AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene40164

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40164.t1 MTR_4g091910 96.667 210 7 0 1 210 1 210 7.10e-151 417
MS.gene40164.t1 MTR_4g091990 47.867 211 90 4 1 209 1 193 2.77e-60 187
MS.gene40164.t1 MTR_8g064700 31.429 175 106 3 42 202 239 413 1.15e-19 86.3
MS.gene40164.t1 MTR_1g112680 30.526 190 92 4 27 183 304 486 8.73e-18 81.3
MS.gene40164.t1 MTR_2g084280 31.737 167 109 3 37 198 121 287 1.07e-15 74.3
MS.gene40164.t1 MTR_4g057270 29.940 167 96 5 46 197 148 308 2.22e-15 73.9
MS.gene40164.t1 MTR_2g038040 27.108 166 103 2 45 192 50 215 1.31e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40164.t1 AT4G21330 45.283 159 75 2 44 192 29 185 8.18e-39 133
MS.gene40164.t1 AT2G16910 32.298 161 82 3 46 179 313 473 9.62e-18 81.3
MS.gene40164.t1 AT5G57150 30.769 169 103 3 38 192 46 214 1.71e-14 69.7
MS.gene40164.t1 AT5G57150 30.769 169 103 3 38 192 45 213 1.92e-14 69.7
MS.gene40164.t1 AT5G57150 30.769 169 103 3 38 192 46 214 2.10e-14 69.7
MS.gene40164.t1 AT5G57150 30.769 169 103 3 38 192 45 213 3.38e-14 69.7
MS.gene40164.t1 AT5G57150 30.769 169 103 3 38 192 46 214 4.37e-14 69.3
MS.gene40164.t1 AT2G28160 27.869 183 119 5 21 191 103 284 6.81e-13 66.6
MS.gene40164.t1 AT2G28160 27.869 183 119 5 21 191 103 284 7.90e-13 66.6
MS.gene40164.t1 AT1G10610 28.571 147 96 1 44 181 231 377 7.99e-13 67.0
MS.gene40164.t1 AT1G10610 28.571 147 96 1 44 181 261 407 1.00e-12 66.6
MS.gene40164.t1 AT1G10610 28.571 147 96 1 44 181 164 310 1.39e-12 65.9
MS.gene40164.t1 AT1G12860 29.870 154 93 2 46 186 266 417 2.82e-12 65.5
MS.gene40164.t1 AT1G12860 29.870 154 93 2 46 186 266 417 2.92e-12 65.1
MS.gene40164.t1 AT3G26744 30.769 156 93 3 46 186 306 461 2.50e-11 62.4
MS.gene40164.t1 AT3G26744 30.769 156 93 3 46 186 306 461 2.58e-11 62.4
MS.gene40164.t1 AT3G26744 30.769 156 93 3 46 186 306 461 2.58e-11 62.4
MS.gene40164.t1 AT3G26744 30.769 156 93 3 46 186 306 461 2.58e-11 62.4
MS.gene40164.t1 AT4G37850 31.818 154 80 4 51 188 156 300 2.82e-11 62.0
MS.gene40164.t1 AT4G37850 31.818 154 80 4 51 188 156 300 2.82e-11 62.0

Find 43 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCAACTATTATCAAGTATT+AGG 0.172705 4.2:+20609350 MS.gene40164:CDS
TCTTTCTGTCTCAAGGTTCT+TGG 0.203142 4.2:-20608186 None:intergenic
TTCTTGGATGTGAACACTTT+TGG 0.236396 4.2:-20608170 None:intergenic
GATGAATAAAATGGGGTTAC+AGG 0.250695 4.2:+20608841 MS.gene40164:CDS
AACTTCATGTTGCAACTTCA+TGG 0.287708 4.2:-20608729 None:intergenic
