AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0626510


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0626510 MtrunA17_Chr4g0003001 97.608 209 4 1 1 209 58 265 3.19e-154 427
Msa0626510 MtrunA17_Chr2g0333351 59.729 221 65 10 1 209 1 209 5.24e-76 227
Msa0626510 MtrunA17_Chr4g0064971 67.033 91 28 2 1 90 1 90 4.43e-34 122
Msa0626510 MtrunA17_Chr2g0304551 61.290 93 33 2 1 92 1 91 3.28e-31 114
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0626510 AT1G15760.1 49.321 221 73 10 3 208 5 201 7.51e-59 184
Msa0626510 AT1G80520.1 50.691 217 72 10 1 208 1 191 3.66e-51 164
Msa0626510 AT2G12462.1 30.980 255 122 9 1 208 1 248 9.22e-28 105

Find 44 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATGCTTTGGAGGAATTCA+TGG 0.284520 4_3:+6124419 None:intergenic
CTATGGAGATTCCCATGCTT+TGG 0.306158 4_3:+6124407 None:intergenic
CCATCTCTTGTATATGAGTA+TGG 0.307188 4_3:-6124493 Msa0626510:CDS
AAACTTGCAAGAAAAGAAAA+AGG 0.339805 4_3:-6124361 Msa0626510:CDS
GAGAATTTCTAGCCTGTGTT+TGG 0.345241 4_3:+6124384 None:intergenic
ATGATCTTTGCCATTGGTCT+TGG 0.351786 4_3:+6124325 None:intergenic
ATCATGATAGCAATGGTTAT+TGG 0.385458 4_3:-6123985 Msa0626510:CDS
CAACCATGGATTGGTTCTCT+TGG 0.390859 4_3:-6124537 None:intergenic
ATCTTTGCCATTGGTCTTGG+TGG 0.398986 4_3:+6124328 None:intergenic
CAGCTGCTGTTGAAGATATC+AGG 0.407684 4_3:-6123961 Msa0626510:CDS
TTCTAGCCTGTGTTTGGCTA+TGG 0.411531 4_3:+6124390 None:intergenic
GCTCCCATGATCTTTGCCAT+TGG 0.442339 4_3:+6124319 None:intergenic
GAGAGGCTGTTGCTTACAAA+TGG 0.465042 4_3:-6124106 Msa0626510:CDS
TGGAGATTCCCATGCTTTGG+AGG 0.467689 4_3:+6124410 None:intergenic
AAGACCAATGGCAAAGATCA+TGG 0.469365 4_3:-6124323 Msa0626510:CDS
GCAGGCATCATTGAAGGACT+AGG 0.479985 4_3:+6124079 None:intergenic
TTGTTGTAGTTCCAACATCA+AGG 0.486008 4_3:-6124219 Msa0626510:CDS
GAAGAGGAATAAGAAGTTGA+AGG 0.494849 4_3:-6124140 Msa0626510:CDS
TAACTACATAATGAGAAAGT+TGG 0.500944 4_3:-6124269 Msa0626510:CDS
TCAACTTACCAACCATGGAT+TGG 0.503114 4_3:-6124546 None:intergenic
GCAAGAGCAGGCATCATTGA+AGG 0.509469 4_3:+6124073 None:intergenic
CATATACAAGAGATGGATCA+AGG 0.528896 4_3:+6124500 None:intergenic
CCATGAATTCCTCCAAAGCA+TGG 0.531392 4_3:-6124419 Msa0626510:CDS
CTACTACTAGCCCTTGATGT+TGG 0.534119 4_3:+6124208 None:intergenic
TTTCATGAAGGAAAGATGAA+AGG 0.538904 4_3:-6124013 Msa0626510:CDS
CCATACTCATATACAAGAGA+TGG 0.559337 4_3:+6124493 None:intergenic
AGACCAATGGCAAAGATCAT+GGG 0.562788 4_3:-6124322 Msa0626510:CDS
GAGGAATAAGAAGTTGAAGG+TGG 0.566010 4_3:-6124137 Msa0626510:CDS
CAGGCATCATTGAAGGACTA+GGG 0.582193 4_3:+6124080 None:intergenic
GAGACAACCACCAAGACCAA+TGG 0.584520 4_3:-6124335 Msa0626510:CDS
CATGAATTCCTCCAAAGCAT+GGG 0.589273 4_3:-6124418 Msa0626510:CDS
TCATGAAAATGATAAACCAT+AGG 0.596177 4_3:+6124028 None:intergenic
GGAAGAGTTCTGTTGTGAAG+AGG 0.606689 4_3:-6124156 Msa0626510:CDS
AAACTATCAAGAGCAAGAGC+AGG 0.606845 4_3:+6124061 None:intergenic
TGTTGTAGTTCCAACATCAA+GGG 0.608033 4_3:-6124218 Msa0626510:CDS
CTGCTGTTGAAGATATCAGG+TGG 0.617099 4_3:-6123958 Msa0626510:CDS
GGAGATGATCATGATAGCAA+TGG 0.631701 4_3:-6123992 Msa0626510:CDS
GCTCATTGTGTGCAAAAGTG+AGG 0.635769 4_3:+6124470 None:intergenic
TGCTGTTGAAGATATCAGGT+GGG 0.636800 4_3:-6123957 Msa0626510:CDS
AAGCCAAGAGAACCAATCCA+TGG 0.643677 4_3:+6124534 None:intergenic
ATTATGGAACAAGATCATCA+TGG 0.658028 4_3:-6124177 Msa0626510:CDS
TGAGCTAGAACAAGAAGACA+TGG 0.668504 4_3:-6124452 Msa0626510:CDS
GAATCTCCATAGCCAAACAC+AGG 0.676222 4_3:-6124396 Msa0626510:CDS
TGAAGGTGGATAAACAAGAG+AGG 0.697861 4_3:-6124123 Msa0626510:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAACTTGCAAGAAAAGAAAA+AGG - chr4_3:6124096-6124115 Msa0626510:CDS 25.0%
