AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39445

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39445.t1 MTR_4g088925 90.909 275 24 1 21 294 34 308 7.74e-175 489
MS.gene39445.t1 MTR_7g096720 66.007 303 88 4 7 294 7 309 4.36e-126 365
MS.gene39445.t1 MTR_8g085760 54.125 303 108 12 16 294 16 311 1.28e-83 257
MS.gene39445.t1 MTR_6g092570 45.977 261 115 12 16 267 11 254 2.70e-50 171
MS.gene39445.t1 MTR_5g079830 40.288 278 128 9 12 272 5 261 2.48e-44 155
MS.gene39445.t1 MTR_8g074610 35.000 320 152 13 10 294 22 320 2.91e-35 132
MS.gene39445.t1 MTR_2g041510 35.331 317 149 12 10 294 3 295 5.93e-35 130
MS.gene39445.t1 MTR_2g041510 35.331 317 149 12 10 294 23 315 8.07e-35 130
MS.gene39445.t1 MTR_4g125090 39.147 258 115 11 16 267 48 269 5.34e-34 127
MS.gene39445.t1 MTR_8g074640 32.923 325 151 13 10 294 3 300 7.98e-34 127
MS.gene39445.t1 MTR_7g096760 63.855 83 28 2 213 294 1 82 2.09e-26 101
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39445.t1 AT2G26160 29.801 302 167 14 10 292 2 277 1.08e-17 82.8
MS.gene39445.t1 AT1G44080 28.716 296 163 12 15 294 7 270 3.17e-16 78.6
MS.gene39445.t1 AT3G25750 26.959 319 157 15 10 293 2 279 4.49e-12 66.6
MS.gene39445.t1 AT3G25750 28.165 316 143 17 10 293 2 265 5.04e-12 66.2
MS.gene39445.t1 AT4G35733 25.407 307 169 14 15 293 8 282 8.93e-12 65.5

Find 63 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTTATGTTGTGGATAAAA+TGG 0.170692 4.2:-22119646 MS.gene39445:CDS
TCTTCTCCATGTTCTAATAA+AGG 0.226945 4.2:-22120026 MS.gene39445:CDS
ATATGTCGTTTCTTCAATAT+TGG 0.240462 4.2:+22119734 None:intergenic
TTGTACTGTTGTGAAGAAAA+TGG 0.292181 4.2:-22119564 MS.gene39445:CDS
TATACTCCTAGTAATCTTAA+AGG 0.306170 4.2:-22119861 MS.gene39445:CDS
GTGAAGAAAATGGGCATATA+AGG 0.309903 4.2:-22119554 MS.gene39445:CDS
GAGATCAAGGAGATAAAGTT+TGG 0.313221 4.2:+22119971 None:intergenic
TGGTTGAATGCGATATATTT+TGG 0.324073 4.2:+22120055 None:intergenic
ATAAAATGGGAACAATATTC+TGG 0.330031 4.2:-22119632 MS.gene39445:CDS
TGAAATACAATGACGGTTAG+AGG 0.334225 4.2:+22120103 None:intergenic
CTTCTCCATGTTCTAATAAA+GGG 0.339621 4.2:-22120025 MS.gene39445:CDS
CATGGTCTTTGCACTGTATT+GGG 0.339972 4.2:-22119772 MS.gene39445:CDS
ATAATTGCCCACAGTTCTTC+GGG 0.362493 4.2:+22120212 None:intergenic
GCATGGTCTTTGCACTGTAT+TGG 0.366088 4.2:-22119773 MS.gene39445:CDS
ATGATGAAAGATATTACAAA+TGG 0.377232 4.2:-22119458 MS.gene39445:CDS
