AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09753


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09753.t1 MTR_5g012930 100.000 199 0 0 1 199 1 199 2.60e-145 403
MS.gene09753.t1 MTR_2g086500 98.995 199 2 0 1 199 1 199 7.23e-144 399
MS.gene09753.t1 MTR_3g070930 97.487 199 5 0 1 199 1 199 6.08e-142 394
MS.gene09753.t1 MTR_3g070930 96.154 130 5 0 1 130 1 130 1.62e-88 257
MS.gene09753.t1 MTR_1g098350 72.527 91 4 1 39 129 47 116 1.34e-20 84.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09753.t1 AT1G08360 91.457 199 17 0 1 199 1 199 1.61e-119 338
MS.gene09753.t1 AT2G27530 90.955 199 18 0 1 199 1 199 8.45e-119 336
MS.gene09753.t1 AT2G27530 90.955 199 18 0 1 199 1 199 8.45e-119 336
MS.gene09753.t1 AT5G22440 90.500 200 18 1 1 199 1 200 2.76e-116 330
MS.gene09753.t1 AT5G22440 90.500 200 18 1 1 199 1 200 2.76e-116 330

Find 41 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAACACTCAGTTGTACATTT+TGG 0.198216 5.4:-6798642 None:intergenic
CAAACAGATTCCTCGTCTTT+TGG 0.210825 5.4:+6798213 MS.gene09753:CDS
TAAGAAACTGGTGAAGAAAT+TGG 0.278623 5.4:+6798150 MS.gene09753:CDS
CCTTAGCCTCAAGAGATTCT+TGG 0.279927 5.4:-6798522 None:intergenic
AACAGCTTCAGAGGCTAAAA+AGG 0.290643 5.4:-6798188 None:intergenic
CAATAGTCTCCACAAATTTA+CGG 0.320435 5.4:-6797221 None:intergenic
CTTGGAATCACCCATGATTC+CGG 0.395102 5.4:-6797190 None:intergenic
AGCTGTTGGCAATGTTAGTA+TGG 0.409393 5.4:+6798603 MS.gene09753:CDS
AGAAGCTATTACCGGAATCA+TGG 0.439289 5.4:+6797179 MS.gene09753:CDS
AAGATGAAAATTTGCATGCT+TGG 0.446340 5.4:+6797330 MS.gene09753:CDS
ATATTGTAGGCTGAGAAAAT+AGG 0.447267 5.4:+6798082 MS.gene09753:intron
TGCACAACACTTTCTTGAGC+TGG 0.451787 5.4:-6798573 None:intergenic
TATTACCTCCTCAACATGTT+GGG 0.453017 5.4:-6797358 None:intergenic
GGATAAACGTTTCAGCGGTT+CGG 0.456511 5.4:+6797281 MS.gene09753:CDS
GAGACTATTGAACTCCAGAT+TGG 0.461376 5.4:+6797234 MS.gene09753:CDS
CCAAGAATCTCTTGAGGCTA+AGG 0.480487 5.4:+6798522 MS.gene09753:CDS
GCTGTGAGAGAAGCTATTAC+CGG 0.513912 5.4:+6797171 MS.gene09753:CDS
CTGTTTGATAACAGCTTCAG+AGG 0.515911 5.4:-6798197 None:intergenic
CGGAATCATGGGTGATTCCA+AGG 0.521957 5.4:+6797191 MS.gene09753:CDS
GAAAATAGGATTGGAATCGA+TGG 0.526298 5.4:+6798096 MS.gene09753:CDS
TTATTACCTCCTCAACATGT+TGG 0.532530 5.4:-6797359 None:intergenic
ATCTTTGGTCTCGGAATGTG+AGG 0.537988 5.4:-6797312 None:intergenic