!!! AAAAAGACAAAAAAGTGCTT+AGG - chr4_3:6124165-6124184 Msa0626510:CDS 25.0%
! TAACTACATAATGAGAAAGT+TGG - chr4_3:6124188-6124207 Msa0626510:CDS 25.0%
! AGTAGTAGTAGTAGTTATTA+TGG - chr4_3:6124264-6124283 Msa0626510:CDS 25.0%
! TCATGAAAATGATAAACCAT+AGG + chr4_3:6124432-6124451 None:intergenic 25.0%
!! ATGGTTTATCATTTTCATGA+AGG - chr4_3:6124432-6124451 Msa0626510:CDS 25.0%
ATTATGGAACAAGATCATCA+TGG - chr4_3:6124280-6124299 Msa0626510:CDS 30.0%
! TAGTTTTTGTAGTACTCCTA+TGG - chr4_3:6124413-6124432 Msa0626510:CDS 30.0%
TTTCATGAAGGAAAGATGAA+AGG - chr4_3:6124444-6124463 Msa0626510:CDS 30.0%
ATCATGATAGCAATGGTTAT+TGG - chr4_3:6124472-6124491 Msa0626510:CDS 30.0%
CATATACAAGAGATGGATCA+AGG + chr4_3:6123960-6123979 None:intergenic 35.0%
CCATACTCATATACAAGAGA+TGG + chr4_3:6123967-6123986 None:intergenic 35.0%
CCATCTCTTGTATATGAGTA+TGG - chr4_3:6123964-6123983 Msa0626510:CDS 35.0%
TTGTTGTAGTTCCAACATCA+AGG - chr4_3:6124238-6124257 Msa0626510:CDS 35.0%
TGTTGTAGTTCCAACATCAA+GGG - chr4_3:6124239-6124258 Msa0626510:CDS 35.0%
GAAGAGGAATAAGAAGTTGA+AGG - chr4_3:6124317-6124336 Msa0626510:CDS 35.0%
TGAGCTAGAACAAGAAGACA+TGG - chr4_3:6124005-6124024 Msa0626510:CDS 40.0%
CATGAATTCCTCCAAAGCAT+GGG - chr4_3:6124039-6124058 Msa0626510:CDS 40.0%
!! GAGAATTTCTAGCCTGTGTT+TGG + chr4_3:6124076-6124095 None:intergenic 40.0%
! ATGATCTTTGCCATTGGTCT+TGG + chr4_3:6124135-6124154 None:intergenic 40.0%
AAGACCAATGGCAAAGATCA+TGG - chr4_3:6124134-6124153 Msa0626510:CDS 40.0%
AGACCAATGGCAAAGATCAT+GGG - chr4_3:6124135-6124154 Msa0626510:CDS 40.0%
GAGGAATAAGAAGTTGAAGG+TGG - chr4_3:6124320-6124339 Msa0626510:CDS 40.0%
TGAAGGTGGATAAACAAGAG+AGG - chr4_3:6124334-6124353 Msa0626510:CDS 40.0%
AAACTATCAAGAGCAAGAGC+AGG + chr4_3:6124399-6124418 None:intergenic 40.0%
GGAGATGATCATGATAGCAA+TGG - chr4_3:6124465-6124484 Msa0626510:CDS 40.0%
TGCTGTTGAAGATATCAGGT+GGG - chr4_3:6124500-6124519 Msa0626510:CDS 40.0%
GCTCATTGTGTGCAAAAGTG+AGG + chr4_3:6123990-6124009 None:intergenic 45.0%
!! CCATGCTTTGGAGGAATTCA+TGG + chr4_3:6124041-6124060 None:intergenic 45.0%
CCATGAATTCCTCCAAAGCA+TGG - chr4_3:6124038-6124057 Msa0626510:CDS 45.0%
CTATGGAGATTCCCATGCTT+TGG + chr4_3:6124053-6124072 None:intergenic 45.0%
GAATCTCCATAGCCAAACAC+AGG - chr4_3:6124061-6124080 Msa0626510:CDS 45.0%
TTCTAGCCTGTGTTTGGCTA+TGG + chr4_3:6124070-6124089 None:intergenic 45.0%
!! ATCTTTGCCATTGGTCTTGG+TGG + chr4_3:6124132-6124151 None:intergenic 45.0%
CTACTACTAGCCCTTGATGT+TGG + chr4_3:6124252-6124271 None:intergenic 45.0%
GGAAGAGTTCTGTTGTGAAG+AGG - chr4_3:6124301-6124320 Msa0626510:CDS 45.0%
! GAGAGGCTGTTGCTTACAAA+TGG - chr4_3:6124351-6124370 Msa0626510:CDS 45.0%
CAGGCATCATTGAAGGACTA+GGG + chr4_3:6124380-6124399 None:intergenic 45.0%
CAGCTGCTGTTGAAGATATC+AGG - chr4_3:6124496-6124515 Msa0626510:CDS 45.0%
CTGCTGTTGAAGATATCAGG+TGG - chr4_3:6124499-6124518 Msa0626510:CDS 45.0%
TGGAGATTCCCATGCTTTGG+AGG + chr4_3:6124050-6124069 None:intergenic 50.0%
GAGACAACCACCAAGACCAA+TGG - chr4_3:6124122-6124141 Msa0626510:CDS 50.0%
GCTCCCATGATCTTTGCCAT+TGG + chr4_3:6124141-6124160 None:intergenic 50.0%
GCAGGCATCATTGAAGGACT+AGG + chr4_3:6124381-6124400 None:intergenic 50.0%
GCAAGAGCAGGCATCATTGA+AGG + chr4_3:6124387-6124406 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 6123925 6124554 6123925 ID=Msa0626510;Name=Msa0626510
chr4_3 mRNA 6123925 6124554 6123925 ID=Msa0626510-mRNA-1;Parent=Msa0626510;Name=Msa0626510-mRNA-1;_AED=0.23;_eAED=0.23;_QI=0|-1|0|1|-1|1|1|0|209
chr4_3 exon 6123925 6124554 6123925 ID=Msa0626510-mRNA-1:exon:1799;Parent=Msa0626510-mRNA-1
chr4_3 CDS 6123925 6124554 6123925 ID=Msa0626510-mRNA-1:cds;Parent=Msa0626510-mRNA-1
Gene Sequence