TATAATTGCCCACAGTTCTT+CGG 0.379606 4.2:+22120211 None:intergenic
TTTATAAGCTTGATCAAGAA+TGG 0.392244 4.2:-22119404 MS.gene39445:CDS
CTTTATGTTGTGGATAAAAT+GGG 0.396836 4.2:-22119645 MS.gene39445:CDS
TATGTATACAGATTTAGATT+CGG 0.409577 4.2:-22119085 MS.gene39445:intron
TGATGAAAGATATTACAAAT+GGG 0.410822 4.2:-22119457 MS.gene39445:CDS
GGCGCACCCTCGTGCAAGAT+CGG 0.416534 4.2:-22119059 MS.gene39445:CDS
ATTTCACCTTTAAGATTACT+AGG 0.418748 4.2:+22119855 None:intergenic
ATGTATACAGATTTAGATTC+GGG 0.419999 4.2:-22119084 MS.gene39445:intron
AACGACATATACCATGTTAG+AGG 0.420963 4.2:-22119721 MS.gene39445:CDS
TCTTGTTAGTGAAGAGATCA+AGG 0.425995 4.2:+22119958 None:intergenic
CAAATGGGGTTACTATTTGA+AGG 0.433128 4.2:-22119442 MS.gene39445:CDS
CTTTGCACTGTATTGGGATA+AGG 0.437651 4.2:-22119766 MS.gene39445:CDS
CGGTTAGAGGGAGATGGAGT+AGG 0.441798 4.2:+22120116 None:intergenic
TGTTTATAGTCTCTTCAGTT+CGG 0.445719 4.2:+22119931 None:intergenic
TGATGATATGATACTTTACA+AGG 0.448437 4.2:-22119673 MS.gene39445:CDS
TAATGCTTTGTCTTTCAAGT+TGG 0.450944 4.2:-22119607 MS.gene39445:CDS
TTATAAGCTTGATCAAGAAT+GGG 0.450966 4.2:-22119403 MS.gene39445:CDS
GAACATGGAGAAGAAGTTGA+TGG 0.458938 4.2:+22120035 None:intergenic
GACCATGCAATGACCCTCAA+TGG 0.463706 4.2:+22119788 None:intergenic
GCGCACCCTCGTGCAAGATC+GGG 0.464655 4.2:-22119058 MS.gene39445:CDS
TTCCATTGAGGGTCATTGCA+TGG 0.485537 4.2:-22119790 MS.gene39445:CDS
TTTGATGAACTTTCGAGTTG+TGG 0.507145 4.2:-22119898 MS.gene39445:CDS
TGTACTGTTGTGAAGAAAAT+GGG 0.510338 4.2:-22119563 MS.gene39445:CDS
CAAGGGACAACTTTATGTTG+TGG 0.530035 4.2:-22119655 MS.gene39445:CDS
AAGCAATTAGTAGAGTATGA+TGG 0.541821 4.2:-22119510 MS.gene39445:CDS
TGAAGAAAATGGGCATATAA+GGG 0.545210 4.2:-22119553 MS.gene39445:CDS
CAATGACGGTTAGAGGGAGA+TGG 0.565114 4.2:+22120110 None:intergenic
GATGAAAGATATTACAAATG+GGG 0.570718 4.2:-22119456 MS.gene39445:CDS
GAAATACAATGACGGTTAGA+GGG 0.587865 4.2:+22120104 None:intergenic
ACTCTTCCCGATCTTGCACG+AGG 0.589668 4.2:+22119052 None:intergenic
CAAATCTTCCCGAAGAACTG+TGG 0.593577 4.2:-22120220 MS.gene39445:CDS
AAATCTTCCCGAAGAACTGT+GGG 0.597436 4.2:-22120219 MS.gene39445:CDS
TCCACCATCGTCCTCTAACA+TGG 0.600678 4.2:+22119710 None:intergenic
AGCCACCCTTTATTAGAACA+TGG 0.603918 4.2:+22120020 None:intergenic
CTCTTCCCGATCTTGCACGA+GGG 0.608888 4.2:+22119053 None:intergenic
CTCCATGTTCTAATAAAGGG+TGG 0.613724 4.2:-22120022 MS.gene39445:CDS