GGCTAAGGTTAACGAGACTA+AGG 0.542276 5.4:+6798537 MS.gene09753:CDS
GTAGGCTGAGAAAATAGGAT+TGG 0.543381 5.4:+6798087 MS.gene09753:intron
GAAGCTATTACCGGAATCAT+GGG 0.561503 5.4:+6797180 MS.gene09753:CDS
GGTCCTGGTCTCAACAAGGC+AGG 0.563119 5.4:+6798235 MS.gene09753:CDS
TAGCCTCAAGAGATTCTTGG+TGG 0.564785 5.4:-6798519 None:intergenic
CTCAAGAAAGTGTTGTGCAT+GGG 0.565229 5.4:+6798577 MS.gene09753:CDS
GGTTAACGAGACTAAGGCTA+TGG 0.565310 5.4:+6798543 MS.gene09753:CDS
TTTGGGTCCTGGTCTCAACA+AGG 0.572628 5.4:+6798231 MS.gene09753:CDS
GCTCAAGAAAGTGTTGTGCA+TGG 0.598477 5.4:+6798576 MS.gene09753:CDS
TCTTGGTGGGAAACAAGTGT+AGG 0.599437 5.4:-6798505 None:intergenic
CTTGGTGGGAAACAAGTGTA+GGG 0.600430 5.4:-6798504 None:intergenic
TGGTGATGCCCAACATGTTG+AGG 0.623552 5.4:+6797350 MS.gene09753:CDS
ATGCCTGCCTTGTTGAGACC+AGG 0.624246 5.4:-6798238 None:intergenic
AGCCTCAAGAGATTCTTGGT+GGG 0.641849 5.4:-6798518 None:intergenic
CAAAAGGATAAACGTTTCAG+CGG 0.645836 5.4:+6797276 MS.gene09753:CDS
TTCCCACCAAGAATCTCTTG+AGG 0.654036 5.4:+6798516 MS.gene09753:CDS
TTGTGCATGGGAGTAGCTGT+TGG 0.683745 5.4:+6798589 MS.gene09753:CDS
AGACCAGGACCCAAAAGACG+AGG 0.696429 5.4:-6798223 None:intergenic
TGATGCCCAACATGTTGAGG+AGG 0.714764 5.4:+6797353 MS.gene09753:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATATAGCACAAAAATAAA+TGG - chr5.4:6797608-6797627 None:intergenic 15.0%
!!! CATTTTTATCAAATCATTAT+CGG - chr5.4:6797446-6797465 None:intergenic 15.0%
!!! TTTATTTTTGTGCTATATTT+TGG + chr5.4:6797608-6797627 MS.gene09753:intron 15.0%
!! GATTAAAGAAGCTTAAAAAA+AGG - chr5.4:6797013-6797032 None:intergenic 20.0%
!! TACTAACATAAAACATAAAC+AGG - chr5.4:6798324-6798343 None:intergenic 20.0%
!!! TAACTGAGATTTGATTTATA+TGG + chr5.4:6797080-6797099 MS.gene09753:intron 20.0%
!!! TTTAAATTACCAACTGTTTT+TGG + chr5.4:6798366-6798385 MS.gene09753:intron 20.0%
! AAACATAAACAGGATATATG+TGG - chr5.4:6798314-6798333 None:intergenic 25.0%
! ATTAGTATGTTGTTGAATTG+TGG - chr5.4:6797950-6797969 None:intergenic 25.0%
! GCTAAACAAAAATAAGAAAC+TGG + chr5.4:6798138-6798157 MS.gene09753:CDS 25.0%
! TGCTAAATAAAATGAAGCAA+CGG - chr5.4:6798404-6798423 None:intergenic 25.0%
!! ATAAATTTTGTGACACTGTT+TGG - chr5.4:6797880-6797899 None:intergenic 25.0%
!!! TGTCTTTCATTTAGTTTTGA+TGG + chr5.4:6797969-6797988 MS.gene09753:intron 25.0%