>Msa0626510

ATGGATTGGTTCTCTTGGCTTTCAAAAACAAACCTTGATCCATCTCTTGTATATGAGTATGGCCTCACTTTTGCACACAATGAGCTAGAACAAGAAGACATGGTTTACTTCAACCATGAATTCCTCCAAAGCATGGGAATCTCCATAGCCAAACACAGGCTAGAAATTCTCAAACTTGCAAGAAAAGAAAAAGGAAAGAGACAACCACCAAGACCAATGGCAAAGATCATGGGAGCAATCAAAAAGACAAAAAAGTGCTTAGGTAACTACATAATGAGAAAGTTGGTTACATGTGAAGAATCAAATTCAGCACTTGTTGTAGTTCCAACATCAAGGGCTAGTAGTAGTAGTAGTTATTATGGAACAAGATCATCATGGAAGAGTTCTGTTGTGAAGAGGAATAAGAAGTTGAAGGTGGATAAACAAGAGAGGCTGTTGCTTACAAATGGAAGCCCTAGTCCTTCAATGATGCCTGCTCTTGCTCTTGATAGTTTTTGTAGTACTCCTATGGTTTATCATTTTCATGAAGGAAAGATGAAAGGAGATGATCATGATAGCAATGGTTATTGGTCAGCTGCTGTTGAAGATATCAGGTGGGATACTATGTTCCAAGATCTAAAACCAAACTAA

Protein sequence

>Msa0626510

MDWFSWLSKTNLDPSLVYEYGLTFAHNELEQEDMVYFNHEFLQSMGISIAKHRLEILKLARKEKGKRQPPRPMAKIMGAIKKTKKCLGNYIMRKLVTCEESNSALVVVPTSRASSSSSYYGTRSSWKSSVVKRNKKLKVDKQERLLLTNGSPSPSMMPALALDSFCSTPMVYHFHEGKMKGDDHDSNGYWSAAVEDIRWDTMFQDLKPN*