TGTTGATGAGATGAATAAAA+TGG 0.288149 4.2:+20608832 MS.gene40164:CDS
TTGGGTTTCAATGCTGAAAA+TGG 0.303250 4.2:+20608095 MS.gene40164:CDS
GCAGAAGACTCTCTTTGTTT+TGG 0.306313 4.2:-20608809 None:intergenic
CCAACTATTATCAAGTATTA+GGG 0.313449 4.2:+20609351 MS.gene40164:CDS
CCCTAATACTTGATAATAGT+TGG 0.313701 4.2:-20609351 None:intergenic
CAATAGACTATGTGTGTCTA+TGG 0.334837 4.2:+20608067 MS.gene40164:CDS
TTCTCTTTCTTTCTGTCTCA+AGG 0.354427 4.2:-20608193 None:intergenic
ATGCTGAAAATGGTAGCAAT+AGG 0.358285 4.2:+20608105 MS.gene40164:CDS
TCTCATTACAGCCTCCTTGC+AGG 0.362149 4.2:+20609112 MS.gene40164:CDS
ATGGTAGCAATAGGGGAAAC+TGG 0.388089 4.2:+20608114 MS.gene40164:CDS
GAAACTCACTAGCAGACTTT+TGG 0.388264 4.2:+20608220 MS.gene40164:CDS
GTGCTTACATTTGTGATGAT+TGG 0.399278 4.2:-20608260 None:intergenic
TGCTGAAAATGGTAGCAATA+GGG 0.418097 4.2:+20608106 MS.gene40164:CDS
GTTGATGAGATGAATAAAAT+GGG 0.433684 4.2:+20608833 MS.gene40164:CDS
AGACCTCAGTGTTACTACTA+TGG 0.457876 4.2:+20609079 MS.gene40164:CDS
GAATGATTTGAACATTGAAA+TGG 0.483853 4.2:+20609055 MS.gene40164:CDS
CACAATAGAGCTTGATGGAA+TGG 0.493719 4.2:+20608760 MS.gene40164:CDS
AGTCTCACAATAGAGCTTGA+TGG 0.495480 4.2:+20608755 MS.gene40164:CDS
GTGCAGGTAGCAAAAGTTGA+TGG 0.518362 4.2:+20608963 MS.gene40164:CDS
ATGCTCATTGAGAAGAAAAG+AGG 0.521277 4.2:+20609005 MS.gene40164:CDS
ATGTGTGTCTATGGAAGAGT+TGG 0.537161 4.2:+20608076 MS.gene40164:CDS
GAACAAAGCAAGCATTATTG+AGG 0.548126 4.2:+20608691 MS.gene40164:CDS
CTTTCTATAGGAAGAGGTGC+AGG 0.549579 4.2:+20608947 MS.gene40164:intron
CTCAGTGTTACTACTATGGC+AGG 0.550252 4.2:+20609083 MS.gene40164:CDS
GCTGAAAATGGTAGCAATAG+GGG 0.556414 4.2:+20608107 MS.gene40164:CDS
GGAATTCGATAAAGTTCAAG+TGG 0.574985 4.2:-20609330 None:intergenic
AATTTATAGTGTCACCTGCA+AGG 0.580808 4.2:-20609126 None:intergenic
AAGTTGATGGAAATAAGCTA+TGG 0.582461 4.2:+20608976 MS.gene40164:CDS
TTGAGACAGAAAGAAAGAGA+AGG 0.583322 4.2:+20608195 MS.gene40164:CDS
AACAAGCACCGTGATAATGA+TGG 0.583729 4.2:+20608143 MS.gene40164:CDS
TGTGTGTCTATGGAAGAGTT+GGG 0.584878 4.2:+20608077 MS.gene40164:CDS
TTGGGACACCATCATTATCA+CGG 0.595132 4.2:-20608151 None:intergenic
TGAGACAGAAAGAAAGAGAA+GGG 0.595420 4.2:+20608196 MS.gene40164:CDS
GCAATAGGGGAAACTGGAGA+AGG 0.660867 4.2:+20608120 MS.gene40164:CDS
TCATTGAGAAGAAAAGAGGA+AGG 0.693261 4.2:+20609009 MS.gene40164:CDS
TTGATGAGATGAATAAAATG+GGG 0.713073 4.2:+20608834 MS.gene40164:CDS
TTATAGTGTCACCTGCAAGG+AGG 0.739971 4.2:-20609123 None:intergenic
