCAAGGTAATTTTTA+TGG - chr2.3:24743407-24743426 MS.gene039227:CDS 35.0%
! TATGAATGTGCTCAGGATTT+TGG - chr2.3:24744185-24744204 MS.gene039227:intron 35.0%
! TCATGAAGATTTGGTCTTTG+AGG - chr2.3:24744257-24744276 MS.gene039227:CDS 35.0%
! TTTAAAATCTGCTGGGAATC+AGG + chr2.3:24744006-24744025 None:intergenic 35.0%
!! GTTTTCAAGAGATGAACAGT+AGG + chr2.3:24744085-24744104 None:intergenic 35.0%
!!! GACCATTGATTTACCTTTTG+AGG - chr2.3:24743921-24743940 MS.gene039227:CDS 35.0%
AATCACAATTCTCGACGGTA+AGG + chr2.3:24744107-24744126 None:intergenic 40.0%
ACTGGAAAAAGGGGTGATTA+AGG - chr2.3:24743825-24743844 MS.gene039227:CDS 40.0%
ATTGTAAGACGGTCATCAAG+TGG + chr2.3:24743381-24743400 None:intergenic 40.0%
CGAATGGTACAACTCTTCAA+GGG + chr2.3:24743751-24743770 None:intergenic 40.0%
CTTTGGTCAAAACTAAGGTC+AGG + chr2.3:24743315-24743334 None:intergenic 40.0%
GGGATGGTTAAGGAAAATAC+TGG - chr2.3:24743807-24743826 MS.gene039227:CDS 40.0%
GTTCTCACAACTTCCATGTA+TGG + chr2.3:24743249-24743268 None:intergenic 40.0%
GTTGCATAGCCATTGTAAGA+CGG + chr2.3:24743392-24743411 None:intergenic 40.0%
TAAAATCTGCTGGGAATCAG+GGG + chr2.3:24744004-24744023 None:intergenic 40.0%
TCCTCCGTTAAGATAATCAC+AGG + chr2.3:24743869-24743888 None:intergenic 40.0%
TCCTGTGATTATCTTAACGG+AGG - chr2.3:24743865-24743884 MS.gene039227:CDS 40.0%
TCGAATGGTACAACTCTTCA+AGG + chr2.3:24743752-24743771 None:intergenic 40.0%
TGACAGAATTCATGCATGAC+AGG - chr2.3:24743642-24743661 MS.gene039227:CDS 40.0%
! ACTTGATGACCGTCTTACAA+TGG - chr2.3:24743380-24743399 MS.gene039227:CDS 40.0%
! AGTCTTCCCGATGAACTTTT+AGG - chr2.3:24743204-24743223 MS.gene039227:intron 40.0%
! GCACGAAGAACTTGAAGTTT+TGG + chr2.3:24744285-24744304 None:intergenic 40.0%
!! TAACGGAGGAGTATTAGACT+TGG - chr2.3:24743879-24743898 MS.gene039227:CDS 40.0%
AAGTGTGCTTTCCAAGCGAT+GGG - chr2.3:24743269-24743288 MS.gene039227:CDS 45.0%
AGATTCTCTACAACCCTTCC+TGG + chr2.3:24743543-24743562 None:intergenic 45.0%
CATGAAGAGTCAACCAGGAA+GGG - chr2.3:24743527-24743546 MS.gene039227:CDS 45.0%
CGGATATTGTGGGATGGTTA+AGG - chr2.3:24743797-24743816 MS.gene039227:CDS 45.0%
TACAATGGCTATGCAACGCA+AGG - chr2.3:24743395-24743414 MS.gene039227:CDS 45.0%
TCATGAAGAGTCAACCAGGA+AGG - chr2.3:24743526-24743545 MS.gene039227:CDS 45.0%
TGTGCAAGTGCGGATATTGT+GGG - chr2.3:24743787-24743806 MS.gene039227:CDS 45.0%
TTGTGCAAGTGCGGATATTG+TGG - chr2.3:24743786-24743805 MS.gene039227:CDS 45.0%
ACAGGTAGCTCCTACAAACG+AGG - chr2.3:24743660-24743679 MS.gene039227:CDS 50.0%
CAAGTGCGGATATTGTGGGA+TGG - chr2.3:24743791-24743810 MS.gene039227:CDS 50.0%
CAAGTGTGCTTTCCAAGCGA+TGG - chr2.3:24743268-24743287 MS.gene039227:CDS 50.0%
CCAAGCGATGGGAGTCATTA+TGG - chr2.3:24743280-24743299 MS.gene039227:CDS 50.0%
CCATAATGACTCCCATCGCT+TGG + chr2.3:24743283-24743302 None:intergenic 50.0%
GACTTGGATGCAATGCTTGC+TGG - chr2.3:24743895-24743914 MS.gene039227:CDS 50.0%
!! ACTCTGAGGCAAGTGTCGAA+TGG + chr2.3:24743767-24743786 None:intergenic 50.0%
AATCTGCTGGGAATCAGGGG+AGG + chr2.3:24744001-24744020 None:intergenic 55.0%
ATCTGCTGGGAATCAGGGGA+GGG + chr2.3:24744000-24744019 None:intergenic 55.0%
GCCTCAGAGTTGTGCAAGTG+CGG - chr2.3:24743777-24743796 MS.gene039227:CDS 55.0%
TCCGCACTTGCACAACTCTG+AGG + chr2.3:24743781-24743800 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 24743141 24744483 24743141 ID=MS.gene039227
chr2.3 mRNA 24743141 24744483 24743141 ID=MS.gene039227.t1;Parent=MS.gene039227
chr2.3 exon 24744208 24744483 24744208 ID=MS.gene039227.t1.exon1;Parent=MS.gene039227.t1
chr2.3 CDS 24744208 24744483 24744208 ID=cds.MS.gene039227.t1;Parent=MS.gene039227.t1
chr2.3 exon 24743223 24743960 24743223 ID=MS.gene039227.t1.exon2;Parent=MS.gene039227.t1
chr2.3 CDS 24743223 24743960 24743223 ID=cds.MS.gene039227.t1;Parent=MS.gene039227.t1
chr2.3 exon 24743141 24743155 24743141 ID=MS.gene039227.t1.exon3;Parent=MS.gene039227.t1
chr2.3 CDS 24743141 24743155 24743141 ID=cds.MS.gene039227.t1;Parent=MS.gene039227.t1
Gene Sequence

