AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49653

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49653.t1 MTR_5g037310 97.417 271 7 0 1 271 26 296 0.0 548
MS.gene49653.t1 MTR_5g037310 97.417 271 7 0 1 271 26 296 0.0 546
MS.gene49653.t1 MTR_8g090055 40.400 250 124 7 1 241 29 262 1.64e-53 176
MS.gene49653.t1 MTR_4g123700 31.276 243 151 8 2 241 34 263 6.34e-26 103
MS.gene49653.t1 MTR_4g105550 29.070 258 151 11 2 241 32 275 5.60e-22 93.2
MS.gene49653.t1 MTR_4g132450 29.572 257 148 11 1 241 37 276 4.06e-20 88.6
MS.gene49653.t1 MTR_2g023970 27.626 257 153 10 1 241 23 262 1.45e-17 81.3
MS.gene49653.t1 MTR_7g112440 27.273 198 120 8 5 197 24 202 6.38e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49653.t1 AT1G10380 53.430 277 119 7 2 271 29 302 1.11e-96 286
MS.gene49653.t1 AT1G10380 58.300 247 95 6 2 243 29 272 3.56e-94 280
MS.gene49653.t1 AT3G17350 33.333 246 145 9 2 239 31 265 5.81e-25 101
MS.gene49653.t1 AT3G17350 33.333 246 145 9 2 239 31 265 6.22e-25 100
MS.gene49653.t1 AT5G50290 31.373 255 150 11 2 241 22 266 1.65e-22 94.7
MS.gene49653.t1 AT1G11915 25.795 283 171 12 1 263 30 293 1.34e-16 78.6

Find 51 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATAGTCAATTGAGGTAAT+AGG 0.216590 5.1:+27965744 None:intergenic
ACAATCTACTAAAGCGAATA+TGG 0.279440 5.1:+27965611 None:intergenic
TTCACATCATCTTACAATAA+TGG 0.287235 5.1:-27965156 MS.gene49653:CDS
GTTCTTTGCCACAATTTCTT+TGG 0.298152 5.1:+27965877 None:intergenic
GAAGCGAGGGTCGCCGCAAC+CGG 0.304646 5.1:+27965827 None:intergenic
GTGCTATCGTCGAAAGTAAA+AGG 0.333825 5.1:+27965633 None:intergenic
CTTCAATGCAGTTCATATAC+AGG 0.342561 5.1:-27965384 MS.gene49653:CDS
CATAGTCAATTGAGGTAATA+GGG 0.351341 5.1:+27965745 None:intergenic
GTGATGTTATGTATTCTTGT+AGG 0.354020 5.1:-27965500 MS.gene49653:CDS
GATCCTCAAAAGTGGAACTA+TGG 0.374420 5.1:-27965333 MS.gene49653:CDS
TTCGGTAGCGGCCCCGGTTG+CGG 0.383447 5.1:-27965840 MS.gene49653:CDS
GCAAAGGCTTCGGCTTAGAT+TGG 0.390000 5.1:-27965662 MS.gene49653:CDS
AGGTTAATATTAGTACTAAT+AGG 0.427315 5.1:+27965477 None:intergenic
TACCCTTTCGGTAGCGGCCC+CGG 0.428105 5.1:-27965846 MS.gene49653:CDS
GTTTATACACCGGTTAATCT+TGG 0.430829 5.1:-27965435 MS.gene49653:CDS
TAAACACAACATGTCGAAAT+CGG 0.436820 5.1:+27965453 None:intergenic
GCTGCATGTGAAAGGAGCTT+TGG 0.444173 5.1:-27965258 MS.gene49653:CDS
AAGCGAGGGTCGCCGCAACC+GGG 0.448647 5.1:+27965828 None:intergenic
AACAAATTGATCCTCAAAAG+TGG 0.460285 5.1:-27965341 MS.gene49653:CDS
