AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54192


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54192.t1 MTR_5g013530 86.413 184 14 3 1 184 1 173 6.28e-111 313
MS.gene54192.t1 MTR_5g013530 85.897 156 11 3 29 184 7 151 9.88e-90 259
MS.gene54192.t1 MTR_5g013520 83.553 152 18 3 30 181 1 145 9.39e-87 251
MS.gene54192.t1 MTR_5g013515 71.034 145 27 5 31 168 1 137 6.14e-64 193
MS.gene54192.t1 MTR_2g042900 47.273 165 43 7 25 163 99 245 8.82e-35 123
MS.gene54192.t1 MTR_2g042900 37.500 168 39 7 25 136 99 256 1.29e-19 83.6
MS.gene54192.t1 MTR_2g044910 30.172 116 72 1 40 146 11 126 2.42e-13 65.1
MS.gene54192.t1 MTR_2g044910 30.172 116 72 1 40 146 54 169 5.45e-13 64.7
MS.gene54192.t1 MTR_8g021380 31.298 131 84 3 19 144 79 208 6.72e-13 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54192.t1 AT1G19180 43.284 134 70 4 37 166 53 184 1.33e-27 102
MS.gene54192.t1 AT1G19180 43.284 134 70 4 37 166 119 250 9.75e-27 102
MS.gene54192.t1 AT1G19180 43.284 134 70 4 37 166 119 250 9.75e-27 102
MS.gene54192.t1 AT1G74950 39.130 138 72 3 37 164 112 247 1.66e-22 91.3
MS.gene54192.t1 AT1G74950 40.000 110 56 2 37 136 112 221 3.38e-17 76.6
MS.gene54192.t1 AT1G17380 35.714 126 73 2 33 150 58 183 9.19e-16 73.2
MS.gene54192.t1 AT1G72450 36.066 122 66 3 39 152 101 218 1.52e-15 72.8
MS.gene54192.t1 AT1G17380 35.714 126 73 2 33 150 87 212 2.75e-15 72.0
MS.gene54192.t1 AT5G20900 37.719 114 58 3 44 147 57 167 7.38e-15 69.7
MS.gene54192.t1 AT1G70700 36.538 104 62 2 44 144 119 221 2.01e-12 63.9
MS.gene54192.t1 AT1G17380 33.929 112 66 2 33 136 87 198 5.28e-11 59.7
MS.gene54192.t1 AT4G14720 33.121 157 85 7 40 181 153 304 6.75e-11 60.1
MS.gene54192.t1 AT4G14720 33.121 157 85 7 40 181 153 304 6.91e-11 60.5

Find 38 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTACAAGAGATTCCTAATT+TGG 0.066386 5.1:+6429613 MS.gene54192:CDS
CCATCTATACCTGTTATTTA+TGG 0.164541 5.1:+6430016 MS.gene54192:CDS
ATTCATCAATTGACTTATTT+AGG 0.185988 5.1:-6431051 None:intergenic
AGCTTCACTTCATCGGTTCT+TGG 0.292747 5.1:+6430160 MS.gene54192:CDS
TACCTGGAGTTTCCCAAATT+AGG 0.318968 5.1:-6429626 None:intergenic
CCAAATTAGGAATCTCTTGT+AGG 0.328797 5.1:-6429613 None:intergenic
CTACAAGAGATTCCTAATTT+GGG 0.331956 5.1:+6429614 MS.gene54192:CDS
GGAAAAGTCCATGATGTCTT+TGG 0.411671 5.1:-6429879 None:intergenic