>MS.gene039227

ATGAGTGAAGGAGAACAGAAAAAAGTGAAAGTGGTAGAGGAGCAAGAAGCAGATTTGATCAACAGTCTTCCCGATGAACTTTTAGGTTCTATCATTTATTTACTTCCATACATGGAAGTTGTGAGAACAAGTGTGCTTTCCAAGCGATGGGAGTCATTATGGAAGAACAGTCCTGACCTTAGTTTTGACCAAAGACAAATGTTGAAGTCTTTGATTGAAGAGTACATTCAAAATTCTCCACTTGATGACCGTCTTACAATGGCTATGCAACGCAAGGTAATTTTTATGGAAATCATGTAAAATAAGTTATGTGTTTTTTTACTATAAGATTTGTGTTTTAATTTATGCTTTATGAATAATTAGATTATTCAAATGGTTCACATTTTCATGAAGAGTCAACCAGGAAGGGTTGTAGAGAATCTAATTACATATTTTAGCTTCCATTTTCTGAATGAAATGAATGAACTTTAATTCTAAACGCGTTTGAGATATGATATATATTGACAGAATTCATGCATGACAGGTAGCTCCTACAAACGAGGAATATTTTGATGTAATTTCTGAAGCAGCCATGATGATTACATCAAATATTGACAATCATATTGGTCCCTTGAAGAGTTGTACCATTCGACACTTGCCTCAGAGTTGTGCAAGTGCGGATATTGTGGGATGGTTAAGGAAAATACTGGAAAAAGGGGTGATTAAGGTTTCAATAGAACGTGAATCCTGTGATTATCTTAACGGAGGAGTATTAGACTTGGATGCAATGCTTGCTGGATCGACCATTGATTTACCTTTTGAGGTTTTCTCCAATTTTAAGGTTCTTGAGTTGAAGAACTATCGTTTTAACACTACACCCTCCCCTGATTCCCAGCAGATTTTAAAAACACTTACTCTTAAGAAAGTGTGTATTATATCAAACACTTTTCACGATATTCTCTCCTACTGTTCATCTCTTGAAAACCTTACCGTCGAGAATTGTGATTTCTTAACAGACGAGCTTAAGATTGTAAGTCCAAGTCTGAAATATATTAAAATTTGTAATATGAATGTGCTCAGGATTTTGGTTTCTGCATTTAATGTTGAAGTCATAGAGATTGACTCCATTATTTGTAGTCATGAAGATTTGGTCTTTGAGGCCCCAAAACTTCAAGTTCTTCGTGCTTACAACGATTTTCAAATTCTTGGAGAAATTTTATTTCTTGATGGAAGAAAGCTTTTGACAGCAAGAGATGTTATAGAAATTTTCGGTGGTATTCTGGTATGTCTTTCTTCACTTCAAGTTTCTGTTTTTTATTCAAGCATATAATACATTTCTTTTTAATTAGTACAGAACCATCTAA
Protein sequence

>MS.gene039227.t1

MSEGEQKKVKVVEEQEADLINSLPDELLGSIIYLLPYMEVVRTSVLSKRWESLWKNSPDLSFDQRQMLKSLIEEYIQNSPLDDRLTMAMQRKVAPTNEEYFDVISEAAMMITSNIDNHIGPLKSCTIRHLPQSCASADIVGWLRKILEKGVIKVSIERESCDYLNGGVLDLDAMLAGSTIDLPFEVFSNFKVLELKNYRFNTTPSPDSQQILKTLTLKKVCIISNTFHDILSYCSSLENLTVENCDFLTDELKIVSPSLKYIKICNMNVLRILVSAFNVEVIEIDSIICSHEDLVFEAPKLQVLRAYNDFQILGEILFLDGRKLLTARDVIEIFGGILYRTI