AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene47260

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47260.t1 MTR_6g027360 82.301 113 20 0 1 113 1 113 3.54e-53 169
MS.gene47260.t1 MTR_6g027370 55.970 134 38 3 1 113 1 134 2.60e-36 126
MS.gene47260.t1 MTR_6g027340 98.039 51 1 0 63 113 1 51 2.62e-30 107
MS.gene47260.t1 MTR_3g089045 61.111 36 14 0 78 113 16 51 1.21e-11 60.1
MS.gene47260.t1 MTR_7g086960 61.111 36 14 0 78 113 89 124 5.95e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene47260.t1 AT1G69560 45.283 53 29 0 61 113 106 158 9.54e-11 57.8
MS.gene47260.t1 AT1G69560 45.283 53 29 0 61 113 90 142 9.73e-11 57.8

Find 33 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAAATCCCAAAGGGTATTT+TGG 0.171827 6.3:-18732296 None:intergenic
TAAAATTTCCTCCATTGTTT+TGG 0.231459 6.3:-18732354 None:intergenic
ATCATCTTCTACTCCCCTTC+AGG 0.338308 6.3:+18732243 MS.gene47260:CDS
CTAAGCCTTTCAAAGCTCAT+TGG 0.383578 6.3:+18732383 MS.gene47260:CDS
GAAAAGTCCAAAATACCCTT+TGG 0.408522 6.3:+18732289 MS.gene47260:CDS
AAAAGTCCAAAATACCCTTT+GGG 0.428010 6.3:+18732290 MS.gene47260:CDS
GGACCATGCTCTCATTAGGT+TGG 0.436179 6.3:-18732333 None:intergenic
AAACAACTTATCGCTGATCA+TGG 0.467600 6.3:+18732430 MS.gene47260:CDS
CTTTGGGATTTCGAACCCTC+CGG 0.484306 6.3:+18732306 MS.gene47260:CDS
AACAACTTATCGCTGATCAT+GGG 0.490010 6.3:+18732431 MS.gene47260:CDS
GAACAACTACAAGGAAGAAC+AGG 0.490599 6.3:+18732478 MS.gene47260:CDS
TTTCAAGTTTAGTGAACTCA+TGG 0.500351 6.3:-18732161 None:intergenic
CTCTCATTAGGTTGGATCAC+CGG 0.504011 6.3:-18732325 None:intergenic
TCATCTTCTACTCCCCTTCA+GGG 0.505070 6.3:+18732244 MS.gene47260:CDS
ACTCCCCTTCAGGGTCATGT+TGG 0.552989 6.3:+18732253 MS.gene47260:CDS
GGTTTCCAATGAGCTTTGAA+AGG 0.559132 6.3:-18732388 None:intergenic
TCATTAGGTTGGATCACCGG+AGG 0.577019 6.3:-18732322 None:intergenic
TTAAGCTTAGCATCTTCAGA+TGG 0.584279 6.3:-18732409 None:intergenic
GAGAGCATGGTCCAAAACAA+TGG 0.587715 6.3:+18732343 MS.gene47260:CDS
GTTACCAACATGACCCTGAA+GGG 0.597809 6.3:-18732257 None:intergenic
AACATTGCTGAACAACTACA+AGG 0.597959 6.3:+18732469 MS.gene47260:CDS
CATTAGGTTGGATCACCGGA+GGG 0.604916 6.3:-18732321 None:intergenic
GGAGGGTTCGAAATCCCAAA+GGG 0.615161 6.3:-18732304 None:intergenic
TGTTACCAACATGACCCTGA+AGG 0.615497 6.3:-18732258 None:intergenic
TGATGTAAGTTGACATGGAA+GGG 0.621849 6.3:-18732221 None:intergenic
GATCCAACCTAATGAGAGCA+TGG 0.627553 6.3:+18732330 MS.gene47260:CDS