ATGTCTTTGGCTTTATCAGC+TGG 0.417227 5.1:-6429866 None:intergenic
GCTGGATTACTTGTTTGATA+AGG 0.423471 5.1:-6431022 None:intergenic
AGTGAAGCTTTCCTAGTCAT+TGG 0.425048 5.1:-6430146 None:intergenic
GACTTATTTAGGAATGCTGC+TGG 0.431039 5.1:-6431040 None:intergenic
GTAGTCTTGAAGAGAATTGT+TGG 0.442893 5.1:-6429984 None:intergenic
CAAATGACAATCTTCTATGA+TGG 0.453411 5.1:+6429818 MS.gene54192:CDS
TGAAGTACTAGTAATTCCTT+TGG 0.455465 5.1:-6429903 None:intergenic
TTCATCGGTTCTTGGAGAAA+AGG 0.463618 5.1:+6430168 MS.gene54192:CDS
GGAAGCTGTTGAAAATTCAT+AGG 0.469618 5.1:-6429581 None:intergenic
CCATAAATAACAGGTATAGA+TGG 0.477854 5.1:-6430016 None:intergenic
AGTACTAGTAATTCCTTTGG+TGG 0.499055 5.1:-6429900 None:intergenic
ATCCATGTCATGGCTATCCT+TGG 0.509457 5.1:+6431072 MS.gene54192:CDS
AGCAAGCATAGTTGTTATTG+TGG 0.514503 5.1:-6429937 None:intergenic
TTCCTAATTTGGGAAACTCC+AGG 0.526778 5.1:+6429624 MS.gene54192:CDS
CTAGGAAAGCTTCACTTCAT+CGG 0.529148 5.1:+6430153 MS.gene54192:CDS
AAATGACAATCTTCTATGAT+GGG 0.538308 5.1:+6429819 MS.gene54192:CDS
CTACATTTAGATTTGTGTTG+CGG 0.547996 5.1:-6431106 None:intergenic
AATGAAGGCTAATATTAAGA+AGG 0.556826 5.1:+6429778 MS.gene54192:CDS
ATCTCTTGTAGGAAGAGATG+AGG 0.564072 5.1:-6429602 None:intergenic
GGCTAATATTAAGAAGGAAG+AGG 0.566182 5.1:+6429784 MS.gene54192:CDS
TCTTGGAGAAAAGGAAGGAT+AGG 0.567398 5.1:+6430177 MS.gene54192:CDS
TGATAAAGCCAAAGACATCA+TGG 0.585378 5.1:+6429871 MS.gene54192:CDS
TCGGTTCTTGGAGAAAAGGA+AGG 0.585705 5.1:+6430172 MS.gene54192:CDS
GTTTCTGCAGAATTGCTGCA+AGG 0.606526 5.1:+6430996 MS.gene54192:intron
ATTCAGATTTACCAATGACT+AGG 0.608086 5.1:+6430135 MS.gene54192:intron
TTTCTGCAGAATTGCTGCAA+GGG 0.611240 5.1:+6430997 MS.gene54192:intron
CAATTGATGAATCCATGTCA+TGG 0.612586 5.1:+6431062 MS.gene54192:CDS
TGCCAAGGATAGCCATGACA+TGG 0.617530 5.1:-6431074 None:intergenic
GATTTGTGTTGCGGTGAATG+TGG 0.627153 5.1:-6431097 None:intergenic
TTGCGGTGAATGTGGTGCCA+AGG 0.648709 5.1:-6431089 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATTTATGGTAATTTTTTT+TGG + chr5.1:6430029-6430048 MS.gene54192:intron 10.0%
!! AAAAAATTACCATAAATAAC+AGG - chr5.1:6430028-6430047 None:intergenic 15.0%
!!! TACACTATTATAATCAATTT+TGG + chr5.1:6430790-6430809 MS.gene54192:intron 15.0%
!!! TGATAGATAAATCAATTTTA+AGG + chr5.1:6430435-6430454 MS.gene54192:intron 15.0%