AAGATGAAAATTTGCATGCT+TGG + chr5.4:6797330-6797349 MS.gene09753:CDS 30.0%
AATGCCTTCTATCAAAATGT+CGG + chr5.4:6797523-6797542 MS.gene09753:intron 30.0%
ATATTGTAGGCTGAGAAAAT+AGG + chr5.4:6798082-6798101 MS.gene09753:intron 30.0%
CAATAGTCTCCACAAATTTA+CGG - chr5.4:6797224-6797243 None:intergenic 30.0%
CACTCTAATATGCATATTGT+AGG + chr5.4:6798069-6798088 MS.gene09753:intron 30.0%
GAAAAACTATGATCCTCAAA+AGG + chr5.4:6797260-6797279 MS.gene09753:CDS 30.0%
TAAGAAACTGGTGAAGAAAT+TGG + chr5.4:6798150-6798169 MS.gene09753:CDS 30.0%
TGTTGAATTGTGGTTACTAA+GGG - chr5.4:6797940-6797959 None:intergenic 30.0%
TTGTTGAATTGTGGTTACTA+AGG - chr5.4:6797941-6797960 None:intergenic 30.0%
! AAATTTACGGTTTTTCTCCT+TGG - chr5.4:6797211-6797230 None:intergenic 30.0%
! AGCATGCAAATTTTCATCTT+TGG - chr5.4:6797330-6797349 None:intergenic 30.0%
! CAAATTTTCATCTTTGGTCT+CGG - chr5.4:6797324-6797343 None:intergenic 30.0%
! TAACACTCAGTTGTACATTT+TGG - chr5.4:6798645-6798664 None:intergenic 30.0%
!! CATAGTTTTTCAAACCAATC+TGG - chr5.4:6797251-6797270 None:intergenic 30.0%
!! CTTCATTTTATTTAGCAACC+AGG + chr5.4:6798407-6798426 MS.gene09753:intron 30.0%
AGACAAGTAGAATAAGAGAG+AGG - chr5.4:6796980-6796999 None:intergenic 35.0%
AGCTCAAGCAACAATTGAAA+TGG - chr5.4:6798449-6798468 None:intergenic 35.0%
CAAAAAAATATCCCATGCTC+CGG - chr5.4:6798009-6798028 None:intergenic 35.0%
CAAAAGGATAAACGTTTCAG+CGG + chr5.4:6797276-6797295 MS.gene09753:CDS 35.0%
CAATTCAGCAATAACTACCT+CGG - chr5.4:6797554-6797573 None:intergenic 35.0%
GAAAATAGGATTGGAATCGA+TGG + chr5.4:6798096-6798115 MS.gene09753:CDS 35.0%
GACAAGTAGAATAAGAGAGA+GGG - chr5.4:6796979-6796998 None:intergenic 35.0%
GAGTATGAACCAAAAACAGT+TGG - chr5.4:6798378-6798397 None:intergenic 35.0%
GGAGAAAAACCGTAAATTTG+TGG + chr5.4:6797212-6797231 MS.gene09753:CDS 35.0%
GGCAAACTTTCAAATAAACC+TGG - chr5.4:6798428-6798447 None:intergenic 35.0%
TATTACCTCCTCAACATGTT+GGG - chr5.4:6797361-6797380 None:intergenic 35.0%
TGTCCTTGTTGAAAAAGAAC+TGG + chr5.4:6798674-6798693 MS.gene09753:CDS 35.0%
TTATTACCTCCTCAACATGT+TGG - chr5.4:6797362-6797381 None:intergenic 35.0%
! AAACAGATTCCTCGTCTTTT+GGG + chr5.4:6798214-6798233 MS.gene09753:CDS 35.0%
! AATTGTTGCTTGAGCTGATT+TGG + chr5.4:6798453-6798472 MS.gene09753:intron 35.0%
! CTGAAACGTTTATCCTTTTG+AGG - chr5.4:6797276-6797295 None:intergenic 35.0%