GATGATGATGTAAGTTGACA+TGG 0.628162 6.3:-18732226 None:intergenic
ACAACTTATCGCTGATCATG+GGG 0.628696 6.3:+18732432 MS.gene47260:CDS
CGGAGGGTTCGAAATCCCAA+AGG 0.641460 6.3:-18732305 None:intergenic
AGCATGGTCCAAAACAATGG+AGG 0.663492 6.3:+18732346 MS.gene47260:CDS
TTACCAACATGACCCTGAAG+GGG 0.664721 6.3:-18732256 None:intergenic
GGGTCATGTTGGTAACAATG+AGG 0.688477 6.3:+18732264 MS.gene47260:CDS
ATGATGTAAGTTGACATGGA+AGG 0.710504 6.3:-18732222 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAAAAACAATTTAAGT+TGG + chr6.3:18733090-18733109 MS.gene47260:intron 10.0%
!! TATTTGTAATTTAACATTTA+GGG + chr6.3:18732734-18732753 MS.gene47260:intron 10.0%
!! TTATTTGTAATTTAACATTT+AGG + chr6.3:18732733-18732752 MS.gene47260:intron 10.0%
!! TTTATGTCAATTAATAAATA+TGG - chr6.3:18732905-18732924 None:intergenic 10.0%
!!! AATAAAAAACAATTTAAGTT+GGG + chr6.3:18733091-18733110 MS.gene47260:intron 10.0%
!!! TACTATTCATTTTTTTTTAT+AGG - chr6.3:18733064-18733083 None:intergenic 10.0%
!! ATATATATAATTGTCTTCAA+GGG - chr6.3:18732930-18732949 None:intergenic 15.0%
!! TAAATTATTGTTTAACGAAA+TGG + chr6.3:18732555-18732574 MS.gene47260:intron 15.0%
!! TATATATATAATTGTCTTCA+AGG - chr6.3:18732931-18732950 None:intergenic 15.0%
!!! ATAAAAAACAATTTAAGTTG+GGG + chr6.3:18733092-18733111 MS.gene47260:intron 15.0%
!! TATAAAGCATAAACATATTG+TGG + chr6.3:18732947-18732966 MS.gene47260:intron 20.0%
!! TTGTTTGGTATAAAAGAAAA+TGG + chr6.3:18732853-18732872 MS.gene47260:intron 20.0%
!!! AAAAATTGAACATTTTCAAG+CGG + chr6.3:18732640-18732659 MS.gene47260:intron 20.0%
!!! TAAAAAACAATTTAAGTTGG+GGG + chr6.3:18733093-18733112 MS.gene47260:intron 20.0%
!!! TAGACTTTTCACATAAAAAA+TGG + chr6.3:18733121-18733140 MS.gene47260:intron 20.0%
! AAAAAGGAAAGAAAGTAATG+TGG - chr6.3:18733202-18733221 None:intergenic 25.0%
! AAAAATGTGTTATGTTGTGT+AGG - chr6.3:18732510-18732529 None:intergenic 25.0%
! AAAAGGAAAGAAAGTAATGT+GGG - chr6.3:18733201-18733220 None:intergenic 25.0%
! AAAATGGAATAGAAAGTTGA+AGG + chr6.3:18732869-18732888 MS.gene47260:intron 25.0%
! AACTTGAAAAATGATGGTTA+TGG + chr6.3:18732175-18732194 MS.gene47260:CDS 25.0%
! AAGAAAAAGAATAGAAAGTG+AGG + chr6.3:18732818-18732837 MS.gene47260:intron 25.0%
! AAGTAAGGAAAGATTAAATG+AGG + chr6.3:18732794-18732813 MS.gene47260:intron 25.0%
! AGAAAAAGAATAGAAAGTGA+GGG + chr6.3:18732819-18732838 MS.gene47260:intron 25.0%
! GTAAAAGGAAAGAAAAAGTA+AGG + chr6.3:18732779-18732798 MS.gene47260:intron 25.0%