!!! TTTTTGTTTATAATAGTGAT+TGG + chr5.1:6430556-6430575 MS.gene54192:intron 15.0%
!! GATAACCAATTTACTAAAAT+TGG - chr5.1:6430886-6430905 None:intergenic 20.0%
!! TATTGCTAAAAATATGTTGA+TGG - chr5.1:6429685-6429704 None:intergenic 20.0%
!!! AATTTTAAGGAACCAATTTT+AGG + chr5.1:6430448-6430467 MS.gene54192:intron 20.0%
!!! AGTGTAATTTTGTGTATTTT+AGG + chr5.1:6430404-6430423 MS.gene54192:intron 20.0%
!!! ATTCATCAATTGACTTATTT+AGG - chr5.1:6431054-6431073 None:intergenic 20.0%
!!! TATAGTTTTTTTCTCTACAT+TGG - chr5.1:6430670-6430689 None:intergenic 20.0%
! AAAAAAAAAGAACATGTACC+TGG - chr5.1:6429645-6429664 None:intergenic 25.0%
! AAACATCATACTAGTAGAAA+AGG - chr5.1:6430942-6430961 None:intergenic 25.0%
! AAATGACAATCTTCTATGAT+GGG + chr5.1:6429819-6429838 MS.gene54192:CDS 25.0%
! AACATACTACTTAACAATTG+AGG - chr5.1:6430273-6430292 None:intergenic 25.0%
! AACATCATACTAGTAGAAAA+GGG - chr5.1:6430941-6430960 None:intergenic 25.0%
! AAGTAGTATGTTTGATTCTA+CGG + chr5.1:6430281-6430300 MS.gene54192:intron 25.0%
! AATGAAGGCTAATATTAAGA+AGG + chr5.1:6429778-6429797 MS.gene54192:CDS 25.0%
! GTTACAAAAATTGATTGAAC+TGG + chr5.1:6430303-6430322 MS.gene54192:intron 25.0%
! TCCTCTCAAAACTATATATA+TGG + chr5.1:6430911-6430930 MS.gene54192:intron 25.0%
! TGGATATATTATGTTTGAGA+GGG + chr5.1:6430049-6430068 MS.gene54192:intron 25.0%
! TTATAGTTTCAATCAGTTTC+TGG + chr5.1:6430692-6430711 MS.gene54192:intron 25.0%
! TTGCGTTTATATAATAGTGA+CGG - chr5.1:6430482-6430501 None:intergenic 25.0%
! TTGGATATATTATGTTTGAG+AGG + chr5.1:6430048-6430067 MS.gene54192:intron 25.0%
!! TTTTCTACTAGTATGATGTT+TGG + chr5.1:6430941-6430960 MS.gene54192:intron 25.0%
!! TTTTCTCTACATTGGATTTT+TGG - chr5.1:6430662-6430681 None:intergenic 25.0%
!!! ATATAGTTTTGAGAGGATAA+CGG - chr5.1:6430908-6430927 None:intergenic 25.0%
ATATTTGATTGAGAGAGATC+TGG - chr5.1:6430211-6430230 None:intergenic 30.0%
ATCCAAATTCTCTACCTTTA+AGG - chr5.1:6430639-6430658 None:intergenic 30.0%
ATTCAGATTTACCAATGACT+AGG + chr5.1:6430135-6430154 MS.gene54192:intron 30.0%
ATTCATGCTAGTATATAGCA+TGG + chr5.1:6429710-6429729 MS.gene54192:intron 30.0%
CAAATGACAATCTTCTATGA+TGG + chr5.1:6429818-6429837 MS.gene54192:CDS 30.0%
CCATAAATAACAGGTATAGA+TGG - chr5.1:6430019-6430038 None:intergenic 30.0%