AATCATATGAAATACAATGA+CGG 0.625198 4.2:+22120096 None:intergenic
AAAGAATAAGAGAGAAAACA+TGG 0.627827 4.2:-22120249 MS.gene39445:CDS
TATAAGCTTGATCAAGAATG+GGG 0.627945 4.2:-22119402 MS.gene39445:intron
GAATAAGAGAGAAAACATGG+AGG 0.633816 4.2:-22120246 MS.gene39445:CDS
ATACAGATTTAGATTCGGGA+TGG 0.640071 4.2:-22119080 MS.gene39445:intron
ATATAGAGAGAAAATATGGA+AGG 0.641170 4.2:-22120278 None:intergenic
AATAAGAGAGAAAACATGGA+GGG 0.643964 4.2:-22120245 MS.gene39445:CDS
GTATCATATCATCAAGACAC+TGG 0.648328 4.2:+22119682 None:intergenic
GAAATAAACTATCGATACTG+CGG 0.667567 4.2:+22120150 None:intergenic
GATGATATGATACTTTACAA+GGG 0.668685 4.2:-22119672 MS.gene39445:CDS
TATACCATGTTAGAGGACGA+TGG 0.699906 4.2:-22119714 MS.gene39445:CDS
ACCATGTTAGAGGACGATGG+TGG 0.704775 4.2:-22119711 MS.gene39445:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGGTTAAAAATAAAAGATT+TGG - chr4.2:22119925-22119944 MS.gene39445:CDS 15.0%
!! TACTATACTTACAAATTAAT+TGG + chr4.2:22120137-22120156 None:intergenic 15.0%
!! TGGTTAAAAATAAAAGATTT+GGG - chr4.2:22119926-22119945 MS.gene39445:CDS 15.0%
!! AATCATATGAAATACAATGA+CGG + chr4.2:22119208-22119227 None:intergenic 20.0%
!! ATGATGAAAGATATTACAAA+TGG - chr4.2:22119843-22119862 MS.gene39445:CDS 20.0%
!! ATGCACATAAATATGATATA+TGG - chr4.2:22120157-22120176 MS.gene39445:CDS 20.0%
!! TATGTATACAGATTTAGATT+CGG - chr4.2:22120216-22120235 MS.gene39445:CDS 20.0%
!! TGATGAAAGATATTACAAAT+GGG - chr4.2:22119844-22119863 MS.gene39445:CDS 20.0%
! AAAGAATAAGAGAGAAAACA+TGG - chr4.2:22119052-22119071 MS.gene39445:CDS 25.0%
! ACTTTATGTTGTGGATAAAA+TGG - chr4.2:22119655-22119674 MS.gene39445:CDS 25.0%
! ATAAAATGGGAACAATATTC+TGG - chr4.2:22119669-22119688 MS.gene39445:CDS 25.0%
! ATGTATACAGATTTAGATTC+GGG - chr4.2:22120217-22120236 MS.gene39445:CDS 25.0%
! CTTTATGTTGTGGATAAAAT+GGG - chr4.2:22119656-22119675 MS.gene39445:CDS 25.0%
! GATGAAAGATATTACAAATG+GGG - chr4.2:22119845-22119864 MS.gene39445:CDS 25.0%
! GATGATATGATACTTTACAA+GGG - chr4.2:22119629-22119648 MS.gene39445:CDS 25.0%
! TATACTCCTAGTAATCTTAA+AGG - chr4.2:22119440-22119459 MS.gene39445:CDS 25.0%
! TGATGATATGATACTTTACA+AGG - chr4.2:22119628-22119647 MS.gene39445:CDS 25.0%
! TTATAAGCTTGATCAAGAAT+GGG - chr4.2:22119898-22119917 MS.gene39445:CDS 25.0%
! TTTATAAGCTTGATCAAGAA+TGG - chr4.2:22119897-22119916 MS.gene39445:CDS 25.0%