CTGCCATAGTAGTAACACTG+AGG 0.765658 4.2:-20609082 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATAATAATTAGGTCATA+CGG - chr4.2:20608529-20608548 None:intergenic 15.0%
!!! AGTTTTTAATTAGTACATTA+TGG + chr4.2:20608634-20608653 MS.gene40164:intron 15.0%
!!! ATTCTATTTTTGTTATTTTC+AGG + chr4.2:20609293-20609312 MS.gene40164:intron 15.0%
!! ATATAGTTTAGAGGATTTAA+TGG - chr4.2:20608348-20608367 None:intergenic 20.0%
!! GATAATGATATATAGTTTAG+AGG - chr4.2:20608357-20608376 None:intergenic 20.0%
!! TTTCATGATTTATCATCTAT+TGG + chr4.2:20608310-20608329 MS.gene40164:intron 20.0%
!!! ATATGTTCTTTTAGTAATGT+TGG + chr4.2:20608916-20608935 MS.gene40164:intron 20.0%
!!! GTTCATCTAAAATCAAATTT+AGG - chr4.2:20608675-20608694 None:intergenic 20.0%
!!! TATGTTCTTTTAGTAATGTT+GGG + chr4.2:20608917-20608936 MS.gene40164:intron 20.0%
! GAATGATTTGAACATTGAAA+TGG + chr4.2:20609055-20609074 MS.gene40164:CDS 25.0%
! TGAAACATTTCATAGACATT+AGG - chr4.2:20608422-20608441 None:intergenic 25.0%
! TTGATGAGATGAATAAAATG+GGG + chr4.2:20608834-20608853 MS.gene40164:CDS 25.0%
!! ATGTTCTTTTAGTAATGTTG+GGG + chr4.2:20608918-20608937 MS.gene40164:intron 25.0%
!! GTTGATGAGATGAATAAAAT+GGG + chr4.2:20608833-20608852 MS.gene40164:CDS 25.0%
!! TGTTGATGAGATGAATAAAA+TGG + chr4.2:20608832-20608851 MS.gene40164:CDS 25.0%
!!! TTTTGTTATTTTCAGGACAT+GGG + chr4.2:20609300-20609319 MS.gene40164:intron 25.0%
!!! TTTTTGTTATTTTCAGGACA+TGG + chr4.2:20609299-20609318 MS.gene40164:intron 25.0%
GATGTTAGAGACTAAATTGA+CGG - chr4.2:20608471-20608490 None:intergenic 30.0%
TATAGATCATGAGACTCATT+AGG - chr4.2:20608899-20608918 None:intergenic 30.0%
TTGATACTTTCTATAGGAAG+AGG + chr4.2:20608941-20608960 MS.gene40164:intron 30.0%
!! AAGTTGATGGAAATAAGCTA+TGG + chr4.2:20608976-20608995 MS.gene40164:CDS 30.0%
AACTTCATGTTGCAACTTCA+TGG - chr4.2:20608732-20608751 None:intergenic 35.0%
AATTTATAGTGTCACCTGCA+AGG - chr4.2:20609129-20609148 None:intergenic 35.0%
ATGCTCATTGAGAAGAAAAG+AGG + chr4.2:20609005-20609024 MS.gene40164:CDS 35.0%
ATGCTGAAAATGGTAGCAAT+AGG + chr4.2:20608105-20608124 MS.gene40164:CDS 35.0%
CAATAGACTATGTGTGTCTA+TGG + chr4.2:20608067-20608086 MS.gene40164:CDS 35.0%
GAACAAAGCAAGCATTATTG+AGG + chr4.2:20608691-20608710 MS.gene40164:CDS 35.0%
GATGAATAAAATGGGGTTAC+AGG + chr4.2:20608841-20608860 MS.gene40164:CDS 35.0%
GGAATTCGATAAAGTTCAAG+TGG - chr4.2:20609333-20609352 None:intergenic 35.0%
GTGCTTACATTTGTGATGAT+TGG - chr4.2:20608263-20608282 None:intergenic 35.0%
TCATTGAGAAGAAAAGAGGA+AGG + chr4.2:20609009-20609028 MS.gene40164:CDS 35.0%
TGAGACAGAAAGAAAGAGAA+GGG + chr4.2:20608196-20608215 MS.gene40164:CDS 35.0%