GTAGTGGTGTTAATTCCATT+AGG 0.460938 5.1:+27965189 None:intergenic
GAACCTCTCAAGTACCCTTT+CGG 0.476764 5.1:-27965858 MS.gene49653:CDS
AAAGCTGGACCAAGATTAAC+CGG 0.476906 5.1:+27965426 None:intergenic
TTGATTTGCATAGTCAATTG+AGG 0.482998 5.1:+27965737 None:intergenic
TGAAGATCCATATCAAAAGC+TGG 0.499024 5.1:+27965411 None:intergenic
ACCCTACCTAGCAAAGGCTT+CGG 0.503040 5.1:-27965672 MS.gene49653:CDS
TGTTGGCTGCAAGTTATATG+TGG 0.504485 5.1:+27965801 None:intergenic
AACCGGGGCCGCTACCGAAA+GGG 0.520766 5.1:+27965844 None:intergenic
CTCAAGTACCCTTTCGGTAG+CGG 0.533088 5.1:-27965852 MS.gene49653:CDS
CAACCGGGGCCGCTACCGAA+AGG 0.537917 5.1:+27965843 None:intergenic
GCCGAAGCCTTTGCTAGGTA+GGG 0.540178 5.1:+27965671 None:intergenic
AAATCAAGAAGTTATGATGA+TGG 0.541719 5.1:-27965564 MS.gene49653:CDS
CAAATGTGCCAAAGAAATTG+TGG 0.553792 5.1:-27965885 MS.gene49653:CDS
TTATATGTGGTTGGAAGCGA+GGG 0.559135 5.1:+27965814 None:intergenic
TCACATGCAGCACAAGAGCT+AGG 0.560587 5.1:+27965270 None:intergenic
AGCGAGGGTCGCCGCAACCG+GGG 0.560831 5.1:+27965829 None:intergenic
GACATGTTGTGTTTATACAC+CGG 0.561125 5.1:-27965445 MS.gene49653:CDS
GCTCTTGTGCTGCATGTGAA+AGG 0.562347 5.1:-27965266 MS.gene49653:CDS
GGCTGCAAGTTATATGTGGT+TGG 0.563811 5.1:+27965805 None:intergenic
GTTATATGTGGTTGGAAGCG+AGG 0.565909 5.1:+27965813 None:intergenic
GGAGCCTGTGTGTGTTGTGA+AGG 0.568111 5.1:+27965770 None:intergenic
AGCCGAAGCCTTTGCTAGGT+AGG 0.568732 5.1:+27965670 None:intergenic
TCTAAGCCGAAGCCTTTGCT+AGG 0.577620 5.1:+27965666 None:intergenic
CAAGAACATGTTGACATGGT+GGG 0.593775 5.1:+27965696 None:intergenic
CACAACATGTCGAAATCGGA+AGG 0.597606 5.1:+27965457 None:intergenic
CTCACCTTCACAACACACAC+AGG 0.609375 5.1:-27965774 MS.gene49653:CDS
GTCAATTGAGGTAATAGGGT+AGG 0.619560 5.1:+27965749 None:intergenic
CTACCGAAAGGGTACTTGAG+AGG 0.634715 5.1:+27965855 None:intergenic
TCTTGTACCCTACCTAGCAA+AGG 0.635014 5.1:-27965678 MS.gene49653:CDS
ACAAGAACATGTTGACATGG+TGG 0.661350 5.1:+27965695 None:intergenic
GGTACAAGAACATGTTGACA+TGG 0.681333 5.1:+27965692 None:intergenic
TGTGAAGAAACAATCTGTAG+TGG 0.691455 5.1:+27965173 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAATATTTTAAAATTATTAT+CGG - chr5.1:27965731-27965750 MS.gene49653:CDS 0.0%
!!! TAAGATTATTTTTTTTGAAA+AGG - chr5.1:27965624-27965643 MS.gene49653:CDS 10.0%
!! TAAAAATGAATGAAAAAAGT+AGG + chr5.1:27965800-27965819 None:intergenic 15.0%
!! AGGTTAATATTAGTACTAAT+AGG + chr5.1:27965212-27965231 None:intergenic 20.0%