!! AGTAATCTTTTATTCCATTG+AGG - chr4.2:22119499-22119518 MS.gene39445:CDS 25.0%
!! ATATGTCGTTTCTTCAATAT+TGG + chr4.2:22119570-22119589 None:intergenic 25.0%
!! CTTACAAATTAATTGGTAAC+AGG + chr4.2:22120130-22120149 None:intergenic 25.0%
!! GTAATCTTTTATTCCATTGA+GGG - chr4.2:22119500-22119519 MS.gene39445:CDS 25.0%
!!! ATTTCACCTTTAAGATTACT+AGG + chr4.2:22119449-22119468 None:intergenic 25.0%
!!! CTATTTCTATTTTGATCACA+AGG - chr4.2:22120030-22120049 MS.gene39445:CDS 25.0%
AAGCAATTAGTAGAGTATGA+TGG - chr4.2:22119791-22119810 MS.gene39445:CDS 30.0%
AATAAGAGAGAAAACATGGA+GGG - chr4.2:22119056-22119075 MS.gene39445:CDS 30.0%
CAAGATTATTATGGATGTGA+AGG - chr4.2:22119998-22120017 MS.gene39445:CDS 30.0%
CTTCTCCATGTTCTAATAAA+GGG - chr4.2:22119276-22119295 MS.gene39445:intron 30.0%
GAAATAAACTATCGATACTG+CGG + chr4.2:22119154-22119173 None:intergenic 30.0%
TATAAGCTTGATCAAGAATG+GGG - chr4.2:22119899-22119918 MS.gene39445:CDS 30.0%
TCTTCTCCATGTTCTAATAA+AGG - chr4.2:22119275-22119294 MS.gene39445:intron 30.0%
TGAAGAAAATGGGCATATAA+GGG - chr4.2:22119748-22119767 MS.gene39445:CDS 30.0%
TGTACTGTTGTGAAGAAAAT+GGG - chr4.2:22119738-22119757 MS.gene39445:CDS 30.0%
TGTTTATAGTCTCTTCAGTT+CGG + chr4.2:22119373-22119392 None:intergenic 30.0%
TTGTACTGTTGTGAAGAAAA+TGG - chr4.2:22119737-22119756 MS.gene39445:CDS 30.0%
! CAAATTAATTGGTAACAGGA+TGG + chr4.2:22120126-22120145 None:intergenic 30.0%
! TAATGCTTTGTCTTTCAAGT+TGG - chr4.2:22119694-22119713 MS.gene39445:CDS 30.0%
! TCACAACAGTACAAGTTTTT+AGG + chr4.2:22119731-22119750 None:intergenic 30.0%
! TGGTTGAATGCGATATATTT+TGG + chr4.2:22119249-22119268 None:intergenic 30.0%
!! CTATTTGAAGGATGTTTTTG+TGG - chr4.2:22119871-22119890 MS.gene39445:CDS 30.0%
!! TTGTTGGCTCAAGATTATTA+TGG - chr4.2:22119989-22120008 MS.gene39445:CDS 30.0%
!!! TATATGGTTTTAGTGTCTTG+TGG - chr4.2:22120173-22120192 MS.gene39445:CDS 30.0%
AACGACATATACCATGTTAG+AGG - chr4.2:22119580-22119599 MS.gene39445:CDS 35.0%
AGACTCAAACTTTGCATTGT+TGG - chr4.2:22119973-22119992 MS.gene39445:CDS 35.0%
ATACAGATTTAGATTCGGGA+TGG - chr4.2:22120221-22120240 MS.gene39445:CDS 35.0%
CAAATGGGGTTACTATTTGA+AGG - chr4.2:22119859-22119878 MS.gene39445:CDS 35.0%
GAAATACAATGACGGTTAGA+GGG + chr4.2:22119200-22119219 None:intergenic 35.0%
GAATAAGAGAGAAAACATGG+AGG - chr4.2:22119055-22119074 MS.gene39445:CDS 35.0%
GAGATCAAGGAGATAAAGTT+TGG + chr4.2:22119333-22119352 None:intergenic 35.0%