TGCTGAAAATGGTAGCAATA+GGG + chr4.2:20608106-20608125 MS.gene40164:CDS 35.0%
TTCTCTTTCTTTCTGTCTCA+AGG - chr4.2:20608196-20608215 None:intergenic 35.0%
TTGAGACAGAAAGAAAGAGA+AGG + chr4.2:20608195-20608214 MS.gene40164:CDS 35.0%
TTGGGTTTCAATGCTGAAAA+TGG + chr4.2:20608095-20608114 MS.gene40164:CDS 35.0%
! ACGGATTTTCGTACACTATA+TGG - chr4.2:20608452-20608471 None:intergenic 35.0%
! TCAACTCTTTTCTCTCTTCT+TGG - chr4.2:20608788-20608807 None:intergenic 35.0%
! TCTTGGATGTGAACACTTTT+GGG - chr4.2:20608172-20608191 None:intergenic 35.0%
! TTCTTGGATGTGAACACTTT+TGG - chr4.2:20608173-20608192 None:intergenic 35.0%
!! TTGGGGTTGATACTTTCTAT+AGG + chr4.2:20608935-20608954 MS.gene40164:intron 35.0%
AGTCTCACAATAGAGCTTGA+TGG + chr4.2:20608755-20608774 MS.gene40164:CDS 40.0%
ATGTGTGTCTATGGAAGAGT+TGG + chr4.2:20608076-20608095 MS.gene40164:CDS 40.0%
CACAATAGAGCTTGATGGAA+TGG + chr4.2:20608760-20608779 MS.gene40164:CDS 40.0%
GCTGAAAATGGTAGCAATAG+GGG + chr4.2:20608107-20608126 MS.gene40164:CDS 40.0%
TCTTTCTGTCTCAAGGTTCT+TGG - chr4.2:20608189-20608208 None:intergenic 40.0%
TGTGTGTCTATGGAAGAGTT+GGG + chr4.2:20608077-20608096 MS.gene40164:CDS 40.0%
TTGGGACACCATCATTATCA+CGG - chr4.2:20608154-20608173 None:intergenic 40.0%
! AACAAGCACCGTGATAATGA+TGG + chr4.2:20608143-20608162 MS.gene40164:CDS 40.0%
! AGACCTCAGTGTTACTACTA+TGG + chr4.2:20609079-20609098 MS.gene40164:CDS 40.0%
! GAAACTCACTAGCAGACTTT+TGG + chr4.2:20608220-20608239 MS.gene40164:CDS 40.0%
!! GCAGAAGACTCTCTTTGTTT+TGG - chr4.2:20608812-20608831 None:intergenic 40.0%
!!! TGTTATTTTCAGGACATGGG+TGG + chr4.2:20609303-20609322 MS.gene40164:intron 40.0%
ATGGTAGCAATAGGGGAAAC+TGG + chr4.2:20608114-20608133 MS.gene40164:CDS 45.0%
CTGCCATAGTAGTAACACTG+AGG - chr4.2:20609085-20609104 None:intergenic 45.0%
GTGCAGGTAGCAAAAGTTGA+TGG + chr4.2:20608963-20608982 MS.gene40164:CDS 45.0%
TTATAGTGTCACCTGCAAGG+AGG - chr4.2:20609126-20609145 None:intergenic 45.0%
! CTCAGTGTTACTACTATGGC+AGG + chr4.2:20609083-20609102 MS.gene40164:CDS 45.0%
! CTTTCTATAGGAAGAGGTGC+AGG + chr4.2:20608947-20608966 MS.gene40164:intron 45.0%
!!! CTAGCAGACTTTTGGTGCTT+AGG + chr4.2:20608228-20608247 MS.gene40164:CDS 45.0%
!! ACTAAATAATTATAATAATT+AGG - chr4.2:20608537-20608556 None:intergenic 5.0%
!!! TATTATAATTATTTAGTTTA+TGG + chr4.2:20608540-20608559 MS.gene40164:intron 5.0%
GCAATAGGGGAAACTGGAGA+AGG + chr4.2:20608120-20608139 MS.gene40164:CDS 50.0%
