AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0623250


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0623250 MtrunA17_Chr1g0212871 95.798 238 8 1 1 238 9 244 6.20e-167 460
Msa0623250 MtrunA17_Chr1g0212861 37.131 237 101 11 43 238 123 352 8.10e-25 100
Msa0623250 MtrunA17_Chr4g0030681 49.524 105 46 4 110 211 178 278 2.05e-23 95.9
Msa0623250 MtrunA17_Chr4g0030731 49.524 105 46 4 110 211 177 277 3.30e-23 95.5
Msa0623250 MtrunA17_Chr1g0169511 32.536 209 109 5 43 226 39 240 2.50e-22 92.0
Msa0623250 MtrunA17_Chr7g0221601 43.902 123 61 3 116 233 267 386 8.45e-22 92.8
Msa0623250 MtrunA17_Chr1g0169291 33.014 209 108 6 43 226 39 240 2.55e-21 89.4
Msa0623250 MtrunA17_Chr4g0030671 32.500 200 105 6 43 214 61 258 6.16e-19 83.6
Msa0623250 MtrunA17_Chr1g0169281 27.888 251 146 5 4 226 3 246 5.86e-18 80.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0623250 AT1G07730.2 36.000 200 97 6 41 211 160 357 1.52e-26 106
Msa0623250 AT2G28670.2 52.830 106 48 2 106 211 91 194 9.12e-26 100
Msa0623250 AT2G28670.1 36.139 202 96 5 41 211 205 404 1.30e-25 103
Msa0623250 AT4G13580.1 33.871 186 98 4 62 224 49 232 1.26e-22 92.8
Msa0623250 AT3G24020.1 32.864 213 113 6 47 236 38 243 2.59e-22 92.0
Msa0623250 AT2G39430.1 31.933 238 114 9 43 236 87 320 1.30e-21 91.7
Msa0623250 AT3G55230.1 30.252 238 120 8 43 237 70 304 2.61e-20 87.8