GTATCATATCATCAAGACAC+TGG + chr4.2:22119622-22119641 None:intergenic 35.0%
GTGAAGAAAATGGGCATATA+AGG - chr4.2:22119747-22119766 MS.gene39445:CDS 35.0%
TATAATTGCCCACAGTTCTT+CGG + chr4.2:22119093-22119112 None:intergenic 35.0%
TCTTGTTAGTGAAGAGATCA+AGG + chr4.2:22119346-22119365 None:intergenic 35.0%
TGAAATACAATGACGGTTAG+AGG + chr4.2:22119201-22119220 None:intergenic 35.0%
TTGATCAAGAATGGGGTAAA+TGG - chr4.2:22119906-22119925 MS.gene39445:CDS 35.0%
!! TTTGATGAACTTTCGAGTTG+TGG - chr4.2:22119403-22119422 MS.gene39445:CDS 35.0%
AAATCTTCCCGAAGAACTGT+GGG - chr4.2:22119082-22119101 MS.gene39445:intron 40.0%
AGCCACCCTTTATTAGAACA+TGG + chr4.2:22119284-22119303 None:intergenic 40.0%
ATAATTGCCCACAGTTCTTC+GGG + chr4.2:22119092-22119111 None:intergenic 40.0%
CAAGGGACAACTTTATGTTG+TGG - chr4.2:22119646-22119665 MS.gene39445:CDS 40.0%
CATGGTCTTTGCACTGTATT+GGG - chr4.2:22119529-22119548 MS.gene39445:CDS 40.0%
CTCCATGTTCTAATAAAGGG+TGG - chr4.2:22119279-22119298 MS.gene39445:intron 40.0%
CTTTGCACTGTATTGGGATA+AGG - chr4.2:22119535-22119554 MS.gene39445:CDS 40.0%
GAACATGGAGAAGAAGTTGA+TGG + chr4.2:22119269-22119288 None:intergenic 40.0%
GTAACAGGATGGAACAAAGT+TGG + chr4.2:22120115-22120134 None:intergenic 40.0%
TATACCATGTTAGAGGACGA+TGG - chr4.2:22119587-22119606 MS.gene39445:CDS 40.0%
!!! ATGGTTTTAGTGTCTTGTGG+TGG - chr4.2:22120176-22120195 MS.gene39445:CDS 40.0%
!!! CTAAGCCTGCTGACATTTTT+TGG - chr4.2:22120083-22120102 MS.gene39445:CDS 40.0%
CAAATCTTCCCGAAGAACTG+TGG - chr4.2:22119081-22119100 MS.gene39445:intron 45.0%
CAAGGCCAAAAAATGTCAGC+AGG + chr4.2:22120091-22120110 None:intergenic 45.0%
GCATGGTCTTTGCACTGTAT+TGG - chr4.2:22119528-22119547 MS.gene39445:CDS 45.0%
GGATGGAACAAAGTTGGACA+AGG + chr4.2:22120109-22120128 None:intergenic 45.0%
TTCCATTGAGGGTCATTGCA+TGG - chr4.2:22119511-22119530 MS.gene39445:CDS 45.0%
ACCATGTTAGAGGACGATGG+TGG - chr4.2:22119590-22119609 MS.gene39445:CDS 50.0%
CAATGACGGTTAGAGGGAGA+TGG + chr4.2:22119194-22119213 None:intergenic 50.0%
GACCATGCAATGACCCTCAA+TGG + chr4.2:22119516-22119535 None:intergenic 50.0%
TCCACCATCGTCCTCTAACA+TGG + chr4.2:22119594-22119613 None:intergenic 50.0%
ACTCTTCCCGATCTTGCACG+AGG + chr4.2:22120252-22120271 None:intergenic 55.0%
CGGTTAGAGGGAGATGGAGT+AGG + chr4.2:22119188-22119207 None:intergenic 55.0%