! TCACTAAACTTGAAAAATGA+TGG + chr6.3:18732169-18732188 MS.gene47260:CDS 25.0%
!! AAAACAATGGAGGAAATTTT+AGG + chr6.3:18732356-18732375 MS.gene47260:CDS 25.0%
!! ATTTTTCTATGGCATACAAT+TGG - chr6.3:18732988-18733007 None:intergenic 25.0%
!! TAAAATTTCCTCCATTGTTT+TGG - chr6.3:18732357-18732376 None:intergenic 25.0%
!! TTCTCTTTTCTTAAGTTTGT+AGG + chr6.3:18733411-18733430 MS.gene47260:intron 25.0%
!! TTTAACATTTAGGGTTTGTT+TGG + chr6.3:18732743-18732762 MS.gene47260:intron 25.0%
!!! AGTGAGTTGATAAAATAAAG+AGG + chr6.3:18733013-18733032 MS.gene47260:intron 25.0%
!!! TTAGACGTATTTTTACTCTA+AGG - chr6.3:18733323-18733342 None:intergenic 25.0%
AAAAGTCCAAAATACCCTTT+GGG + chr6.3:18732290-18732309 MS.gene47260:CDS 30.0%
AAGATTGAGGAAGAAAAGAT+TGG - chr6.3:18733285-18733304 None:intergenic 30.0%
AGCATAAACATATTGTGGTT+AGG + chr6.3:18732952-18732971 MS.gene47260:intron 30.0%
CCAAACTATGGAACAATATT+TGG + chr6.3:18733237-18733256 MS.gene47260:intron 30.0%
CCAAATATTGTTCCATAGTT+TGG - chr6.3:18733240-18733259 None:intergenic 30.0%
GAAAAAGAATAGAAAGTGAG+GGG + chr6.3:18732820-18732839 MS.gene47260:intron 30.0%
GGATGATCAAAGAAAGTAAA+AGG + chr6.3:18732764-18732783 MS.gene47260:intron 30.0%
GTTCAAGGGAACAATTAAAA+AGG - chr6.3:18733218-18733237 None:intergenic 30.0%
!! CTCACTCTTTCATTTTTCTA+TGG - chr6.3:18732999-18733018 None:intergenic 30.0%
!!! TTTTACTCTAAGGCTTTGTT+TGG - chr6.3:18733313-18733332 None:intergenic 30.0%
AAACAACTTATCGCTGATCA+TGG + chr6.3:18732430-18732449 MS.gene47260:CDS 35.0%
AACAACTTATCGCTGATCAT+GGG + chr6.3:18732431-18732450 MS.gene47260:CDS 35.0%
AACATTGCTGAACAACTACA+AGG + chr6.3:18732469-18732488 MS.gene47260:CDS 35.0%
GAAAAGTCCAAAATACCCTT+TGG + chr6.3:18732289-18732308 MS.gene47260:CDS 35.0%
TTAAGCTTAGCATCTTCAGA+TGG - chr6.3:18732412-18732431 None:intergenic 35.0%
! AAGAAAAGATTGGTTGTGGA+TGG - chr6.3:18733275-18733294 None:intergenic 35.0%
! ATGATGTAAGTTGACATGGA+AGG - chr6.3:18732225-18732244 None:intergenic 35.0%
! GATGATGATGTAAGTTGACA+TGG - chr6.3:18732229-18732248 None:intergenic 35.0%
! TGATGTAAGTTGACATGGAA+GGG - chr6.3:18732224-18732243 None:intergenic 35.0%
! TGTTCCATAGTTTGGTTCAA+GGG - chr6.3:18733232-18733251 None:intergenic 35.0%
! TTGTTCCATAGTTTGGTTCA+AGG - chr6.3:18733233-18733252 None:intergenic 35.0%
!!! AGGGGATTGTTTTGATTGTT+TGG + chr6.3:18732838-18732857 MS.gene47260:intron 35.0%
ACAAAAAGAGTAGAGCCACA+TGG - chr6.3:18733375-18733394 None:intergenic 40.0%