CTACAAGAGATTCCTAATTT+GGG + chr5.1:6429614-6429633 MS.gene54192:CDS 30.0%
CTACATTTAGATTTGTGTTG+CGG - chr5.1:6431109-6431128 None:intergenic 30.0%
GACAAACTTATCAGTCAATA+TGG - chr5.1:6430973-6430992 None:intergenic 30.0%
TGCGTTTATATAATAGTGAC+GGG - chr5.1:6430481-6430500 None:intergenic 30.0%
! CCATCTATACCTGTTATTTA+TGG + chr5.1:6430016-6430035 MS.gene54192:CDS 30.0%
! GTGATTTTGCTAAAAGTGAA+TGG + chr5.1:6430336-6430355 MS.gene54192:intron 30.0%
! TGAAGTACTAGTAATTCCTT+TGG - chr5.1:6429906-6429925 None:intergenic 30.0%
! TTTATATAATAGTGACGGGA+TGG - chr5.1:6430477-6430496 None:intergenic 30.0%
!! AGGAGCCAATTTTAGTAAAT+TGG + chr5.1:6430878-6430897 MS.gene54192:intron 30.0%
!! GTTTTATTACAGTGCAATGA+AGG + chr5.1:6429763-6429782 MS.gene54192:intron 30.0%
!!! GCCATATATATAGTTTTGAG+AGG - chr5.1:6430915-6430934 None:intergenic 30.0%
!!! GTCAATAGACTTCACTTTTT+AGG + chr5.1:6430243-6430262 MS.gene54192:intron 30.0%
AGATATAGTGACTTTGGTGA+TGG + chr5.1:6430363-6430382 MS.gene54192:intron 35.0%
AGTACTAGTAATTCCTTTGG+TGG - chr5.1:6429903-6429922 None:intergenic 35.0%
CAATTGATGAATCCATGTCA+TGG + chr5.1:6431062-6431081 MS.gene54192:CDS 35.0%
CCAAATTAGGAATCTCTTGT+AGG - chr5.1:6429616-6429635 None:intergenic 35.0%
CCTACAAGAGATTCCTAATT+TGG + chr5.1:6429613-6429632 MS.gene54192:CDS 35.0%
CTACAAAAATAACACAGAGG+TGG - chr5.1:6431134-6431153 None:intergenic 35.0%
GATACCATGAACAAAAGTGA+AGG + chr5.1:6430858-6430877 MS.gene54192:intron 35.0%
GCTGGATTACTTGTTTGATA+AGG - chr5.1:6431025-6431044 None:intergenic 35.0%
GGAAGCTGTTGAAAATTCAT+AGG - chr5.1:6429584-6429603 None:intergenic 35.0%
GGATTGAGATATAGTGACTT+TGG + chr5.1:6430357-6430376 MS.gene54192:intron 35.0%
GGCTAATATTAAGAAGGAAG+AGG + chr5.1:6429784-6429803 MS.gene54192:CDS 35.0%
TGATAAAGCCAAAGACATCA+TGG + chr5.1:6429871-6429890 MS.gene54192:CDS 35.0%
TTAAGGCGAAAAAGTCATCA+TGG - chr5.1:6430622-6430641 None:intergenic 35.0%
! AGCAAGCATAGTTGTTATTG+TGG - chr5.1:6429940-6429959 None:intergenic 35.0%
! GATATAGTGACTTTGGTGAT+GGG + chr5.1:6430364-6430383 MS.gene54192:intron 35.0%
! GTAGTCTTGAAGAGAATTGT+TGG - chr5.1:6429987-6430006 None:intergenic 35.0%
!!! TGATGACTTTTTCGCCTTAA+AGG + chr5.1:6430622-6430641 MS.gene54192:intron 35.0%
AGTGAAGCTTTCCTAGTCAT+TGG - chr5.1:6430149-6430168 None:intergenic 40.0%
ATCTCTTGTAGGAAGAGATG+AGG - chr5.1:6429605-6429624 None:intergenic 40.0%