Find 51 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATTTCAAGAGCTGGAATT+TGG 0.209367 4_3:+439411 Msa0623250:CDS
GGTTTCTCTGTATTAATATT+AGG 0.221299 4_3:-439243 None:intergenic
AGCTGAGGAAAATTTGTTTA+TGG 0.235026 4_3:-439127 None:intergenic
GATGGCCATGGTAGTGATTA+GGG 0.312185 4_3:-439170 None:intergenic
GTTTGAGTTGATTGTGGAAT+TGG 0.329326 4_3:-439339 None:intergenic
TGATGGCCATGGTAGTGATT+AGG 0.343261 4_3:-439171 None:intergenic
GAGTCACATGTTGCAGTTAT+TGG 0.351309 4_3:+439636 Msa0623250:CDS
CTTCTCTTCTAGCAATTGTC+AGG 0.383847 4_3:+439085 Msa0623250:CDS
GGAATTGGAATCCCTCCATT+TGG 0.399195 4_3:-439324 None:intergenic
GTTAAGGTTGTGGATAAAGT+AGG 0.408640 4_3:+439699 Msa0623250:CDS
GTAGGGTCTAGTACAGTAGA+AGG 0.416844 4_3:+439717 Msa0623250:CDS
GGAAAGTACCATGGTGCTAA+TGG 0.420735 4_3:+439666 Msa0623250:CDS
TCTTGAAATGCTGCTCTAGT+AGG 0.424130 4_3:-439399 None:intergenic
TGAAGGGTGGGTATGAAGAC+GGG 0.435836 4_3:+439577 Msa0623250:CDS
TAATGGCTATGCTGTTGTTA+AGG 0.440993 4_3:+439683 Msa0623250:CDS
ACACTTGATCTTTCCACCAT+TGG 0.449523 4_3:+439366 Msa0623250:CDS
GTTGCAGTTATTGGTGGTAC+TGG 0.455685 4_3:+439645 Msa0623250:CDS
TTGAAGGGTGGGTATGAAGA+CGG 0.461286 4_3:+439576 Msa0623250:CDS
TGCTAGAAGAGAAGGGAGAT+TGG 0.464219 4_3:-439076 None:intergenic
CTATGCTGTTGTTAAGGTTG+TGG 0.492544 4_3:+439689 Msa0623250:CDS
AGAGAAACCTTCCACTACTA+AGG 0.495734 4_3:+439257 Msa0623250:CDS
CTGACAATTGCTAGAAGAGA+AGG 0.504357 4_3:-439084 None:intergenic
TAGAGCAGCATTTCAAGAGC+TGG 0.504564 4_3:+439404 Msa0623250:CDS
GACGAGGAACTACTAGTTGA+AGG 0.506266 4_3:+439450 Msa0623250:CDS
TATGTAGCTAGTGAAGAGGA+TGG 0.509172 4_3:+439519 Msa0623250:CDS
GTTTGTGTTTGAGTTGATTG+TGG 0.515184 4_3:-439345 None:intergenic
TTAAGGTTGTGGATAAAGTA+GGG 0.516469 4_3:+439700 Msa0623250:CDS
TCACTGTCATAGCAACCATA+TGG 0.517871 4_3:-439548 None:intergenic
GAAGATGAACTAAAGAAACT+TGG 0.528902 4_3:+439480 Msa0623250:CDS
TCTGTATTAATATTAGGACT+AGG 0.530173 4_3:-439237 None:intergenic
ATTGGAATCCCTCCATTTGG+AGG 0.538267 4_3:-439321 None:intergenic
CCATGGTAGTGATTAGGGGT+TGG 0.550854 4_3:-439165 None:intergenic
AGAGGATGGAAGTAGCCATA+TGG 0.562281 4_3:+439533 Msa0623250:CDS
TTTGTGACCTTAGTAGTGGA+AGG 0.562764 4_3:-439264 None:intergenic
TTGATTTGTGACCTTAGTAG+TGG 0.562901 4_3:-439268 None:intergenic
ATGTTATTCTATGATGGCCA+TGG 0.591384 4_3:-439182 None:intergenic
GGTGTATGTAGCTAGTGAAG+AGG 0.591556 4_3:+439515 Msa0623250:CDS
TAAAATACACGTCATACAGA+AGG 0.595028 4_3:-439761 None:intergenic
TCACATGTTGCAGTTATTGG+TGG 0.626055 4_3:+439639 Msa0623250:CDS
AAGAAACTTGGAAAAGCACA+AGG 0.629760 4_3:+439492 Msa0623250:CDS
TGACAATTGCTAGAAGAGAA+GGG 0.634492 4_3:-439083 None:intergenic
AGGAAAAGAGAAACCAATGG+TGG 0.644162 4_3:-439379 None:intergenic
AGTAGGAAAAGAGAAACCAA+TGG 0.647659 4_3:-439382 None:intergenic
CCAACCCCTAATCACTACCA+TGG 0.665385 4_3:+439165 Msa0623250:CDS
GAAACTTGGAAAAGCACAAG+GGG 0.665476 4_3:+439494 Msa0623250:CDS
CAGCATAGCCATTAGCACCA+TGG 0.679074 4_3:-439674 None:intergenic
ATGGCCATGGTAGTGATTAG+GGG 0.679512 4_3:-439169 None:intergenic
AGAAACTTGGAAAAGCACAA+GGG 0.691717 4_3:+439493 Msa0623250:CDS
ATTACCAAGAGTTCTAGCTG+AGG 0.711799 4_3:-439142 None:intergenic
ATCAGTAACATCGATCGACG+AGG 0.719628 4_3:+439434 Msa0623250:CDS
GGTGGTACTGGAAAGTACCA+TGG 0.742516 4_3:+439657 Msa0623250:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAAAATGTTATTCTATGA+TGG - chr4_3:439191-439210 None:intergenic 15.0%
! TCTGTATTAATATTAGGACT+AGG - chr4_3:439240-439259 None:intergenic 25.0%
! GGTTTCTCTGTATTAATATT+AGG - chr4_3:439246-439265 None:intergenic 25.0%
! AGCTGAGGAAAATTTGTTTA+TGG - chr4_3:439130-439149 None:intergenic 30.0%
GAAGATGAACTAAAGAAACT+TGG + chr4_3:439480-439499 Msa0623250:CDS 30.0%
!!! TATGACAGTGAGTTTTTTGA+AGG + chr4_3:439560-439579 Msa0623250:CDS 30.0%
!!! ATGACAGTGAGTTTTTTGAA+GGG + chr4_3:439561-439580 Msa0623250:CDS 30.0%
TTAAGGTTGTGGATAAAGTA+GGG + chr4_3:439700-439719 Msa0623250:CDS 30.0%
TAAAATACACGTCATACAGA+AGG - chr4_3:439764-439783 None:intergenic 30.0%
TGACAATTGCTAGAAGAGAA+GGG - chr4_3:439086-439105 None:intergenic 35.0%
ATGTTATTCTATGATGGCCA+TGG - chr4_3:439185-439204 None:intergenic 35.0%
!! TTGATTTGTGACCTTAGTAG+TGG - chr4_3:439271-439290 None:intergenic 35.0%
! TTACCTTTTCCAAAACCTCT+AGG + chr4_3:439291-439310 Msa0623250:CDS 35.0%