!!! ACACTAAAATTTAAGATTAG+AGG - chr5.1:27965648-27965667 MS.gene49653:CDS 20.0%
!!! CACTAAAATTTAAGATTAGA+GGG - chr5.1:27965649-27965668 MS.gene49653:CDS 20.0%
!!! TACAATAATGGTTTTAGAAA+TGG - chr5.1:27965542-27965561 MS.gene49653:CDS 20.0%
! AAATCAAGAAGTTATGATGA+TGG - chr5.1:27965122-27965141 MS.gene49653:intron 25.0%
! ATGCAATTGACAAATAAGAA+AGG + chr5.1:27965583-27965602 None:intergenic 25.0%
! TGCAATTGACAAATAAGAAA+GGG + chr5.1:27965582-27965601 None:intergenic 25.0%
! TTCACATCATCTTACAATAA+TGG - chr5.1:27965530-27965549 MS.gene49653:CDS 25.0%
!!! TCATTTTTAATGACTTGTTC+TGG - chr5.1:27965811-27965830 MS.gene49653:CDS 25.0%
AACAAATTGATCCTCAAAAG+TGG - chr5.1:27965345-27965364 MS.gene49653:CDS 30.0%
ACAATCTACTAAAGCGAATA+TGG + chr5.1:27965078-27965097 None:intergenic 30.0%
ATTGAATGTAACAACTGTGT+TGG + chr5.1:27965711-27965730 None:intergenic 30.0%
CATAGTCAATTGAGGTAATA+GGG + chr5.1:27964944-27964963 None:intergenic 30.0%
GTGATGTTATGTATTCTTGT+AGG - chr5.1:27965186-27965205 MS.gene49653:CDS 30.0%
TAAACACAACATGTCGAAAT+CGG + chr5.1:27965236-27965255 None:intergenic 30.0%
! TATAGAGTACTACACAAACA+CGG + chr5.1:27965772-27965791 None:intergenic 30.0%
! TTTTTATGCAACTGTCCTAA+TGG - chr5.1:27965482-27965501 MS.gene49653:CDS 30.0%
!! ATTTTGATCACATTGAAGCT+TGG + chr5.1:27965156-27965175 None:intergenic 30.0%
!! TTGATTTGCATAGTCAATTG+AGG + chr5.1:27964952-27964971 None:intergenic 30.0%
CTTCAATGCAGTTCATATAC+AGG - chr5.1:27965302-27965321 MS.gene49653:CDS 35.0%
GACATGTTGTGTTTATACAC+CGG - chr5.1:27965241-27965260 MS.gene49653:CDS 35.0%
GCATAGTCAATTGAGGTAAT+AGG + chr5.1:27964945-27964964 None:intergenic 35.0%
GTTCTTTGCCACAATTTCTT+TGG + chr5.1:27964812-27964831 None:intergenic 35.0%
TGAAGATCCATATCAAAAGC+TGG + chr5.1:27965278-27965297 None:intergenic 35.0%
TGTGAAGAAACAATCTGTAG+TGG + chr5.1:27965516-27965535 None:intergenic 35.0%
! CTTTTGCATGGTCTTTGATT+AGG - chr5.1:27965870-27965889 MS.gene49653:CDS 35.0%
! GGATGATATATGCTTTTGCA+TGG - chr5.1:27965858-27965877 MS.gene49653:CDS 35.0%
! GTAGTGGTGTTAATTCCATT+AGG + chr5.1:27965500-27965519 None:intergenic 35.0%
! GTTTATACACCGGTTAATCT+TGG - chr5.1:27965251-27965270 MS.gene49653:CDS 35.0%
! TTGTGAAGGTGAGTTTTTGT+TGG + chr5.1:27964905-27964924 None:intergenic 35.0%
!! ATTATTATCGGTGTTGTGTC+AGG - chr5.1:27965743-27965762 MS.gene49653:CDS 35.0%
!! ATTCCATAGTTCCACTTTTG+AGG + chr5.1:27965359-27965378 None:intergenic 35.0%
AAAGCTGGACCAAGATTAAC+CGG + chr5.1:27965263-27965282 None:intergenic 40.0%