CGCCTTAAAGGTAGAGAATT+TGG + chr5.1:6430634-6430653 MS.gene54192:intron 40.0%
CTAGGAAAGCTTCACTTCAT+CGG + chr5.1:6430153-6430172 MS.gene54192:CDS 40.0%
GACTTATTTAGGAATGCTGC+TGG - chr5.1:6431043-6431062 None:intergenic 40.0%
GGAAAAGTCCATGATGTCTT+TGG - chr5.1:6429882-6429901 None:intergenic 40.0%
TACCTGGAGTTTCCCAAATT+AGG - chr5.1:6429629-6429648 None:intergenic 40.0%
TCTTGGAGAAAAGGAAGGAT+AGG + chr5.1:6430177-6430196 MS.gene54192:CDS 40.0%
TTCCTAATTTGGGAAACTCC+AGG + chr5.1:6429624-6429643 MS.gene54192:CDS 40.0%
TTTCTGCAGAATTGCTGCAA+GGG + chr5.1:6430997-6431016 MS.gene54192:intron 40.0%
! ATCATGGACTTTTCCACCAA+AGG + chr5.1:6429887-6429906 MS.gene54192:CDS 40.0%
!! AGGGTGTTTGATTTGTGTCA+TGG + chr5.1:6430068-6430087 MS.gene54192:intron 40.0%
!! ATGTCTTTGGCTTTATCAGC+TGG - chr5.1:6429869-6429888 None:intergenic 40.0%
!! TTCATCGGTTCTTGGAGAAA+AGG + chr5.1:6430168-6430187 MS.gene54192:CDS 40.0%
ACGGGATGGAGTCCTAAAAT+TGG - chr5.1:6430463-6430482 None:intergenic 45.0%
ATCCATGTCATGGCTATCCT+TGG + chr5.1:6431072-6431091 MS.gene54192:CDS 45.0%
GACATGACTCAGTGTATCCT+CGG - chr5.1:6430833-6430852 None:intergenic 45.0%
GATTTGTGTTGCGGTGAATG+TGG - chr5.1:6431100-6431119 None:intergenic 45.0%
GTTTCTGCAGAATTGCTGCA+AGG + chr5.1:6430996-6431015 MS.gene54192:intron 45.0%
TCGGTTCTTGGAGAAAAGGA+AGG + chr5.1:6430172-6430191 MS.gene54192:CDS 45.0%
TTGATTGAGAGAGATCTGGC+AGG - chr5.1:6430207-6430226 None:intergenic 45.0%
!! AGCTTCACTTCATCGGTTCT+TGG + chr5.1:6430160-6430179 MS.gene54192:CDS 45.0%
!! GGCTCCTTCACTTTTGTTCA+TGG - chr5.1:6430865-6430884 None:intergenic 45.0%
TGCCAAGGATAGCCATGACA+TGG - chr5.1:6431077-6431096 None:intergenic 50.0%
! TGTATCCTCGGCTCGACTTT+AGG - chr5.1:6430821-6430840 None:intergenic 50.0%
CTCATCCTAAAGTCGAGCCG+AGG + chr5.1:6430813-6430832 MS.gene54192:intron 55.0%
! TTGCGGTGAATGTGGTGCCA+AGG - chr5.1:6431092-6431111 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 6429560 6431153 6429560 ID=MS.gene54192
chr5.1 mRNA 6429560 6431153 6429560 ID=MS.gene54192.t1;Parent=MS.gene54192
chr5.1 exon 6429560 6429645 6429560 ID=MS.gene54192.t1.exon1;Parent=MS.gene54192.t1
chr5.1 CDS 6429560 6429645 6429560 ID=cds.MS.gene54192.t1;Parent=MS.gene54192.t1
chr5.1 exon 6429775 6430037 6429775 ID=MS.gene54192.t1.exon2;Parent=MS.gene54192.t1