! GATATTTTGCATGGCTTTTC+AGG + chr5.4:6798475-6798494 MS.gene09753:intron 35.0%
!! GCTGTTTTCATAAGCTATCT+TGG + chr5.4:6797786-6797805 MS.gene09753:intron 35.0%
!!! GATGGTATTGATTTTGCATC+CGG + chr5.4:6797987-6798006 MS.gene09753:intron 35.0%
!!! GCTGATTTGGATATTTTGCA+TGG + chr5.4:6798466-6798485 MS.gene09753:intron 35.0%
!!! TTGCCAGTTCTTTTTCAACA+AGG - chr5.4:6798680-6798699 None:intergenic 35.0%
AACAGCTTCAGAGGCTAAAA+AGG - chr5.4:6798191-6798210 None:intergenic 40.0%
ACAAACACGAAACACTGACA+CGG + chr5.4:6797415-6797434 MS.gene09753:intron 40.0%
AGAAGCTATTACCGGAATCA+TGG + chr5.4:6797179-6797198 MS.gene09753:CDS 40.0%
AGCTGTTGGCAATGTTAGTA+TGG + chr5.4:6798603-6798622 MS.gene09753:CDS 40.0%
CACTCTATCAAACACGTGTT+CGG - chr5.4:6797500-6797519 None:intergenic 40.0%
GAAGCTATTACCGGAATCAT+GGG + chr5.4:6797180-6797199 MS.gene09753:CDS 40.0%
GAGACTATTGAACTCCAGAT+TGG + chr5.4:6797234-6797253 MS.gene09753:CDS 40.0%
GATACTGTTGTATGCGACTT+AGG + chr5.4:6797681-6797700 MS.gene09753:intron 40.0%
GCTTATCTGAGCTTATCTAC+TGG - chr5.4:6797904-6797923 None:intergenic 40.0%
GTAGGCTGAGAAAATAGGAT+TGG + chr5.4:6798087-6798106 MS.gene09753:intron 40.0%
GTTGCACTCAAACTGTTTGT+TGG + chr5.4:6797388-6797407 MS.gene09753:intron 40.0%
TGTGTCATCTGACTCATATC+AGG - chr5.4:6797659-6797678 None:intergenic 40.0%
! CAAACAGATTCCTCGTCTTT+TGG + chr5.4:6798213-6798232 MS.gene09753:CDS 40.0%
! CTGTTTGATAACAGCTTCAG+AGG - chr5.4:6798200-6798219 None:intergenic 40.0%
! GCAGGCATGTGTTTTCTTTT+GGG + chr5.4:6798253-6798272 MS.gene09753:intron 40.0%
! GTGTTTTCTTTTGGGCGTTT+TGG + chr5.4:6798261-6798280 MS.gene09753:intron 40.0%
!! CTCAAGAAAGTGTTGTGCAT+GGG + chr5.4:6798577-6798596 MS.gene09753:CDS 40.0%
!!! AGCACCGACATTTTGATAGA+AGG - chr5.4:6797530-6797549 None:intergenic 40.0%
!!! TCTTTTTCAACAAGGACACG+AGG - chr5.4:6798672-6798691 None:intergenic 40.0%
AGCCTCAAGAGATTCTTGGT+GGG - chr5.4:6798521-6798540 None:intergenic 45.0%
ATCTTTGGTCTCGGAATGTG+AGG - chr5.4:6797315-6797334 None:intergenic 45.0%
CCAAGAATCTCTTGAGGCTA+AGG + chr5.4:6798522-6798541 MS.gene09753:CDS 45.0%
CCTTAGCCTCAAGAGATTCT+TGG - chr5.4:6798525-6798544 None:intergenic 45.0%
CGAACACGTGTTTGATAGAG+TGG + chr5.4:6797498-6797517 MS.gene09753:intron 45.0%
CTTCAGAGGCTAAAAAGGCA+TGG - chr5.4:6798186-6798205 None:intergenic 45.0%
CTTGGAATCACCCATGATTC+CGG - chr5.4:6797193-6797212 None:intergenic 45.0%