ACAACTTATCGCTGATCATG+GGG + chr6.3:18732432-18732451 MS.gene47260:CDS 40.0%
CTAAGCCTTTCAAAGCTCAT+TGG + chr6.3:18732383-18732402 MS.gene47260:CDS 40.0%
CTGATCATGGGGCTAAAAAT+TGG + chr6.3:18732443-18732462 MS.gene47260:CDS 40.0%
GAACAACTACAAGGAAGAAC+AGG + chr6.3:18732478-18732497 MS.gene47260:CDS 40.0%
TGTTCCCTTGAACCAAACTA+TGG + chr6.3:18733225-18733244 MS.gene47260:intron 40.0%
! GAGGAAGAAAAGATTGGTTG+TGG - chr6.3:18733279-18733298 None:intergenic 40.0%
! TTGTTTGGTTCGCAAGATTG+AGG - chr6.3:18733298-18733317 None:intergenic 40.0%
! TTTTGGACCATGCTCTCATT+AGG - chr6.3:18732340-18732359 None:intergenic 40.0%
!! GCAGAAAGGTTTTTAGGCAT+GGG + chr6.3:18733174-18733193 MS.gene47260:intron 40.0%
!! GGTTTCCAATGAGCTTTGAA+AGG - chr6.3:18732391-18732410 None:intergenic 40.0%
!!! CGAAATCCCAAAGGGTATTT+TGG - chr6.3:18732299-18732318 None:intergenic 40.0%
AAGAGTAGAGCCACATGGTT+CGG - chr6.3:18733370-18733389 None:intergenic 45.0%
AGCATGGTCCAAAACAATGG+AGG + chr6.3:18732346-18732365 MS.gene47260:CDS 45.0%
ATCATCTTCTACTCCCCTTC+AGG + chr6.3:18732243-18732262 MS.gene47260:CDS 45.0%
CAAGAGTAAACCGAACCATG+TGG + chr6.3:18733357-18733376 MS.gene47260:intron 45.0%
GATCCAACCTAATGAGAGCA+TGG + chr6.3:18732330-18732349 MS.gene47260:CDS 45.0%
GTTACCAACATGACCCTGAA+GGG - chr6.3:18732260-18732279 None:intergenic 45.0%
TCATCTTCTACTCCCCTTCA+GGG + chr6.3:18732244-18732263 MS.gene47260:CDS 45.0%
TGTTACCAACATGACCCTGA+AGG - chr6.3:18732261-18732280 None:intergenic 45.0%
TTACCAACATGACCCTGAAG+GGG - chr6.3:18732259-18732278 None:intergenic 45.0%
TTGGTTGTGGATGGAAAGCA+CGG - chr6.3:18733266-18733285 None:intergenic 45.0%
! AGCAGCGCAGAAAGGTTTTT+AGG + chr6.3:18733168-18733187 MS.gene47260:intron 45.0%
! GAGAGCATGGTCCAAAACAA+TGG + chr6.3:18732343-18732362 MS.gene47260:CDS 45.0%
!! CGCAGAAAGGTTTTTAGGCA+TGG + chr6.3:18733173-18733192 MS.gene47260:intron 45.0%
!! CTCTCATTAGGTTGGATCAC+CGG - chr6.3:18732328-18732347 None:intergenic 45.0%
!! GGGTCATGTTGGTAACAATG+AGG + chr6.3:18732264-18732283 MS.gene47260:CDS 45.0%
AAAACCTTTCTGCGCTGCTG+AGG - chr6.3:18733167-18733186 None:intergenic 50.0%
GGACCATGCTCTCATTAGGT+TGG - chr6.3:18732336-18732355 None:intergenic 50.0%
GGAGGGTTCGAAATCCCAAA+GGG - chr6.3:18732307-18732326 None:intergenic 50.0%
!! CATTAGGTTGGATCACCGGA+GGG - chr6.3:18732324-18732343 None:intergenic 50.0%
!! CTTTGGGATTTCGAACCCTC+CGG + chr6.3:18732306-18732325 MS.gene47260:CDS 50.0%
!! TCATTAGGTTGGATCACCGG+AGG - chr6.3:18732325-18732344 None:intergenic 50.0%