!!! AATCCTAGAGGTTTTGGAAA+AGG - chr4_3:439297-439316 None:intergenic 35.0%
! GGAAAAAATCCTAGAGGTTT+TGG - chr4_3:439303-439322 None:intergenic 35.0%
TTTGGAGGAAAAAATCCTAG+AGG - chr4_3:439309-439328 None:intergenic 35.0%
!!! CTAGGATTTTTTCCTCCAAA+TGG + chr4_3:439309-439328 Msa0623250:CDS 35.0%
!!! GATTTTTTCCTCCAAATGGA+GGG + chr4_3:439313-439332 Msa0623250:CDS 35.0%
!! GTTTGAGTTGATTGTGGAAT+TGG - chr4_3:439342-439361 None:intergenic 35.0%
!! GTTTGTGTTTGAGTTGATTG+TGG - chr4_3:439348-439367 None:intergenic 35.0%
AGTAGGAAAAGAGAAACCAA+TGG - chr4_3:439385-439404 None:intergenic 35.0%
! AAGAAACTTGGAAAAGCACA+AGG + chr4_3:439492-439511 Msa0623250:CDS 35.0%
! AGAAACTTGGAAAAGCACAA+GGG + chr4_3:439493-439512 Msa0623250:CDS 35.0%
!!! TGAGACTTTTTGGAGTTCAT+AGG + chr4_3:439601-439620 Msa0623250:CDS 35.0%
TAATGGCTATGCTGTTGTTA+AGG + chr4_3:439683-439702 Msa0623250:CDS 35.0%
GTTAAGGTTGTGGATAAAGT+AGG + chr4_3:439699-439718 Msa0623250:CDS 35.0%
CTGACAATTGCTAGAAGAGA+AGG - chr4_3:439087-439106 None:intergenic 40.0%
CTTCTCTTCTAGCAATTGTC+AGG + chr4_3:439085-439104 Msa0623250:CDS 40.0%
! TTTTCCTCAGCTAGAACTCT+TGG + chr4_3:439138-439157 Msa0623250:CDS 40.0%
! ATTACCAAGAGTTCTAGCTG+AGG - chr4_3:439145-439164 None:intergenic 40.0%
AGAGAAACCTTCCACTACTA+AGG + chr4_3:439257-439276 Msa0623250:CDS 40.0%
! TTTGTGACCTTAGTAGTGGA+AGG - chr4_3:439267-439286 None:intergenic 40.0%
!!! GGATTTTTTCCTCCAAATGG+AGG + chr4_3:439312-439331 Msa0623250:CDS 40.0%
ACACTTGATCTTTCCACCAT+TGG + chr4_3:439366-439385 Msa0623250:CDS 40.0%
AGGAAAAGAGAAACCAATGG+TGG - chr4_3:439382-439401 None:intergenic 40.0%
TCTTGAAATGCTGCTCTAGT+AGG - chr4_3:439402-439421 None:intergenic 40.0%
GCATTTCAAGAGCTGGAATT+TGG + chr4_3:439411-439430 Msa0623250:CDS 40.0%
! GAAACTTGGAAAAGCACAAG+GGG + chr4_3:439494-439513 Msa0623250:CDS 40.0%
TATGTAGCTAGTGAAGAGGA+TGG + chr4_3:439519-439538 Msa0623250:CDS 40.0%
TCACTGTCATAGCAACCATA+TGG - chr4_3:439551-439570 None:intergenic 40.0%
!!! ACAGTGAGTTTTTTGAAGGG+TGG + chr4_3:439564-439583 Msa0623250:CDS 40.0%
!!! CAGTGAGTTTTTTGAAGGGT+GGG + chr4_3:439565-439584 Msa0623250:CDS 40.0%
GAGTCACATGTTGCAGTTAT+TGG + chr4_3:439636-439655 Msa0623250:CDS 40.0%
TCACATGTTGCAGTTATTGG+TGG + chr4_3:439639-439658 Msa0623250:CDS 40.0%
CTATGCTGTTGTTAAGGTTG+TGG + chr4_3:439689-439708 Msa0623250:CDS 40.0%
TGCTAGAAGAGAAGGGAGAT+TGG - chr4_3:439079-439098 None:intergenic 45.0%
! ATGGCCATGGTAGTGATTAG+GGG - chr4_3:439172-439191 None:intergenic 45.0%
! GATGGCCATGGTAGTGATTA+GGG - chr4_3:439173-439192 None:intergenic 45.0%
! TGATGGCCATGGTAGTGATT+AGG - chr4_3:439174-439193 None:intergenic 45.0%
ATTGGAATCCCTCCATTTGG+AGG - chr4_3:439324-439343 None:intergenic 45.0%
GGAATTGGAATCCCTCCATT+TGG - chr4_3:439327-439346 None:intergenic 45.0%
TAGAGCAGCATTTCAAGAGC+TGG + chr4_3:439404-439423 Msa0623250:CDS 45.0%
ATCAGTAACATCGATCGACG+AGG + chr4_3:439434-439453 Msa0623250:CDS 45.0%
GACGAGGAACTACTAGTTGA+AGG + chr4_3:439450-439469 Msa0623250:CDS 45.0%
GGTGTATGTAGCTAGTGAAG+AGG + chr4_3:439515-439534 Msa0623250:CDS 45.0%
AGAGGATGGAAGTAGCCATA+TGG + chr4_3:439533-439552 Msa0623250:CDS 45.0%
TTGAAGGGTGGGTATGAAGA+CGG + chr4_3:439576-439595 Msa0623250:CDS 45.0%
!!! GAAGACGGGTTGAGACTTTT+TGG + chr4_3:439591-439610 Msa0623250:CDS 45.0%
! GTTGCAGTTATTGGTGGTAC+TGG + chr4_3:439645-439664 Msa0623250:CDS 45.0%
!! GGAAAGTACCATGGTGCTAA+TGG + chr4_3:439666-439685 Msa0623250:CDS 45.0%
GTAGGGTCTAGTACAGTAGA+AGG + chr4_3:439717-439736 Msa0623250:CDS 45.0%
! CCATGGTAGTGATTAGGGGT+TGG - chr4_3:439168-439187 None:intergenic 50.0%
CCAACCCCTAATCACTACCA+TGG + chr4_3:439165-439184 Msa0623250:CDS 50.0%
TGAAGGGTGGGTATGAAGAC+GGG + chr4_3:439577-439596 Msa0623250:CDS 50.0%
!! GGTGGTACTGGAAAGTACCA+TGG + chr4_3:439657-439676 Msa0623250:CDS 50.0%
CAGCATAGCCATTAGCACCA+TGG - chr4_3:439677-439696 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 439072 439788 439072 ID=Msa0623250;Name=Msa0623250
chr4_3 mRNA 439072 439788 439072 ID=Msa0623250-mRNA-1;Parent=Msa0623250;Name=Msa0623250-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|238
chr4_3 exon 439072 439788 439072 ID=Msa0623250-mRNA-1:exon:119;Parent=Msa0623250-mRNA-1
chr4_3 CDS 439072 439788 439072 ID=Msa0623250-mRNA-1:cds;Parent=Msa0623250-mRNA-1
Gene Sequence