CTTGGTGGGAAACAAGTGTA+GGG - chr5.4:6798507-6798526 None:intergenic 45.0%
GCTGTGAGAGAAGCTATTAC+CGG + chr5.4:6797171-6797190 MS.gene09753:CDS 45.0%
GGATAAACGTTTCAGCGGTT+CGG + chr5.4:6797281-6797300 MS.gene09753:CDS 45.0%
GGCTAAGGTTAACGAGACTA+AGG + chr5.4:6798537-6798556 MS.gene09753:CDS 45.0%
GGTTAACGAGACTAAGGCTA+TGG + chr5.4:6798543-6798562 MS.gene09753:CDS 45.0%
TAGCCTCAAGAGATTCTTGG+TGG - chr5.4:6798522-6798541 None:intergenic 45.0%
TCTTGGTGGGAAACAAGTGT+AGG - chr5.4:6798508-6798527 None:intergenic 45.0%
TGCACAACACTTTCTTGAGC+TGG - chr5.4:6798576-6798595 None:intergenic 45.0%
TTCCCACCAAGAATCTCTTG+AGG + chr5.4:6798516-6798535 MS.gene09753:CDS 45.0%
! GGCAGGCATGTGTTTTCTTT+TGG + chr5.4:6798252-6798271 MS.gene09753:intron 45.0%
! TGATTTTGCATCCGGAGCAT+GGG + chr5.4:6797995-6798014 MS.gene09753:intron 45.0%
! TTGATTTTGCATCCGGAGCA+TGG + chr5.4:6797994-6798013 MS.gene09753:intron 45.0%
!! GCTCAAGAAAGTGTTGTGCA+TGG + chr5.4:6798576-6798595 MS.gene09753:CDS 45.0%
CGGAATCATGGGTGATTCCA+AGG + chr5.4:6797191-6797210 MS.gene09753:CDS 50.0%
TGATGCCCAACATGTTGAGG+AGG + chr5.4:6797353-6797372 MS.gene09753:CDS 50.0%
TTGTGCATGGGAGTAGCTGT+TGG + chr5.4:6798589-6798608 MS.gene09753:CDS 50.0%
TTTGGGTCCTGGTCTCAACA+AGG + chr5.4:6798231-6798250 MS.gene09753:CDS 50.0%
! TGGTGATGCCCAACATGTTG+AGG + chr5.4:6797350-6797369 MS.gene09753:CDS 50.0%
!! ATTCCTCGTCTTTTGGGTCC+TGG + chr5.4:6798220-6798239 MS.gene09753:CDS 50.0%
!! TCAAAATGTCGGTGCTACCG+AGG + chr5.4:6797534-6797553 MS.gene09753:intron 50.0%
AGACCAGGACCCAAAAGACG+AGG - chr5.4:6798226-6798245 None:intergenic 55.0%
! ATGCCTGCCTTGTTGAGACC+AGG - chr5.4:6798241-6798260 None:intergenic 55.0%
GGTCCTGGTCTCAACAAGGC+AGG + chr5.4:6798235-6798254 MS.gene09753:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 6796957 6798702 6796957 ID=MS.gene09753
chr5.4 mRNA 6796957 6798702 6796957 ID=MS.gene09753.t1;Parent=MS.gene09753
chr5.4 exon 6796957 6796961 6796957 ID=MS.gene09753.t1.exon1;Parent=MS.gene09753.t1
chr5.4 CDS 6796957 6796961 6796957 ID=cds.MS.gene09753.t1;Parent=MS.gene09753.t1
chr5.4 exon 6797155 6797374 6797155 ID=MS.gene09753.t1.exon2;Parent=MS.gene09753.t1
chr5.4 CDS 6797155 6797374 6797155 ID=cds.MS.gene09753.t1;Parent=MS.gene09753.t1
chr5.4 exon 6798091 6798256 6798091 ID=MS.gene09753.t1.exon3;Parent=MS.gene09753.t1