chr5.1 CDS 6429775 6430037 6429775 ID=cds.MS.gene54192.t1;Parent=MS.gene54192.t1
chr5.1 exon 6430141 6430198 6430141 ID=MS.gene54192.t1.exon3;Parent=MS.gene54192.t1
chr5.1 CDS 6430141 6430198 6430141 ID=cds.MS.gene54192.t1;Parent=MS.gene54192.t1
chr5.1 exon 6431006 6431153 6431006 ID=MS.gene54192.t1.exon4;Parent=MS.gene54192.t1
chr5.1 CDS 6431006 6431153 6431006 ID=cds.MS.gene54192.t1;Parent=MS.gene54192.t1
Gene Sequence

>MS.gene54192

ATGAAGCATCACAACATAACACCTATGAATTTTCAACAGCTTCCTCATCTCTTCCTACAAGAGATTCCTAATTTGGGAAACTCCAGGTACATGTTCTTTTTTTTTACTTTAACTTGTTAAGTCCATCAACATATTTTTAGCAATATTCAAATTCATGCTAGTATATAGCATGGTCAATTTGCATTAAATTAATTGTTAATGTTGTTTTATTACAGTGCAATGAAGGCTAATATTAAGAAGGAAGAGGCTAGATGTGCACAAATGACAATCTTCTATGATGGGAAAGTAATTGTGTTTGATGATGTTCCAGCTGATAAAGCCAAAGACATCATGGACTTTTCCACCAAAGGAATTACTAGTACTTCACAAGCACAAAACCACAATAACAACTATGCTTGCTCTTCATTTCTTGCTAGAAATTCTGCCAACAATTCTCTTCAAGACTACTATCAAGTACCATCTATACCTGTTATTTATGGTAATTTTTTTTGGATATATTATGTTTGAGAGGGTGTTTGATTTGTGTCATGGTTTTGTTTTTTGTGTGTTTTTAACTCATGAAATTATTTTTATGTATTCAGATTTACCAATGACTAGGAAAGCTTCACTTCATCGGTTCTTGGAGAAAAGGAAGGATAGGTAAGCCTGCCAGATCTCTCTCAATCAAATATTGTTTGATCTTTGTCAATAGACTTCACTTTTTAGGAAAACCTCAATTGTTAAGTAGTATGTTTGATTCTACGGTTACAAAAATTGATTGAACTGGTTATTTAAAAGTGATTTTGCTAAAAGTGAATGGATTGAGATATAGTGACTTTGGTGATGGGAAAGTAATTATTACTATAGTGTAATTTTGTGTATTTTAGGAAAGAAAATGATAGATAAATCAATTTTAAGGAACCAATTTTAGGACTCCATCCCGTCACTATTATATAAACGCAAAAAATCACTTTTAAATTTATTCAATAATGTATTGAATGAATCTTAAAAGTTGTTTTTTTGTTTATAATAGTGATTGGATGAAGTATATATATATAAAAGTGAAAGATAAACACAAAGCCATGATGACTTTTTCGCCTTAAAGGTAGAGAATTTGGATCCAAAAATCCAATGTAGAGAAAAAAACTATAAATTATAGTTTCAATCAGTTTCTGGAAGCAAAATCAATTTCACTTCAAAAACATTCAAACATTTGTTTTTGAAAGAAAGAAAACATGTCAAAATCAATTCTACACTATTATAATCAATTTTGGCTCATCCTAAAGTCGAGCCGAGGATACACTGAGTCATGTCAAATTGATACCATGAACAAAAGTGAAGGAGCCAATTTTAGTAAATTGGTTATCCGTTATCCTCTCAAAACTATATATATGGCTGACCCTTTTCTACTAGTATGATGTTTGGAATTATCCATATTGACTGATAAGTTTGTCTATGTTTCTGCAGAATTGCTGCAAGGGCACCTTATCAAACAAGTAATCCAGCAGCATTCCTAAATAAGTCAATTGATGAATCCATGTCATGGCTATCCTTGGCACCACATTCACCGCAACACAAATCTAAATGTAGCTCCACCTCTGTGTTATTTTTGTAG

Protein sequence

>MS.gene54192.t1

MKHHNITPMNFQQLPHLFLQEIPNLGNSSAMKANIKKEEARCAQMTIFYDGKVIVFDDVPADKAKDIMDFSTKGITSTSQAQNHNNNYACSSFLARNSANNSLQDYYQVPSIPVIYDLPMTRKASLHRFLEKRKDRIAARAPYQTSNPAAFLNKSIDESMSWLSLAPHSPQHKSKCSSTSVLFL