CTCTTCCCGATCTTGCACGA+GGG + chr4.2:22120251-22120270 None:intergenic 55.0%
GCGCACCCTCGTGCAAGATC+GGG - chr4.2:22120243-22120262 MS.gene39445:CDS 65.0%
GGCGCACCCTCGTGCAAGAT+CGG - chr4.2:22120242-22120261 MS.gene39445:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 22119038 22120285 22119038 ID=MS.gene39445
chr4.2 mRNA 22119038 22120285 22119038 ID=MS.gene39445.t1;Parent=MS.gene39445
chr4.2 exon 22119403 22120285 22119403 ID=MS.gene39445.t1.exon1;Parent=MS.gene39445.t1
chr4.2 CDS 22119403 22120285 22119403 ID=cds.MS.gene39445.t1;Parent=MS.gene39445.t1
chr4.2 exon 22119038 22119096 22119038 ID=MS.gene39445.t1.exon2;Parent=MS.gene39445.t1
chr4.2 CDS 22119038 22119096 22119038 ID=cds.MS.gene39445.t1;Parent=MS.gene39445.t1
Gene Sequence

>MS.gene39445

ATGGAAGGTGAACGAAAGAATAAGAGAGAAAACATGGAGGGTTCAAATCTTCCCGAAGAACTGTGGGCAATTATATCAAAAAAATTGAACACTACTATTGATGTTGTTCGATTCCGCAGTATCGATAGTTTATTTCGCTCTCTTCTTCCTACTCCATCTCCCTCTAACCGTCATTGTATTTCATATGATTGTTATTTTCTACTACAAACCAAAATATATCGCATTCAACCATCAACTTCTTCTCCATGTTCTAATAAAGGGTGGCTCATTAGAGTTTTTCAGTCGAATTCATCCAAACTTTATCTCCTTGATCTCTTCACTAACAAGAAACTCCGAACTGAAGAGACTATAAACAAAGTTTTGAATTTGATGAACTTTCGAGTTGTGGAGTTGTTTGAACTATATACTCCTAGTAATCTTAAAGGTGAAATTGATTTTAATTATTTTTGCAGCTTTTGCAAAGTAATCTTTTATTCCATTGAGGGTCATTGCATGGTCTTTGCACTGTATTGGGATAAGGTGATAGTTTCCAATATTGAAGAAACGACATATACCATGTTAGAGGACGATGGTGGAGAAAACCAGTGTCTTGATGATATGATACTTTACAAGGGACAACTTTATGTTGTGGATAAAATGGGAACAATATTCTGGTTTAATGCTTTGTCTTTCAAGTTGGTTCAATTTTCACCTAAAAACTTGTACTGTTGTGAAGAAAATGGGCATATAAGGGTGAATGCTTGTGAAAACAAAAAGCAATTAGTAGAGTATGATGGAAGTCTCTATGTAGTTGACTTGTATATTAATGATGAAAGATATTACAAATGGGGTTACTATTTGAAGGATGTTTTTGTGGAAGTTTATAAGCTTGATCAAGAATGGGGTAAATGGTTAAAAATAAAAGATTTGGGTGATGTTTCGTTTGTTTTGAGTAAAGACTCAAACTTTGCATTGTTGGCTCAAGATTATTATGGATGTGAAGGAAATTGCATCTATTTCTATTTTGATCACAAGGCTTCTTGTTTCAACTTGAAGAATTTAGAGACTAAGCCTGCTGACATTTTTTGGCCTTGTCCAACTTTGTTCCATCCTGTTACCAATTAATTTGTAAGTATAGTAATGCACATAAATATGATATATGGTTTTAGTGTCTTGTGGTGGTGACTTGTCTTTTTTAATATGTATACAGATTTAGATTCGGGATGGCGCACCCTCGTGCAAGATCGGGAAGAGTCAGCAATTCATTGA
Protein sequence

>MS.gene39445.t1

MEGERKNKRENMEGSNLPEELWAIISKKLNTTIDVVRFRSIDSLFRSLLPTPSPSNRHCISYDCYFLLQTKIYRIQPSTSSPCSNKGWLIRVFQSNSSKLYLLDLFTNKKLRTEETINKVLNLMNFRVVELFELYTPSNLKGEIDFNYFCSFCKVIFYSIEGHCMVFALYWDKVIVSNIEETTYTMLEDDGGENQCLDDMILYKGQLYVVDKMGTIFWFNALSFKLVQFSPKNLYCCEENGHIRVNACENKKQLVEYDGSLYVVDLYINDERYYKWGYYLKDVFVEVYKLDQEWDLDSGWRTLVQDREESAIH