ACAAGAACATGTTGACATGG+TGG + chr5.1:27964994-27965013 None:intergenic 40.0%
AGCAAACCCTGAAAACAGAA+AGG + chr5.1:27965837-27965856 None:intergenic 40.0%
CAAGAACATGTTGACATGGT+GGG + chr5.1:27964993-27965012 None:intergenic 40.0%
GATCCTCAAAAGTGGAACTA+TGG - chr5.1:27965353-27965372 MS.gene49653:CDS 40.0%
GGTACAAGAACATGTTGACA+TGG + chr5.1:27964997-27965016 None:intergenic 40.0%
GTCAATTGAGGTAATAGGGT+AGG + chr5.1:27964940-27964959 None:intergenic 40.0%
GTGCTATCGTCGAAAGTAAA+AGG + chr5.1:27965056-27965075 None:intergenic 40.0%
TTATATGTGGTTGGAAGCGA+GGG + chr5.1:27964875-27964894 None:intergenic 40.0%
! TCTTGGTCCAGCTTTTGATA+TGG - chr5.1:27965268-27965287 MS.gene49653:CDS 40.0%
! TGTTGGCTGCAAGTTATATG+TGG + chr5.1:27964888-27964907 None:intergenic 40.0%
!! TTCTGGCCTTTCTGTTTTCA+GGG - chr5.1:27965828-27965847 MS.gene49653:CDS 40.0%
!! TTCTGTTTTCAGGGTTTGCT+TGG - chr5.1:27965837-27965856 MS.gene49653:CDS 40.0%
!!! GAAAGGAGCTTTGGATTTTG+TGG - chr5.1:27965437-27965456 MS.gene49653:CDS 40.0%
CACAACATGTCGAAATCGGA+AGG + chr5.1:27965232-27965251 None:intergenic 45.0%
GAACCTCTCAAGTACCCTTT+CGG - chr5.1:27964828-27964847 MS.gene49653:CDS 45.0%
GGCTGCAAGTTATATGTGGT+TGG + chr5.1:27964884-27964903 None:intergenic 45.0%
GTTATATGTGGTTGGAAGCG+AGG + chr5.1:27964876-27964895 None:intergenic 45.0%
TCTTGTACCCTACCTAGCAA+AGG - chr5.1:27965008-27965027 MS.gene49653:intron 45.0%
!! GTTCTGGCCTTTCTGTTTTC+AGG - chr5.1:27965827-27965846 MS.gene49653:CDS 45.0%
ACCCTACCTAGCAAAGGCTT+CGG - chr5.1:27965014-27965033 MS.gene49653:intron 50.0%
CTCAAGTACCCTTTCGGTAG+CGG - chr5.1:27964834-27964853 MS.gene49653:CDS 50.0%
CTCACCTTCACAACACACAC+AGG - chr5.1:27964912-27964931 MS.gene49653:intron 50.0%
GCAAAGGCTTCGGCTTAGAT+TGG - chr5.1:27965024-27965043 MS.gene49653:intron 50.0%
GCTCTTGTGCTGCATGTGAA+AGG - chr5.1:27965420-27965439 MS.gene49653:CDS 50.0%
GCTGCATGTGAAAGGAGCTT+TGG - chr5.1:27965428-27965447 MS.gene49653:CDS 50.0%
TCACATGCAGCACAAGAGCT+AGG + chr5.1:27965419-27965438 None:intergenic 50.0%
TCTAAGCCGAAGCCTTTGCT+AGG + chr5.1:27965023-27965042 None:intergenic 50.0%
!! CTACCGAAAGGGTACTTGAG+AGG + chr5.1:27964834-27964853 None:intergenic 50.0%
AGCCGAAGCCTTTGCTAGGT+AGG + chr5.1:27965019-27965038 None:intergenic 55.0%
GCCGAAGCCTTTGCTAGGTA+GGG + chr5.1:27965018-27965037 None:intergenic 55.0%
GGAGCCTGTGTGTGTTGTGA+AGG + chr5.1:27964919-27964938 None:intergenic 55.0%
AACCGGGGCCGCTACCGAAA+GGG + chr5.1:27964845-27964864 None:intergenic 65.0%