chr5.4 CDS 6798091 6798256 6798091 ID=cds.MS.gene09753.t1;Parent=MS.gene09753.t1
chr5.4 exon 6798497 6798702 6798497 ID=MS.gene09753.t1.exon4;Parent=MS.gene09753.t1
chr5.4 CDS 6798497 6798702 6798497 ID=cds.MS.gene09753.t1;Parent=MS.gene09753.t1
Gene Sequence

>MS.gene09753

ATGAGGTTATTTTTTTTTTCCCTCTCTCTTATTCTACTTGTCTTTTTTTATCACCTTTTTTTAAGCTTCTTTAATCTTTTTTTTTATATATAAATTGAGTTACAAATTGTTATTTTTCATTGATAACTGAGATTTGATTTATATGGATTTTAATGTAGCAATGTTAATTATTCAACGAATTGTTGATTGATTGTGCAGTAAGCTTCAGAGTGATGCTGTGAGAGAAGCTATTACCGGAATCATGGGTGATTCCAAGGAGAAAAACCGTAAATTTGTGGAGACTATTGAACTCCAGATTGGTTTGAAAAACTATGATCCTCAAAAGGATAAACGTTTCAGCGGTTCGGTTAAGTTGCCTCACATTCCGAGACCAAAGATGAAAATTTGCATGCTTGGTGATGCCCAACATGTTGAGGAGGTAATAATCTCATGTTGCACTCAAACTGTTTGTTGGATTCACAAACACGAAACACTGACACGGAGACACCGATAATGATTTGATAAAAATGACATAATTGAATGTAATCACAAGCGTCATTGCCGAACACGTGTTTGATAGAGTGGCAAATGCCTTCTATCAAAATGTCGGTGCTACCGAGGTAGTTATTGCTGAATTGAAGTGAACACGAGTTTCAAATGTGTGAATTGCCATTTATTTTTGTGCTATATTTTGGTTGATTGCTATTAATCACTTATTTTCCTGATATGAGTCAGATGACACAATGATACTGTTGTATGCGACTTAGGATTAAGCTGATAATCGCTTATGCATAAGCTATTTCTATAGCAAAAGATAAAATAAAGTTAGATTGTTTTGTATAAATTATAAGCTGTTTTCATAAGCTATCTTGGAGAACTTATGAAAATAAGCTGAAAACAGCTTATGAACAATGAAAATAAGCTGTTTTAAACAAGTTCTTCCAAACAGTGTCACAAAATTTATGCCAGTAGATAAGCTCAGATAAGCAAATTCAAACAGACCCTTAGTAACCACAATTCAACAACATACTAATGTCTTTCATTTAGTTTTGATGGTATTGATTTTGCATCCGGAGCATGGGATATTTTTTTGAATATATGTTTGTTGCTAAGTTTCTTGTGTTAATGTCTTACACTCTAATATGCATATTGTAGGCTGAGAAAATAGGATTGGAATCGATGGATGTTGAAGCTTTGAAGAAGCTAAACAAAAATAAGAAACTGGTGAAGAAATTGGCAAAGAAGTACCATGCCTTTTTAGCCTCTGAAGCTGTTATCAAACAGATTCCTCGTCTTTTGGGTCCTGGTCTCAACAAGGCAGGCATGTGTTTTCTTTTGGGCGTTTTGGAATGCTGTCTCTTTAGTTATATGTTGTCCACATATATCCTGTTTATGTTTTATGTTAGTAATACATGTATGTATTGAATCATTTTAAATTACCAACTGTTTTTGGTTCATACTCTATCCGTTGCTTCATTTTATTTAGCAACCAGGTTTATTTGAAAGTTTGCCATTTCAATTGTTGCTTGAGCTGATTTGGATATTTTGCATGGCTTTTCAGGAAAGTTCCCTACACTTGTTTCCCACCAAGAATCTCTTGAGGCTAAGGTTAACGAGACTAAGGCTATGGTCAAATTCCAGCTCAAGAAAGTGTTGTGCATGGGAGTAGCTGTTGGCAATGTTAGTATGGACGAAAAACAAATATTCCAAAATGTACAACTGAGTGTTAACTTCCTCGTGTCCTTGTTGAAAAAGAACTGGCAAAAT

Protein sequence

>MS.gene09753.t1

MSKLQSDAVREAITGIMGDSKEKNRKFVETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKICMLGDAQHVEEAEKIGLESMDVEALKKLNKNKKLVKKLAKKYHAFLASEAVIKQIPRLLGPGLNKAGKFPTLVSHQESLEAKVNETKAMVKFQLKKVLCMGVAVGNVSMDEKQIFQNVQLSVNFLVSLLKKNWQN