ACTCCCCTTCAGGGTCATGT+TGG + chr6.3:18732253-18732272 MS.gene47260:CDS 55.0%
CGGAGGGTTCGAAATCCCAA+AGG - chr6.3:18732308-18732327 None:intergenic 55.0%
ACCTTTCTGCGCTGCTGAGG+AGG - chr6.3:18733164-18733183 None:intergenic 60.0%
CCTTTCTGCGCTGCTGAGGA+GGG - chr6.3:18733163-18733182 None:intergenic 60.0%
CCCTCCTCAGCAGCGCAGAA+AGG + chr6.3:18733160-18733179 MS.gene47260:intron 65.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 18732163 18733449 18732163 ID=MS.gene47260
chr6.3 mRNA 18732163 18733449 18732163 ID=MS.gene47260.t1;Parent=MS.gene47260
chr6.3 exon 18732163 18732499 18732163 ID=MS.gene47260.t1.exon1;Parent=MS.gene47260.t1
chr6.3 CDS 18732163 18732499 18732163 ID=cds.MS.gene47260.t1;Parent=MS.gene47260.t1
chr6.3 exon 18733433 18733449 18733433 ID=MS.gene47260.t1.exon2;Parent=MS.gene47260.t1
chr6.3 CDS 18733433 18733449 18733433 ID=cds.MS.gene47260.t1;Parent=MS.gene47260.t1
Gene Sequence

>MS.gene47260

ATGAGTTCACTAAACTTGAAAAATGATGGTTATGGTTTCTTTTTAGACTTGAAAATTTCCCTTCCATGTCAACTTACATCATCATCTTCTACTCCCCTTCAGGGTCATGTTGGTAACAATGAGGCTGAAAAGTCCAAAATACCCTTTGGGATTTCGAACCCTCCGGTGATCCAACCTAATGAGAGCATGGTCCAAAACAATGGAGGAAATTTTAGGAACACTAAGCCTTTCAAAGCTCATTGGAAACCATCTGAAGATGCTAAGCTTAAACAACTTATCGCTGATCATGGGGCTAAAAATTGGAACAACATTGCTGAACAACTACAAGGAAGAACAGGTTTGATCCTACACAACATAACACATTTTTATTTATTAAATTTTAAAAATTTTACTAAATTATTGTTTAACGAAATGGTTTTTTTTATATTGTTAATAATTAATTTTTAATTTAATTTTTTTTACAAAAATAAATATTTAAAAAATTGAACATTTTCAAGCGGTACGTTTAGTATTTTTAATAAAATTGCATAAGTATTGTATTTTGATTAGACATTTCTTTAATTTCGCTATTTATTTGTAATTTAACATTTAGGGTTTGTTTGGATGATCAAAGAAAGTAAAAGGAAAGAAAAAGTAAGGAAAGATTAAATGAGGAAAGAAAAAGAATAGAAAGTGAGGGGATTGTTTTGATTGTTTGGTATAAAAGAAAATGGAATAGAAAGTTGAAGGAAAGAAAGATCCATATTTATTAATTGACATAAATACCCTTGAAGACAATTATATATATAAAGCATAAACATATTGTGGTTAGGTGTGAGTAGTCCAATTGTATGCCATAGAAAAATGAAAGAGTGAGTTGATAAAATAAAGAGGAGACAACAAACGAATATAGCTATAACCTATAAAAAAAAATGAATAGTAAAAAGTAAATAAAAAACAATTTAAGTTGGGGGCGTTTTAGACTTTTCACATAAAAAATGGTTGTTTCTCAATCTTTCCCTCCTCAGCAGCGCAGAAAGGTTTTTAGGCATGGGTCCCACATTACTTTCTTTCCTTTTTAATTGTTCCCTTGAACCAAACTATGGAACAATATTTGGTTTCCGTGCTTTCCATCCACAACCAATCTTTTCTTCCTCAATCTTGCGAACCAAACAAAGCCTTAGAGTAAAAATACGTCTAAATGATATCTCACATCAAGAGTAAACCGAACCATGTGGCTCTACTCTTTTTGTTTTCTTTGCTTAGTTCTTCTCTTTTCTTAAGTTTGTAGGAAATGAGAATAACTAA
Protein sequence

>MS.gene47260.t1

MSSLNLKNDGYGFFLDLKISLPCQLTSSSSTPLQGHVGNNEAEKSKIPFGISNPPVIQPNESMVQNNGGNFRNTKPFKAHWKPSEDAKLKQLIADHGAKNWNNIAEQLQGRTGNENN