TCTCATTACAGCCTCCTTGC+AGG + chr4.2:20609112-20609131 MS.gene40164:CDS 50.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 20608050 20609371 20608050 ID=MS.gene40164
chr4.2 mRNA 20608050 20609371 20608050 ID=MS.gene40164.t1;Parent=MS.gene40164
chr4.2 exon 20608050 20608274 20608050 ID=MS.gene40164.t1.exon1;Parent=MS.gene40164.t1
chr4.2 CDS 20608050 20608274 20608050 ID=cds.MS.gene40164.t1;Parent=MS.gene40164.t1
chr4.2 exon 20608689 20608862 20608689 ID=MS.gene40164.t1.exon2;Parent=MS.gene40164.t1
chr4.2 CDS 20608689 20608862 20608689 ID=cds.MS.gene40164.t1;Parent=MS.gene40164.t1
chr4.2 exon 20608957 20609133 20608957 ID=MS.gene40164.t1.exon3;Parent=MS.gene40164.t1
chr4.2 CDS 20608957 20609133 20608957 ID=cds.MS.gene40164.t1;Parent=MS.gene40164.t1
chr4.2 exon 20609315 20609371 20609315 ID=MS.gene40164.t1.exon4;Parent=MS.gene40164.t1
chr4.2 CDS 20609315 20609371 20609315 ID=cds.MS.gene40164.t1;Parent=MS.gene40164.t1
Gene Sequence

>MS.gene40164

ATGGAACAAGTAAATAACAATAGACTATGTGTGTCTATGGAAGAGTTGGGTTTCAATGCTGAAAATGGTAGCAATAGGGGAAACTGGAGAAGGAACAAGCACCGTGATAATGATGGTGTCCCAAAAGTGTTCACATCCAAGAACCTTGAGACAGAAAGAAAGAGAAGGGAGAAACTCACTAGCAGACTTTTGGTGCTTAGGTCTTTAGTACCAATCATCACAAATGTAAGCACATAAACTTCACTCACTATCTTATAGTCTTTCATGATTTATCATCTATTGGATTTTGAATTAACCATTAAATCCTCTAAACTATATATCATTATCTTTTCAAATTTTTTCTTGAACTATATAAAGATATTAAGCTATCCTAATGTCTATGAAATGTTTCAATTTAATCCATATAGTGTACGAAAATCCGTCAATTTAGTCTCTAACATCTTAATAACAATTATTAACTCGATTGATTATATATACCGTATGACCTAATTATTATAATTATTTAGTTTATGGACTAAAGTGAAGAGAGCGATAGCATAGAGACTAAATTGATAGTTTATTCATTGAATATATTTACTTTGCTTAGTTTTTAATTAGTACATTATGGTAAATGACTATGAATCCTAAATTTGATTTTAGATGAACAAAGCAAGCATTATTGAGGATGCTATCACTTATACCATGAAGTTGCAACATGAAGTTGAGAGTCTCACAATAGAGCTTGATGGAATGGAACCAAGAAGAGAGAAAAGAGTTGAGCCAAAACAAAGAGAGTCTTCTGCTGTTGATGAGATGAATAAAATGGGGTTACAGGTTTTGCATAAATTCATTTATTTATTTTATTAACCTAATGAGTCTCATGATCTATATGTTCTTTTAGTAATGTTGGGGTTGATACTTTCTATAGGAAGAGGTGCAGGTAGCAAAAGTTGATGGAAATAAGCTATGGATTAAGATGCTCATTGAGAAGAAAAGAGGAAGGTTCAACAAATTAATACAAGACTTGAATGATTTGAACATTGAAATGGTAGACCTCAGTGTTACTACTATGGCAGGAGCATATCTCATTACAGCCTCCTTGCAGGTGACACTATAAATTTAAGATAAGAAATTAATATCATAAACTCATTCTATAAGACTAAAACATGAACTTTGTTTCATCTTTTGAGAAGCTTTTTAATACATGTTAATCTATTATTTGCTTTAATTTGAAATTTTGAACATATGCTAGACTTTTATGTTGATTCTATTTTTGTTATTTTCAGGACATGGGTGGTGAACCACTTGAACTTTATCGAATTCCAACTATTATCAAGTATTAG
Protein sequence

>MS.gene40164.t1

MEQVNNNRLCVSMEELGFNAENGSNRGNWRRNKHRDNDGVPKVFTSKNLETERKRREKLTSRLLVLRSLVPIITNMNKASIIEDAITYTMKLQHEVESLTIELDGMEPRREKRVEPKQRESSAVDEMNKMGLQEEVQVAKVDGNKLWIKMLIEKKRGRFNKLIQDLNDLNIEMVDLSVTTMAGAYLITASLQDMGGEPLELYRIPTIIKY