! TACCCTTTCGGTAGCGGCCC+CGG - chr5.1:27964840-27964859 MS.gene49653:CDS 65.0%
AAGCGAGGGTCGCCGCAACC+GGG + chr5.1:27964861-27964880 None:intergenic 70.0%
CAACCGGGGCCGCTACCGAA+AGG + chr5.1:27964846-27964865 None:intergenic 70.0%
GAAGCGAGGGTCGCCGCAAC+CGG + chr5.1:27964862-27964881 None:intergenic 70.0%
! TTCGGTAGCGGCCCCGGTTG+CGG - chr5.1:27964846-27964865 MS.gene49653:intron 70.0%
AGCGAGGGTCGCCGCAACCG+GGG + chr5.1:27964860-27964879 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 27964804 27965904 27964804 ID=MS.gene49653
chr5.1 mRNA 27964804 27965904 27964804 ID=MS.gene49653.t1;Parent=MS.gene49653
chr5.1 exon 27965145 27965904 27965145 ID=MS.gene49653.t1.exon1;Parent=MS.gene49653.t1
chr5.1 CDS 27965145 27965904 27965145 ID=cds.MS.gene49653.t1;Parent=MS.gene49653.t1
chr5.1 exon 27964804 27964859 27964804 ID=MS.gene49653.t1.exon2;Parent=MS.gene49653.t1
chr5.1 CDS 27964804 27964859 27964804 ID=cds.MS.gene49653.t1;Parent=MS.gene49653.t1
Gene Sequence

>MS.gene49653

ATGTGCCAAAGAAATTGTGGCAAAGAACCTCTCAAGTACCCTTTCGGTAGCGGCCCCGGTTGCGGCGACCCTCGCTTCCAACCACATATAACTTGCAGCCAACAAAAACTCACCTTCACAACACACACAGGCTCCTACCCTATTACCTCAATTGACTATGCAAATCAAGTCATATACATTTCAGATCCCACCATGTCAACATGTTCTTGTACCCTACCTAGCAAAGGCTTCGGCTTAGATTGGAACGCGCCTTTTACTTTCGACGATAGCACCATATTCGCTTTAGTAGATTGTTCGATGAACTCATCATCGATATGTAAATCAAGAAGTTATGATGATGGAAGCAATTCCAAGCTTCAATGTGATCAAAATACACAAATTTGTGATGTTATGTATTCTTGTAGGCCTATTAGTACTAATATTAACCTTCCGATTTCGACATGTTGTGTTTATACACCGGTTAATCTTGGTCCAGCTTTTGATATGGATCTTCAAAAGCTTCAATGCAGTTCATATACAGGTTTTTACAATTACAATGATCAACAAATTGATCCTCAAAAGTGGAACTATGGAATTGCACTTAAGTATAAGTTTAGTGTTACAAATGATTATCCTAGCTCTTGTGCTGCATGTGAAAGGAGCTTTGGATTTTGTGGATATAGTGAAGTTTATAATTCATTTTTATGCAACTGTCCTAATGGAATTAACACCACTACAGATTGTTTCTTCACATCATCTTACAATAATGGTTTTAGAAATGGTAAGCAAAGTTATTCCCTTTCTTATTTGTCAATTGCATCATCTATATAACACTAGTATTTAAGATTATTTTTTTTGAAAAGGAACACTAAAATTTAAGATTAGAGGGTGTCTACACGTGTCTGTGTCAAACACTGATATGACACCAACACAGTTGTTACATTCAATTAATATTTTAAAATTATTATCGGTGTTGTGTCAGGTTTCCGTGTTTGTGTAGTACTCTATAAGTAGCCTACTTTTTTCATTCATTTTTAATGACTTGTTCTGGCCTTTCTGTTTTCAGGGTTTGCTTGGATGATATATGCTTTTGCATGGTCTTTGATTAGGCTCATCTTATAA
Protein sequence

>MS.gene49653.t1

MCQRNCGKEPLKYPFGSGPGCGDPRFQPHITCSQQKLTFTTHTGSYPITSIDYANQVIYISDPTMSTCSCTLPSKGFGLDWNAPFTFDDSTIFALVDCSMNSSSICKSRSYDDGSNSKLQCDQNTQICDVMYSCRPISTNINLPISTCCVYTPVNLGPAFDMDLQKLQCSSYTGFYNYNDQQIDPQKWNYGIALKYKFSVTNDYPSSCAACERSFGFCGYSEVYNSFLCNCPNGINTTTDCFFTSSYNNGFRNGFAWMIYAFAWSLIRLIL