>Msa0623250

ATGGCCAATCTCCCTTCTCTTCTAGCAATTGTCAGGTTACTTTTGCTAATGACTACCATAAACAAATTTTCCTCAGCTAGAACTCTTGGTAATCCAACCCCTAATCACTACCATGGCCATCATAGAATAACATTTTTAATGAAGCATATGCTCAATGATACACATCCTAGTCCTAATATTAATACAGAGAAACCTTCCACTACTAAGGTCACAAATCAATTACCTTTTCCAAAACCTCTAGGATTTTTTCCTCCAAATGGAGGGATTCCAATTCCACAATCAACTCAAACACAAACACTTGATCTTTCCACCATTGGTTTCTCTTTTCCTACTAGAGCAGCATTTCAAGAGCTGGAATTTGGATCAGTAACATCGATCGACGAGGAACTACTAGTTGAAGGTGATCATGAAGATGAACTAAAGAAACTTGGAAAAGCACAAGGGGTGTATGTAGCTAGTGAAGAGGATGGAAGTAGCCATATGGTTGCTATGACAGTGAGTTTTTTGAAGGGTGGGTATGAAGACGGGTTGAGACTTTTTGGAGTTCATAGGAGTGATGTTTTTGAGTCACATGTTGCAGTTATTGGTGGTACTGGAAAGTACCATGGTGCTAATGGCTATGCTGTTGTTAAGGTTGTGGATAAAGTAGGGTCTAGTACAGTAGAAGGAAAAGTTACAAGTTCTAAGTTCCTTCTGTATGACGTGTATTTTAGTTAG

Protein sequence

>Msa0623250

MANLPSLLAIVRLLLLMTTINKFSSARTLGNPTPNHYHGHHRITFLMKHMLNDTHPSPNINTEKPSTTKVTNQLPFPKPLGFFPPNGGIPIPQSTQTQTLDLSTIGFSFPTRAAFQELEFGSVTSIDEELLVEGDHEDELKKLGKAQGVYVASEEDGSSHMVAMTVSFLKGGYEDGLRLFGVHRSDVFESHVAVIGGTGKYHGANGYAVVKVVDKVGSSTVEGKVTSSKFLLYDVYFS*